Comments (22)
leepc12
commented on July 21, 2024
Could you post a full STDOUT/STDERR and chipseq.bds.20170529_194354_069.report.html here?
from chipseq_pipeline.
rdali
commented on July 21, 2024
STDOUT
== git info
Latest git commit : f26ac96 (Tue May 9 23:50:11 2017)
Reading parameters from section (default) in file(tools/TF_chipseq_pipeline/default.env)...
== configuration file info
Hostname : lm-1r16-n02.guillimin.clumeq.ca
Configuration file :
Environment file : tools/TF_chipseq_pipeline/default.env
Warning: Maximum # threads (-nth) for a pipeline is <= 1. Turning off parallelization... (-no_par)
== parallelization info
No parallel jobs : true
Maximum # threads : 1
== cluster/system info
Walltime (general) : 5h50m
Max. memory (general) : 7G
Force to use a system : local
Process priority (niceness) : 0
Retiral for failed tasks : 0
Submit tasks to a cluster queue :
Unlimited cluster mem./walltime : false
== shell environment info
Conda env. : aquas_chipseq
Conda env. for python3 : aquas_chipseq_py3
Conda bin. directory :
Shell cmd. for init. : if [[ -f
Shell cmd. for init.(py3) : if [[ -f
Shell cmd. for fin. : TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
Cluster task min. len. : 60
Cluster task delay : 0
== output directory/title info
Output dir. : project/ChIPSeq/160130_CTCF
Title (prefix) : 160130_CTCF
Reading parameters from section (default) in file(tools/TF_chipseq_pipeline/default.env)...
== species settings
Species : hg19
Species file :
Species name (WashU browser) : hg19
Ref. genome seq. fasta :
Chr. sizes file : tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes
Black list bed :
Ref. genome seq. dir. :
== ENCODE accession settings
ENCODE experiment accession :
ENCODE award RFA :
ENCODE assay category :
ENCODE assay title :
ENCODE award :
ENCODE lab :
ENCODE assembly genome :
ENCODE alias prefix : KLAB_PIPELINE
== report settings
URL root for output directory :
Genome coord. for browser tracks :
== align bwa settings
Param. for bwa : -q 5 -l 32 -k 2
BWA index : tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa
Walltime (bwa) : 47h
Max. memory (bwa) : 12G
== align multimapping settings
alignments reported for multimapping : 0
== postalign bam settings
MAPQ reads rm thresh. : 30
Rm. tag reads with str. :
No dupe removal in filtering raw bam : false
Walltime (bam filter) : 23h
Max. memory (bam filter) : 12G
Dup marker : picard
Use sambamba markdup (instead of picard) : false
== postalign bed/tagalign settings
Max. memory for UNIX shuf : 12G
== postalign cross-corr. analysis settings
Max. memory for UNIX shuf : 12G
User-defined cross-corr. peak strandshift : -1
Extra parameters for cross-corr. analysis :
== callpeak spp settings
Threshold for # peak : 300000
Walltime (spp) : 47h
Max. memory (spp) : 12G
Stack size for run_spp.R :
Use-defined cross-corr. peak strandshift; if -1, use frag. len. :-1
Extra parameters for run_spp.R :
== callpeak gem settings
Threshold for # peak in GEM : 300000
Min. length of k-mers in GEM : 6
Max. length of k-mers in GEM : 13
Q-value threshold for GEM : 0.0
Read distribution txt for GEM : tools/TF_chipseq_pipeline/etc/Read_Distribution_default.txt
Extra parameters for GEM :
Walltime (GEM) : 47h
Max. memory (GEM) : 15G
== callpeak PeakSeq settings
Target FDR for PeakSeq :0.05
Number of simulations for PeakSeq :10
Enrichment mapped frag. len. for PeakSeq :-1
Minimum interpeak distance for PeakSeq :-1
Mappability map file for PeakSeq :
Maximum Q-value for PeakSeq :0.1
Background model for PeakSeq :Simulated
Extra parameters for PeakSeq :
Walltime (PeakSeq) : 47h
Max. memory (PeakSeq) : 12G
== callpeak macs2 settings
Genome size (hs,mm) : hs
Walltime (macs2) : 23h
Max. memory (macs2) : 15G
P-value cutoff (macs2 callpeak) : 0.01
--keep-dup (macs2 callpeak) : all
--extsize (macs2 callpeak); if -1 then use frag. len. : -1
--shift (macs2 callpeak) : 0
Extra parameters for macs2 callpeak :
== callpeak naiver overlap settings
Bedtools intersect -nonamecheck : false
== IDR settings
Append IDR threshold to IDR out_dir : false
== chipseq pipeline settings
replicates : 1
Type of ChIP-Seq pipeline : TF
Final stage for ChIP-Seq : peak
Signal tracks for pooled rep. only : false
Aligner to map raw reads : bwa
reads to subsample for cross-corr. analysis : 15000000
reads to subsample exp. replicates (0: no subsampling): 0
reads to subsample controls (0: no subsampling) : 0
Generate anonymized filt. bam : false
Peak caller for IDR analysis : spp
Control rep. depth ratio : 1.2
Scoring column for IDR : signal.value
IDR threshold : 0.05
Force to use pooled ctl : false
Peak calling for true reps only : false
No peak calling for self pseudo reps : false
Disable cross-correlation analysis : false
Disable g. peak filt. thru. n. peak : false
== checking chipseq parameters ...
== checking input files ...
Rep1 fastq (PE) :
project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq
project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq
Control Rep1 fastq (PE) :
project/ChIPSeq/HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq
project/ChIPSeq/HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq
Distributing 1 to ...
{rep1=1, ctl1=1}
Distributing 1 to ...
[1, 1]
bds -c tools/TF_chipseq_pipeline/bds.config -v tools/TF_chipseq_pipeline/chipseq.bds -title 160130_CTCF -final_stage peak -gensz hs -out_dir project/ChIPSeq/160130_CTCF -chrsz tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -nth 1 -type TF -species hg19 -bwa_idx tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa -pe1 -fastq1_1:1 HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq -fastq1_2:1 HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq -ctl_pe1 -ctl_fastq1_1:1 HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq -ctl_fastq1_2:1 HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq
########################################################################
STDError
00:00:00.000 Bds 0.99999e (build 2016-08-26 06:34), by Pablo Cingolani
00:00:00.294 Parsing
00:00:15.989 Initializing
00:00:16.077 Process ID: chipseq.bds.20170529_194354_069
00:00:16.082 Running
00:00:23.200 Executioner factory: Creating new executioner type 'LOCAL'
00:00:23.336 ExecutionerLocal 'Local[41]': Queuing task: chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10
00:00:23.337 Waiting for all tasks to finish.
00:00:23.338 Wait: Waiting for task to finish: chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: SCHEDULED
00:00:23.340 ExecutionerLocal 'Local[41]': Started running
00:00:23.342 ExecutionerLocal 'Local[41]': Task selected 'chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' on host 'localhost'
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[bwt_restore_sa] fail to open file 'tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa.sa' : No such file or directory
Task failed:
Program & line : 'tools/TF_chipseq_pipeline/modules/align_bwa.bds', line 181
Task Name : 'bwa_sam_PE rep1'
Task ID : 'chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10'
Task PID : '31877'
Task hint : 'bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai project/ChIPSeq/160130_CTCF/align/re'
Task resources : 'cpus: 1 mem: -1.0 B wall-timeout: 8640000'
State : 'ERROR'
Dependency state : 'ERROR'
Retries available : '1'
Input files : '[project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai, project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai]'
Output files : '[project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam, project/ChIPSeq/160130_CTCF/qc/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.flagstat.qc]'
Script file : 'project/ChIPSeq/chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10.sh'
Exit status : '1'
Program :
# SYS command. line 183
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
# SYS command. line 185
bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq project/ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq | pigz -p 1 -nc > project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz
# SYS command. line 194
pigz -p 1 -cd project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz \
| awk 'BEGIN {FS="\t" ; OFS="\t"} ! /^@/ && $6!="*" { cigar=$6; gsub("[0-9]+D","",cigar); n = split(cigar,vals,"[A-Z]"); s = 0; for (i=1;i<=n;i++) s=s+vals[i]; seqlen=length($10) ; if (s!=seqlen) print $1"\t"; }' \
| sort | uniq > project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads
# SYS command. line 199
if [ $(cat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads | wc -l) -gt 0 ]; then \
zcat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz | grep -v -F -f project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads | samtools view -Su - | samtools sort - project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE; \
else \
samtools view -Su project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz | samtools sort - project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE; \
fi
# SYS command. line 211
samtools flagstat project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam > project/ChIPSeq/160130_CTCF/qc/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.flagstat.qc
# SYS command. line 212
samtools index project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam
# SYS command. line 216
rm -f project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.badReads project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.sam.gz
# SYS command. line 218
TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
StdErr (100000000 lines) :
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[bwt_restore_sa] fail to open file 'tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa.sa' : No such file or directory
00:00:50.885 Wait: Task 'chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished.
Fatal error: tools/TF_chipseq_pipeline/modules/align_bwa.bds, line 87, pos 3. Task/s failed.
chipseq.bds, line 76 : main()
chipseq.bds, line 79 : void main() { // chipseq pipeline starts here
chipseq.bds, line 87 : align() // align and postalign
chipseq.bds, line 318 : void align() {
chipseq.bds, line 355 : for ( int ctl=0; ctl <= 1; ctl++) { // iterate through inputs (ctl==0 : exp. replicate, ctl==1 : control)
chipseq.bds, line 358 : for ( int rep=1; rep <= get_num_rep( ctl ); rep++) {
chipseq.bds, line 364 : if ( no_par ) align( ctl, rep, nth_rep{group} ) // parallel jobs for align() for each replicate and each control
chipseq.bds, line 374 : void align( int ctl, int rep, int nth_rep ) {
chipseq.bds, line 376 : if ( is_se( ctl, rep ) ) align_SE( ctl, rep, nth_rep )
chipseq.bds, line 377 : else align_PE( ctl, rep, nth_rep )
chipseq.bds, line 550 : void align_PE( int ctl, int rep, int nth_rep ) {
chipseq.bds, line 563 : if ( is_input_fastq( ctl, rep ) ) {
chipseq.bds, line 582 : if ( aligner == "bwa" ) {
chipseq.bds, line 583 : ( bam_, flagstat_qc_ ) = bwa_PE( pooled_fastq_pair1, pooled_fastq_pair2, aln_o_dir, qc_o_dir, group, nth_rep )
align_bwa.bds, line 66 : string[] bwa_PE( string fastq1, string fastq2, string o_dir, string log_o_dir, string group, int nth_bwa ) {
align_bwa.bds, line 76 : if ( out <- in ) { // compare file timestamps of in and out (to check if job is already done or not)
align_bwa.bds, line 87 : wait
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
00:00:51.033 Writing report file 'chipseq.bds.20170529_194354_069.report.html'
00:00:51.155 Program 'chipseq.bds.20170529_194354_069' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: bwa_sam_PE rep1.
00:00:51.156 Finished. Exit code: 1
00:00:51.156 ExecutionerLocal 'Local[41]': Killed
############################################################################
cat chipseq.bds.20170529_194354_069.report.html
<style type="text/css"> pre { width:1200px; overflow: auto; word-wrap: normal; white-space: pre; } </style> <script src="http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js"></script> <script src="http://cytoscape.github.io/cytoscape.js/api/cytoscape.js-latest/cytoscape.min.js"></script> <script src="chipseq.bds.20170529_194354_069.dag.js"></script>BigDataScript report: chipseq.bds
<table class="table table-striped">
<tr> <th> Script file </th><td> tools/TF_chipseq_pipeline/chipseq.bds </td></tr>
<tr> <th> Program ID </th><td> chipseq.bds.20170529_194354_069 </td></tr>
<tr> <th> Start time </th><td> 2017-05-29 19:43:54 </td></tr>
<tr> <th> Run time </th><td> 00:00:34.931 </td></tr>
<tr> <th> Tasks executed </th><td> 1 </td></tr>
<tr> <th> Tasks failed </th><td> 1 </td></tr>
<tr> <th> Tasks failed names </th><td> <pre>bwa_sam_PE rep1</pre> </td></tr>
<tr> <th> Arguments* </th><td> [-title, 160130_CTCF, -final_stage, peak, -gensz, hs, -out_dir, project/ChIPSeq/160130_CTCF, -chrsz, tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes, -nth, 1, -type, TF, -species, hg19, -bwa_idx, tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa, -pe1, -fastq1_1:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, -fastq1_2:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, -ctl_pe1, -ctl_fastq1_1:1, HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq, -ctl_fastq1_2:1, HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq] </td></tr>
<tr> <th> System* </th><td> local </td></tr>
<tr> <th> Cpus* </th><td> -1 </td></tr>
<tr> <th> Exit value </th><td style="background-color: #ffc0c0"> 1 </td></tr>
</table>
<b>*</b> Values in global scope when program finished execution.
Timeline
<script type="text/javascript" src="https://www.google.com/jsapi?autoload={'modules':[{'name':'visualization','version':'1','packages':['timeline']}]}"></script> <script type="text/javascript"> google.setOnLoadCallback(drawChart);function drawChart() {
var container = document.getElementById('bdsTimeline');
var chart = new google.visualization.Timeline(container);
var dataTable = new google.visualization.DataTable();
dataTable.addColumn({ type: 'string', id: 'TaskName' });
dataTable.addColumn({ type: 'string', id: 'TaskHint' });
dataTable.addColumn({ type: 'date', id: 'Start' });
dataTable.addColumn({ type: 'date', id: 'End' });
dataTable.addRows([
[ 'bwa_sam_PE rep1', 'bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa project/ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai project/ChIPSeq/160130_CTCF/align/re', new Date(2017,4,29,19,44,01), new Date(2017,4,29,19,44,01) ],
]);
var options = {
timeline: { groupByRowLabel: false }
};
chart.draw(dataTable, options);
}
</script>
<div id="bdsTimeline" style="width: 900px; height: 126px;"></div>
Task Graph
Parallel (threads) details
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | chipseq.bds.20170529_194354_069/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10 |
Task details
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
|
| # SYS command. line 183
|
Global scope
Note: Global scope when program finished execution.| Type | Name | Value |
|---|---|---|
| string | _ | /home/rdali/.bds/bds |
| string | _LMFILES_ | /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles/perl/5.16:/sb/software/CentOS-6/eb/modules/all/Core/Java/1.8.0_45.lua |
| string | _ModuleTable001_ | 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 |
| string | _ModuleTable002_ | 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 |
| string | _ModuleTable003_ | bGwvTGludXgiLCIvc2Ivc29mdHdhcmUvQ2VudE9TLTYvZWIvbW9kdWxlcy9hbGwvQ29yZSIsIi9zYi9ob21lL3JkYWxpL21vZHVsZWZpbGVzIix9LFsic3lzdGVtQmFzZU1QQVRIIl09Ii9zYi9zb2Z0d2FyZS9DZW50T1MtNi90b29scy9Nb2R1bGVzLzMuMi45L21vZHVsZWZpbGVzOi9zYi9zb2Z0d2FyZS9DZW50T1MtNi9lYi9tb2R1bGVzL2FsbC9MaW51eDovc2Ivc29mdHdhcmUvQ2VudE9TLTYvZWIvbW9kdWxlcy9hbGwvQ29yZTovc2IvaG9tZS9yZGFsaS9tb2R1bGVmaWxlcyIsWyJ2ZXJzaW9uIl09Mix9 |
| string | _ModuleTable_Sz_ | 3 |
| bool | allowEmpty | false |
| string[] | args | [-title, 160130_CTCF, -final_stage, peak, -gensz, hs, -out_dir, project/ChIPSeq/160130_CTCF, -chrsz, tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes, -nth, 1, -type, TF, -species, hg19, -bwa_idx, tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa, -pe1, -fastq1_1:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, -fastq1_2:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, -ctl_pe1, -ctl_fastq1_1:1, HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq, -ctl_fastq1_2:1, HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq] |
| string | BASH_ENV | /software/CentOS-6/tools/lmod/lmod/init/bash |
| string | BASH_FUNC_ml() | () { eval $( |
| string | BASH_FUNC_module() | () { eval $( |
| bool | canFail | false |
| string | CONDA_DEFAULT_ENV | aquas_chipseq |
| string | CONDA_PATH_BACKUP | tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin |
| string | CONDA_PREFIX | tools/miniconda3/envs/aquas_chipseq |
| string | CONDA_PS1_BACKUP | |
| string | CPATH | /software/CentOS-6/eb/software/Core/Java/1.8.0_45/include |
| int | cpus | -1 |
| int | cpusLocal | 32 |
| string | CVS_RSH | ssh |
| int | day | 86400 |
| real | E | 2.718281828459045 |
| string | EBDEVELJAVA | /software/CentOS-6/eb/software/Core/Java/1.8.0_45/easybuild/Core-Java-1.8.0_45-easybuild-devel |
| string | EBROOTJAVA | /software/CentOS-6/eb/software/Core/Java/1.8.0_45 |
| string | EBVERSIONJAVA | 1.8.0_45 |
| string | ENVIRONMENT | BATCH |
| int | G | 1073741824 |
| string | G_BROKEN_FILENAMES | 1 |
| string | HDF5_DIR | tools/hdf5-1.8.14/bin |
| string | HISTCONTROL | ignoreboth:erasedups |
| string | HISTIGNORE | ls:pwd:logout:rm*:mkdir*:rdali:hic:q |
| string | HISTSIZE | 1000000 |
| string | HISTTIMEFORMAT | %F %T |
| string | HOME | /home/rdali |
| string | HOSTNAME | lm-1r16-n02 |
| int | hour | 3600 |
| string | JAVA_HOME | /software/CentOS-6/eb/software/Core/Java/1.8.0_45 |
| int | K | 1024 |
| string | LANG | C |
| string | LD_LIBRARY_PATH | /gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/lib/amd64/server:/gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/lib/amd64:/gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/../lib/amd64:/software/CentOS-6/eb/software/Core/Java/1.8.0_45/lib:$LD_LIBRARY_PATH:~/software/lib:/home/rdali/software/lib:tools/hdf5-1.8.14/lib/:/home/rdali/tools/ghmm-0.9-rc3/lib:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/bin/glnxa64:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:~/software/lib:/home/rdali/software/lib:tools/hdf5-1.8.14/lib:/home/rdali/tools/ghmm-0.9-rc3/lib:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/bin/glnxa64:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server |
| string | LESSOPEN | ||/usr/bin/lesspipe.sh %s |
| string | LIBRARY_PATH | /software/CentOS-6/eb/software/Core/Java/1.8.0_45/lib |
| string | LMOD_arch | x86_64 |
| string | LMOD_CMD | /software/CentOS-6/tools/lmod/lmod/libexec/lmod |
| string | LMOD_COLORIZE | yes |
| string | LMOD_DEFAULT_MODULEPATH | /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles:/sb/software/CentOS-6/eb/modules/all/Linux:/sb/software/CentOS-6/eb/modules/all/Core:/sb/home/rdali/modulefiles |
| string | LMOD_DIR | /software/CentOS-6/tools/lmod/lmod/libexec |
| string | LMOD_FULL_SETTARG_SUPPORT | no |
| string | LMOD_PKG | /software/CentOS-6/tools/lmod/lmod |
| string | LMOD_PREPEND_BLOCK | normal |
| string | LMOD_SETTARG_CMD | : |
| string | LMOD_sys | Linux |
| string | LMOD_VERSION | 6.1 |
| string | LOADEDMODULES | perl/5.16:Java/1.8.0_45 |
| string | LOGNAME | rdali |
| string | LSCRATCH | /localscratch/91162790.gm-1r16-n04.guillimin.clumeq.ca |
| int | M | 1048576 |
| string | /var/spool/mail/rdali | |
| string | MANPATH | /software/CentOS-6/eb/software/Core/Java/1.8.0_45/man:/software/CentOS-6/tools/perl-5.16/man:/software/CentOS-6/tools/lmod/lmod/share/man:: |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULEPATH | /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles:/sb/software/CentOS-6/eb/modules/all/Linux:/sb/software/CentOS-6/eb/modules/all/Core:/sb/home/rdali/modulefiles |
| string | MODULEPATH_ROOT | /sb/software/CentOS-6/eb/modules/all |
| string | MODULESHOME | /software/CentOS-6/tools/lmod/lmod |
| string | NLSPATH | /usr/dt/lib/nls/msg/%L/%N.cat |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /software/CentOS-6/eb/software/Core/Java/1.8.0_45:/software/CentOS-6/eb/software/Core/Java/1.8.0_45/bin:tools/miniconda3/envs/aquas_chipseq/extra/phantompeakqualtools:tools/miniconda3/envs/aquas_chipseq/bin:tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin:tools/miniconda3/envs/aquas_chipseq/extra/align2rawsignal/bin |
| string | PBS_ENVIRONMENT | PBS_BATCH |
| string | PBS_GPUFILE | /var/spool/pbs/aux//91162790.gm-1r16-n04.guillimin.clumeq.cagpu |
| string | PBS_JOBCOOKIE | 9AA928B60B64CD98E7E1F385AD8E7205 |
| string | PBS_JOBID | 91162790.gm-1r16-n04.guillimin.clumeq.ca |
| string | PBS_JOBNAME | AQUAS-160130_CTCF |
| string | PBS_MICFILE | /var/spool/pbs/aux//91162790.gm-1r16-n04.guillimin.clumeq.camic |
| string | PBS_MOMPORT | 15003 |
| string | PBS_NODEFILE | /var/spool/pbs/aux//91162790.gm-1r16-n04.guillimin.clumeq.ca |
| string | PBS_NODENUM | 0 |
| string | PBS_NP | 1 |
| string | PBS_NUM_NODES | 1 |
| string | PBS_NUM_PPN | 1 |
| string | PBS_O_HOME | /home/rdali |
| string | PBS_O_HOST | lg-1r17-n04.guillimin.clumeq.ca |
| string | PBS_O_LANG | en_CA.UTF-8 |
| string | PBS_O_LOGNAME | rdali |
| string | PBS_O_MAIL | /var/spool/mail/rdali |
| string | PBS_O_PATH | tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/opt/moab/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:/sb/software/tools/scripts:/usr/lpp/mmfs/bin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin |
| string | PBS_O_QUEUE | metaq |
| string | PBS_O_SERVER | gm-schrmat |
| string | PBS_O_SHELL | /bin/bash |
| string | PBS_O_SUBMIT_FILTER | /opt/torque/x86_64/libexec/qsub_filter |
| string | PBS_O_WORKDIR | project/ChIPSeq |
| string | PBS_QUEUE | xlm2 |
| string | PBS_TASKNUM | 1 |
| string | PBS_VERSION | TORQUE-5.1.3 |
| string | PBS_VNODENUM | 0 |
| string | PBS_WALLTIME | 86400 |
| string | PBSCOREDUMP | 1 |
| string | PERL5LIB | tools/perl5/lib/perl5:/home/rdali/tools/vcftools_0.1.12b/perl |
| string | PERL_LOCAL_LIB_ROOT | tools/perl5 |
| string | PERL_MB_OPT | --install_base \"tools/perl5\" |
| string | PERL_MM_OPT | INSTALL_BASE=tools/perl5 |
| real | PI | 3.141592653589793 |
| string | ppwd | project/ChIPSeq |
| string | programName | chipseq.bds |
| string | programPath | tools/TF_chipseq_pipeline/chipseq.bds |
| string | PROMPT_COMMAND | history -a |
| string | PWD | project/ChIPSeq |
| string | QTDIR | /usr/lib64/qt-3.3 |
| string | QTINC | /usr/lib64/qt-3.3/include |
| string | QTLIB | /usr/lib64/qt-3.3/lib |
| string | queue | |
| string | R_LIBS | tools/R_LIBS |
| string | RAMDISK | /dev/shm/91162790.gm-1r16-n04.guillimin.clumeq.ca |
| int | retry | 0 |
| string | SCRATCH | /gs/scratch/rdali |
| string | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_ASKPASS | /usr/libexec/openssh/gnome-ssh-askpass |
| string | system | local |
| int | T | 1099511627776 |
| int | timeout | -1 |
| string | USER | rdali |
| string | VDB_PWFILE | keys/prj_6419.ngc |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | XAPPLRESDIR | tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/X11/app-defaults |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |
from chipseq_pipeline.
leepc12
commented on July 21, 2024
Did you use install_genome_data.sh for genome data installation? What files do you have in tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index?
from chipseq_pipeline.
rdali
commented on July 21, 2024
I did use the install_genome_data.sh. I followed the instructions on github.
I have the following files:
total 3.7G
lrwxrwxrwx male.hg19.fa -> ../male.hg19.fa
-rw-r--r-- male.hg19.fa.bwt
-rw-r--r-- male.hg19.fa.pac
-rw-r--r-- male.hg19.fa.ann
-rw-r--r-- male.hg19.fa.amb
from chipseq_pipeline.
leepc12
commented on July 21, 2024
It looks like BWA index is not installed correctly. You need one more file on it (male.hg19.fa.sa). Did you see any error while running install_genome_data.sh?
from chipseq_pipeline.
rdali
commented on July 21, 2024
None that I can recall. I am running it again and I will re-run the pipeline and will report back when it is done.
from chipseq_pipeline.
rdali
commented on July 21, 2024
So I reran the install_genome_data.sh and now the male.hg19.fa.sa is installed, however, I still get an error; see below:
################################### STDERR for Genome Installation ###################################
################################### STDERR for Genome Installation ###################################
################################### STDERR for Genome Installation ###################################
--2017-06-02 08:53:47-- http://mitra.stanford.edu/kundaje/genome_data/hg19/globalmap_k20tok54.tgz
Resolving mitra.stanford.edu... 171.65.76.236
Connecting to mitra.stanford.edu|171.65.76.236|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
--2017-06-02 08:53:47-- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/referenceSequences/male.hg19.fa.gz
Resolving hgdownload.cse.ucsc.edu... 128.114.119.163
Connecting to hgdownload.cse.ucsc.edu|128.114.119.163|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
--2017-06-02 08:53:48-- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz
Resolving hgdownload.cse.ucsc.edu... 128.114.119.163
Connecting to hgdownload.cse.ucsc.edu|128.114.119.163|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/hg19_gencode_tss_unique.bed.gz
Resolving mitra.stanford.edu... 171.65.76.236
Connecting to mitra.stanford.edu|171.65.76.236|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.bed.gz
Resolving mitra.stanford.edu... 171.65.76.236
Connecting to mitra.stanford.edu|171.65.76.236|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_prom_p2.bed.gz
Resolving mitra.stanford.edu... 171.65.76.236
Connecting to mitra.stanford.edu|171.65.76.236|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/reg2map_honeybadger2_dnase_enh_p2.bed.gz
Resolving mitra.stanford.edu... 171.65.76.236
Connecting to mitra.stanford.edu|171.65.76.236|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/dnase_avgs_reg2map_p10_merged_named.pvals.gz
Resolving mitra.stanford.edu... 171.65.76.236
Connecting to mitra.stanford.edu|171.65.76.236|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
--2017-06-02 08:53:48-- http://mitra.stanford.edu/kundaje/genome_data/hg19/ataqc/eid_to_mnemonic.txt
Resolving mitra.stanford.edu... 171.65.76.236
Connecting to mitra.stanford.edu|171.65.76.236|:80... connected.
HTTP request sent, awaiting response... 416 Requested Range Not Satisfiable
The file is already fully retrieved; nothing to do.
tar: globalmap_k20tok54: skipping existing file
tar: globalmap_k20tok54/chr17.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chrY.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chrM.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr22.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr12.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr2.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr18.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr15.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr9.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr19.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr6.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr13.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr10.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr20.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr21.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr8.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr7.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr4.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr1.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chrX.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr14.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr3.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr11.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr16.uint8.unique: skipping existing file
tar: globalmap_k20tok54/chr5.uint8.unique: skipping existing file
[bwa_index] Pack FASTA... 37.49 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=6191387966, availableWord=447648912
[BWTIncConstructFromPacked] 10 iterations done. 99999998 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 199999998 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 299999998 characters processed.
[BWTIncConstructFromPacked] 40 iterations done. 399999998 characters processed.
[BWTIncConstructFromPacked] 50 iterations done. 499999998 characters processed.
[BWTIncConstructFromPacked] 60 iterations done. 599999998 characters processed.
[BWTIncConstructFromPacked] 70 iterations done. 699999998 characters processed.
[BWTIncConstructFromPacked] 80 iterations done. 799999998 characters processed.
[BWTIncConstructFromPacked] 90 iterations done. 899999998 characters processed.
[BWTIncConstructFromPacked] 100 iterations done. 999999998 characters processed.
[BWTIncConstructFromPacked] 110 iterations done. 1099999998 characters processed.
[BWTIncConstructFromPacked] 120 iterations done. 1199999998 characters processed.
[BWTIncConstructFromPacked] 130 iterations done. 1299999998 characters processed.
[BWTIncConstructFromPacked] 140 iterations done. 1399999998 characters processed.
[BWTIncConstructFromPacked] 150 iterations done. 1499999998 characters processed.
[BWTIncConstructFromPacked] 160 iterations done. 1599999998 characters processed.
[BWTIncConstructFromPacked] 170 iterations done. 1699999998 characters processed.
[BWTIncConstructFromPacked] 180 iterations done. 1799999998 characters processed.
[BWTIncConstructFromPacked] 190 iterations done. 1899999998 characters processed.
[BWTIncConstructFromPacked] 200 iterations done. 1999999998 characters processed.
[BWTIncConstructFromPacked] 210 iterations done. 2099999998 characters processed.
[BWTIncConstructFromPacked] 220 iterations done. 2199999998 characters processed.
[BWTIncConstructFromPacked] 230 iterations done. 2299999998 characters processed.
[BWTIncConstructFromPacked] 240 iterations done. 2399999998 characters processed.
[BWTIncConstructFromPacked] 250 iterations done. 2499999998 characters processed.
[BWTIncConstructFromPacked] 260 iterations done. 2599999998 characters processed.
[BWTIncConstructFromPacked] 270 iterations done. 2699999998 characters processed.
[BWTIncConstructFromPacked] 280 iterations done. 2799999998 characters processed.
[BWTIncConstructFromPacked] 290 iterations done. 2899999998 characters processed.
[BWTIncConstructFromPacked] 300 iterations done. 2999999998 characters processed.
[BWTIncConstructFromPacked] 310 iterations done. 3099999998 characters processed.
[BWTIncConstructFromPacked] 320 iterations done. 3199999998 characters processed.
[BWTIncConstructFromPacked] 330 iterations done. 3299999998 characters processed.
[BWTIncConstructFromPacked] 340 iterations done. 3399999998 characters processed.
[BWTIncConstructFromPacked] 350 iterations done. 3499999998 characters processed.
[BWTIncConstructFromPacked] 360 iterations done. 3599999998 characters processed.
[BWTIncConstructFromPacked] 370 iterations done. 3699999998 characters processed.
[BWTIncConstructFromPacked] 380 iterations done. 3799999998 characters processed.
[BWTIncConstructFromPacked] 390 iterations done. 3899999998 characters processed.
[BWTIncConstructFromPacked] 400 iterations done. 3999999998 characters processed.
[BWTIncConstructFromPacked] 410 iterations done. 4099999998 characters processed.
[BWTIncConstructFromPacked] 420 iterations done. 4199999998 characters processed.
[BWTIncConstructFromPacked] 430 iterations done. 4299999998 characters processed.
[BWTIncConstructFromPacked] 440 iterations done. 4399999998 characters processed.
[BWTIncConstructFromPacked] 450 iterations done. 4499999998 characters processed.
[BWTIncConstructFromPacked] 460 iterations done. 4599999998 characters processed.
[BWTIncConstructFromPacked] 470 iterations done. 4699999998 characters processed.
[BWTIncConstructFromPacked] 480 iterations done. 4799999998 characters processed.
[BWTIncConstructFromPacked] 490 iterations done. 4899999998 characters processed.
[BWTIncConstructFromPacked] 500 iterations done. 4999999998 characters processed.
[BWTIncConstructFromPacked] 510 iterations done. 5099999998 characters processed.
[BWTIncConstructFromPacked] 520 iterations done. 5199999998 characters processed.
[BWTIncConstructFromPacked] 530 iterations done. 5299999998 characters processed.
[BWTIncConstructFromPacked] 540 iterations done. 5399999998 characters processed.
[BWTIncConstructFromPacked] 550 iterations done. 5499999998 characters processed.
[BWTIncConstructFromPacked] 560 iterations done. 5596003406 characters processed.
[BWTIncConstructFromPacked] 570 iterations done. 5681458862 characters processed.
[BWTIncConstructFromPacked] 580 iterations done. 5757407918 characters processed.
[BWTIncConstructFromPacked] 590 iterations done. 5824907614 characters processed.
[BWTIncConstructFromPacked] 600 iterations done. 5884897502 characters processed.
[BWTIncConstructFromPacked] 610 iterations done. 5938212670 characters processed.
[BWTIncConstructFromPacked] 620 iterations done. 5985595326 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 6027705102 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 6065128334 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 6098386190 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 6127941854 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 6154206942 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 6177547390 characters processed.
[bwa_index] 3584.13 seconds elapse.
[bwa_index] Update BWT... 21.54 sec
[bwa_index] Pack forward-only FASTA... 24.44 sec
[bwa_index] Construct SA from BWT and Occ... 968.91 sec
[main] Version: 0.7.13-r1126
[main] CMD: bwa index male.hg19.fa
[main] Real time: 4697.887 sec; CPU: 4636.520 sec
################################### STDOUT for Genome Installation ###################################
################################### STDOUT for Genome Installation ###################################
################################### STDOUT for Genome Installation ###################################
tools/TF_chipseq_pipeline/Genomes
Downloading files...
globalmap_k20tok54/
globalmap_k20tok54/chr17.uint8.unique
globalmap_k20tok54/chrY.uint8.unique
globalmap_k20tok54/chrM.uint8.unique
globalmap_k20tok54/chr22.uint8.unique
globalmap_k20tok54/chr12.uint8.unique
globalmap_k20tok54/chr2.uint8.unique
globalmap_k20tok54/chr18.uint8.unique
globalmap_k20tok54/chr15.uint8.unique
globalmap_k20tok54/chr9.uint8.unique
globalmap_k20tok54/chr19.uint8.unique
globalmap_k20tok54/chr6.uint8.unique
globalmap_k20tok54/chr13.uint8.unique
globalmap_k20tok54/chr10.uint8.unique
globalmap_k20tok54/chr20.uint8.unique
globalmap_k20tok54/chr21.uint8.unique
globalmap_k20tok54/chr8.uint8.unique
globalmap_k20tok54/chr7.uint8.unique
globalmap_k20tok54/chr4.uint8.unique
globalmap_k20tok54/chr1.uint8.unique
globalmap_k20tok54/chrX.uint8.unique
globalmap_k20tok54/chr14.uint8.unique
globalmap_k20tok54/chr3.uint8.unique
globalmap_k20tok54/chr11.uint8.unique
globalmap_k20tok54/chr16.uint8.unique
globalmap_k20tok54/chr5.uint8.unique
Extracting/processing data files...
Building bwa index...
[bwt_gen] Finished constructing BWT in 687 iterations.
Creating species file... (tools/TF_chipseq_pipeline/Genomes/aquas_chipseq_species.conf)
=== Genome data (hg19) has been successfully installed. ===
################################### content of the Genomes/hg19/bwa_index ###################################
################################### content of the Genomes/hg19/bwa_index ###################################
################################### content of the Genomes/hg19/bwa_index ###################################
$ ls -ltrh Genomes/hg19/bwa_index/
total 5.1G
lrwxrwxrwx 1 15 Jun 2 09:01 male.hg19.fa -> ../male.hg19.fa
-rw-r--r-- 1 2.9G Jun 2 10:02 male.hg19.fa.bwt
-rw-r--r-- 1 739M Jun 2 10:03 male.hg19.fa.pac
-rw-r--r-- 1 944 Jun 2 10:03 male.hg19.fa.ann
-rw-r--r-- 1 6.4K Jun 2 10:03 male.hg19.fa.amb
-rw-r--r-- 1 1.5G Jun 2 10:19 male.hg19.fa.sa
from chipseq_pipeline.
rdali
commented on July 21, 2024
################################### STDERROR of ChIPSeq pipeline ###################################
################################### STDERROR of ChIPSeq pipeline ###################################
################################### STDERROR of ChIPSeq pipeline ###################################
00:00:00.000 Bds 0.99999e (build 2016-08-26 06:34), by Pablo Cingolani
00:00:00.214 Parsing
00:00:13.628 Initializing
00:00:13.704 Process ID: chipseq.bds.20170602_104615_132
00:00:13.704 Running
00:00:21.261 Executioner factory: Creating new executioner type 'LOCAL'
00:00:21.340 ExecutionerLocal 'Local[38]': Queuing task: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10
00:00:21.341 Waiting for all tasks to finish.
00:00:21.341 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: SCHEDULED
00:00:21.343 ExecutionerLocal 'Local[38]': Started running
00:00:21.344 ExecutionerLocal 'Local[38]': Task selected 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' on host 'localhost'
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 225438 pairs: 243.286 +/- 54.364
[infer_isize] skewness: 0.538; kurtosis: 0.215; ap_prior: 5.31e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.77 sec
[bwa_sai2sam_pe_core] changing coordinates of 3673 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9767 out of 10967 Q17 singletons are mated.
[bwa_paired_sw] 294 out of 2210 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.18 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 241492 pairs: 242.723 +/- 54.198
[infer_isize] skewness: 0.537; kurtosis: 0.219; ap_prior: 5.16e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.51 sec
[bwa_sai2sam_pe_core] changing coordinates of 1098 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9024 out of 10229 Q17 singletons are mated.
[bwa_paired_sw] 41 out of 2130 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.82 sec
[bwa_sai2sam_pe_core] print alignments... 00:01:22.625 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:01:22.879 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
1.40 sec
[bwa_sai2sam_pe_core] 524288 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 240809 pairs: 241.415 +/- 54.160
[infer_isize] skewness: 0.560; kurtosis: 0.271; ap_prior: 7.05e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.61 sec
[bwa_sai2sam_pe_core] changing coordinates of 1463 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7369 out of 8510 Q17 singletons are mated.
[bwa_paired_sw] 89 out of 2716 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 786432 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 193449 pairs: 241.079 +/- 54.501
[infer_isize] skewness: 0.551; kurtosis: 0.227; ap_prior: 1.42e-04
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.97 sec
[bwa_sai2sam_pe_core] changing coordinates of 6994 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 25842 out of 27807 Q17 singletons are mated.
[bwa_paired_sw] 3030 out of 12986 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 3.99 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec
[bwa_sai2sam_pe_core] print alignments... 00:02:23.726 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:02:23.890 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
1.41 sec
[bwa_sai2sam_pe_core] 1048576 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 200644 pairs: 242.543 +/- 54.549
[infer_isize] skewness: 0.549; kurtosis: 0.240; ap_prior: 5.19e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.78 sec
[bwa_sai2sam_pe_core] changing coordinates of 11570 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8913 out of 9939 Q17 singletons are mated.
[bwa_paired_sw] 567 out of 2654 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.19 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec
[bwa_sai2sam_pe_core] print alignments... 1.47 sec
[bwa_sai2sam_pe_core] 1310720 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239159 pairs: 241.662 +/- 54.133
[infer_isize] skewness: 0.555; kurtosis: 0.271; ap_prior: 6.82e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.60 sec
[bwa_sai2sam_pe_core] changing coordinates of 1707 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7599 out of 8778 Q17 singletons are mated.
[bwa_paired_sw] 89 out of 2607 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.99 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 1572864 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 237, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 242340 pairs: 241.311 +/- 54.204
[infer_isize] skewness: 0.571; kurtosis: 0.276; ap_prior: 7.63e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
00:03:24.787 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:03:24.900 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
[bwa_sai2sam_pe_core] time elapses: 7.90 sec
[bwa_sai2sam_pe_core] changing coordinates of 1303 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6817 out of 7968 Q17 singletons are mated.
[bwa_paired_sw] 67 out of 2787 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 1835008 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 241325 pairs: 242.727 +/- 53.973
[infer_isize] skewness: 0.532; kurtosis: 0.239; ap_prior: 5.15e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.75 sec
[bwa_sai2sam_pe_core] changing coordinates of 1497 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7764 out of 8920 Q17 singletons are mated.
[bwa_paired_sw] 48 out of 2150 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.82 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 2097152 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 237866 pairs: 241.906 +/- 53.992
[infer_isize] skewness: 0.544; kurtosis: 0.246; ap_prior: 6.36e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.58 sec
[bwa_sai2sam_pe_core] changing coordinates of 1856 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7057 out of 8173 Q17 singletons are mated.
[bwa_paired_sw] 81 out of 2503 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec
[bwa_sai2sam_pe_core] print alignments... 00:04:25.835 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:04:25.910 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
1.40 sec
[bwa_sai2sam_pe_core] 2359296 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 236883 pairs: 241.639 +/- 54.175
[infer_isize] skewness: 0.556; kurtosis: 0.249; ap_prior: 6.79e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.89 sec
[bwa_sai2sam_pe_core] changing coordinates of 2192 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8494 out of 9686 Q17 singletons are mated.
[bwa_paired_sw] 149 out of 2672 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 2621440 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 239923 pairs: 242.138 +/- 54.082
[infer_isize] skewness: 0.543; kurtosis: 0.228; ap_prior: 6.51e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.19 sec
[bwa_sai2sam_pe_core] changing coordinates of 865 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9328 out of 11155 Q17 singletons are mated.
[bwa_paired_sw] 61 out of 2558 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 00:05:26.884 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:05:26.920 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
1.38 sec
[bwa_sai2sam_pe_core] 2883584 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241349 pairs: 241.734 +/- 54.166
[infer_isize] skewness: 0.555; kurtosis: 0.263; ap_prior: 6.91e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.43 sec
[bwa_sai2sam_pe_core] changing coordinates of 1241 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8196 out of 9436 Q17 singletons are mated.
[bwa_paired_sw] 48 out of 2547 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.03 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 3145728 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 172352 pairs: 241.563 +/- 54.324
[infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 7.33e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.92 sec
[bwa_sai2sam_pe_core] changing coordinates of 10130 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7724 out of 8696 Q17 singletons are mated.
[bwa_paired_sw] 948 out of 3502 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.24 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec
[bwa_sai2sam_pe_core] print alignments... 00:06:27.928 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:06:27.933 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
1.32 sec
[bwa_sai2sam_pe_core] 3407872 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 222023 pairs: 241.686 +/- 54.293
[infer_isize] skewness: 0.553; kurtosis: 0.245; ap_prior: 7.01e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.25 sec
[bwa_sai2sam_pe_core] changing coordinates of 5699 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7165 out of 8362 Q17 singletons are mated.
[bwa_paired_sw] 216 out of 2754 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 3670016 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 240218 pairs: 241.140 +/- 53.914
[infer_isize] skewness: 0.554; kurtosis: 0.242; ap_prior: 7.17e-05
[infer_isize] inferred maximum insert size: 615 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.64 sec
[bwa_sai2sam_pe_core] changing coordinates of 1472 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7182 out of 8405 Q17 singletons are mated.
[bwa_paired_sw] 99 out of 2734 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 00:07:28.942 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:07:28.960 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.41 sec
[bwa_sai2sam_pe_core] 3932160 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241089 pairs: 241.318 +/- 54.044
[infer_isize] skewness: 0.565; kurtosis: 0.273; ap_prior: 7.18e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.18 sec
[bwa_sai2sam_pe_core] changing coordinates of 1451 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7645 out of 8811 Q17 singletons are mated.
[bwa_paired_sw] 100 out of 2706 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 4194304 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 237981 pairs: 242.180 +/- 54.232
[infer_isize] skewness: 0.549; kurtosis: 0.232; ap_prior: 6.82e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.26 sec
[bwa_sai2sam_pe_core] changing coordinates of 2050 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8988 out of 10230 Q17 singletons are mated.
[bwa_paired_sw] 158 out of 2672 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.10 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 00:08:29.953 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:08:30.008 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.39 sec
[bwa_sai2sam_pe_core] 4456448 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241952 pairs: 241.881 +/- 54.067
[infer_isize] skewness: 0.551; kurtosis: 0.257; ap_prior: 6.72e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.86 sec
[bwa_sai2sam_pe_core] changing coordinates of 1268 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7525 out of 8753 Q17 singletons are mated.
[bwa_paired_sw] 77 out of 2647 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.99 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 4718592 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 240858 pairs: 242.001 +/- 53.908
[infer_isize] skewness: 0.543; kurtosis: 0.239; ap_prior: 6.25e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.24 sec
[bwa_sai2sam_pe_core] changing coordinates of 1080 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8431 out of 9750 Q17 singletons are mated.
[bwa_paired_sw] 114 out of 2579 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 00:09:30.963 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:09:31.051 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.40 sec
[bwa_sai2sam_pe_core] 4980736 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (203, 237, 277)
[infer_isize] low and high boundaries: 125 and 425 for estimating avg and std
[infer_isize] inferred external isize from 240327 pairs: 241.033 +/- 54.127
[infer_isize] skewness: 0.565; kurtosis: 0.269; ap_prior: 7.44e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.75 sec
[bwa_sai2sam_pe_core] changing coordinates of 1705 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6876 out of 8054 Q17 singletons are mated.
[bwa_paired_sw] 89 out of 2797 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 5242880 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 240821 pairs: 241.744 +/- 54.086
[infer_isize] skewness: 0.546; kurtosis: 0.236; ap_prior: 6.68e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.04 sec
[bwa_sai2sam_pe_core] changing coordinates of 1832 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7051 out of 8278 Q17 singletons are mated.
[bwa_paired_sw] 128 out of 2687 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec
[bwa_sai2sam_pe_core] print alignments... 00:10:31.974 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:10:32.089 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.40 sec
[bwa_sai2sam_pe_core] 5505024 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 238571 pairs: 241.322 +/- 54.103
[infer_isize] skewness: 0.561; kurtosis: 0.262; ap_prior: 6.96e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.82 sec
[bwa_sai2sam_pe_core] changing coordinates of 1915 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8050 out of 9325 Q17 singletons are mated.
[bwa_paired_sw] 156 out of 2792 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.03 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 5767168 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 233693 pairs: 242.018 +/- 54.014
[infer_isize] skewness: 0.544; kurtosis: 0.226; ap_prior: 6.09e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.32 sec
[bwa_sai2sam_pe_core] changing coordinates of 2837 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7822 out of 9072 Q17 singletons are mated.
[bwa_paired_sw] 202 out of 2541 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.03 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 6029312 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:11:32.984 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:11:33.115 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 193233 pairs: 241.293 +/- 54.170
[infer_isize] skewness: 0.569; kurtosis: 0.260; ap_prior: 8.38e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.76 sec
[bwa_sai2sam_pe_core] changing coordinates of 1940 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7543 out of 8634 Q17 singletons are mated.
[bwa_paired_sw] 263 out of 2722 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.05 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.83 sec
[bwa_sai2sam_pe_core] print alignments... 1.21 sec
[bwa_sai2sam_pe_core] 6291456 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 236541 pairs: 241.292 +/- 54.154
[infer_isize] skewness: 0.568; kurtosis: 0.269; ap_prior: 7.80e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.72 sec
[bwa_sai2sam_pe_core] changing coordinates of 2010 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8347 out of 9632 Q17 singletons are mated.
[bwa_paired_sw] 124 out of 3002 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.99 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 6553600 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:12:33.994 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:12:34.145 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (203, 237, 277)
[infer_isize] low and high boundaries: 125 and 425 for estimating avg and std
[infer_isize] inferred external isize from 239347 pairs: 240.791 +/- 54.158
[infer_isize] skewness: 0.576; kurtosis: 0.286; ap_prior: 7.98e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.77 sec
[bwa_sai2sam_pe_core] changing coordinates of 2427 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6503 out of 7723 Q17 singletons are mated.
[bwa_paired_sw] 116 out of 2984 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.92 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 6815744 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 240281 pairs: 240.937 +/- 53.952
[infer_isize] skewness: 0.552; kurtosis: 0.235; ap_prior: 7.56e-05
[infer_isize] inferred maximum insert size: 615 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.27 sec
[bwa_sai2sam_pe_core] changing coordinates of 2012 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6640 out of 7894 Q17 singletons are mated.
[bwa_paired_sw] 108 out of 2899 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.94 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 7077888 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:13:35.004 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:13:35.177 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239755 pairs: 241.239 +/- 54.064
[infer_isize] skewness: 0.559; kurtosis: 0.265; ap_prior: 7.83e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.05 sec
[bwa_sai2sam_pe_core] changing coordinates of 1549 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8247 out of 9546 Q17 singletons are mated.
[bwa_paired_sw] 116 out of 2969 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.05 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.10 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 7340032 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 233124 pairs: 241.583 +/- 54.418
[infer_isize] skewness: 0.568; kurtosis: 0.257; ap_prior: 8.01e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.85 sec
[bwa_sai2sam_pe_core] changing coordinates of 3221 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7800 out of 9095 Q17 singletons are mated.
[bwa_paired_sw] 251 out of 3123 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 7602176 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 234349 pairs: 240.959 +/- 53.752
[infer_isize] skewness: 0.559; kurtosis: 0.261; ap_prior: 7.72e-05
[infer_isize] inferred maximum insert size: 614 (6.94 sigma)
00:14:36.013 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:14:36.214 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[bwa_sai2sam_pe_core] time elapses: 8.25 sec
[bwa_sai2sam_pe_core] changing coordinates of 3343 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7231 out of 8437 Q17 singletons are mated.
[bwa_paired_sw] 178 out of 2970 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 7864320 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 224990 pairs: 241.336 +/- 54.117
[infer_isize] skewness: 0.559; kurtosis: 0.265; ap_prior: 6.96e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.75 sec
[bwa_sai2sam_pe_core] changing coordinates of 3464 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6777 out of 7945 Q17 singletons are mated.
[bwa_paired_sw] 106 out of 2651 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 8126464 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (203, 237, 277)
[infer_isize] low and high boundaries: 125 and 425 for estimating avg and std
[infer_isize] inferred external isize from 239668 pairs: 240.865 +/- 54.172
[infer_isize] skewness: 0.570; kurtosis: 0.266; ap_prior: 8.10e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.54 sec
[bwa_sai2sam_pe_core] changing coordinates of 2219 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7007 out of 8265 Q17 singletons are mated.
[bwa_paired_sw] 105 out of 3048 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.97 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 00:15:37.023 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:15:37.243 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
0.86 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 8388608 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 240999 pairs: 240.997 +/- 54.002
[infer_isize] skewness: 0.548; kurtosis: 0.227; ap_prior: 7.84e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.18 sec
[bwa_sai2sam_pe_core] changing coordinates of 1584 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6983 out of 8260 Q17 singletons are mated.
[bwa_paired_sw] 105 out of 3003 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 8650752 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 241818 pairs: 242.106 +/- 53.944
[infer_isize] skewness: 0.538; kurtosis: 0.229; ap_prior: 5.80e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.59 sec
[bwa_sai2sam_pe_core] changing coordinates of 982 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8846 out of 10204 Q17 singletons are mated.
[bwa_paired_sw] 169 out of 2541 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.04 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 00:16:38.035 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:16:38.334 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.40 sec
[bwa_sai2sam_pe_core] 8912896 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 242516 pairs: 241.863 +/- 54.087
[infer_isize] skewness: 0.550; kurtosis: 0.243; ap_prior: 6.43e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.97 sec
[bwa_sai2sam_pe_core] changing coordinates of 1028 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7618 out of 8924 Q17 singletons are mated.
[bwa_paired_sw] 65 out of 2562 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.97 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 9175040 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 230394 pairs: 242.300 +/- 54.089
[infer_isize] skewness: 0.530; kurtosis: 0.193; ap_prior: 5.54e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.21 sec
[bwa_sai2sam_pe_core] changing coordinates of 2970 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9675 out of 10954 Q17 singletons are mated.
[bwa_paired_sw] 116 out of 2348 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.13 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 9437184 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:17:39.046 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:17:39.370 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239699 pairs: 241.969 +/- 54.184
[infer_isize] skewness: 0.565; kurtosis: 0.277; ap_prior: 6.32e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.66 sec
[bwa_sai2sam_pe_core] changing coordinates of 1142 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9145 out of 10510 Q17 singletons are mated.
[bwa_paired_sw] 83 out of 2524 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 9699328 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 241996 pairs: 242.065 +/- 53.988
[infer_isize] skewness: 0.539; kurtosis: 0.234; ap_prior: 6.31e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.72 sec
[bwa_sai2sam_pe_core] changing coordinates of 952 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8374 out of 9615 Q17 singletons are mated.
[bwa_paired_sw] 80 out of 2557 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.05 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 9961472 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (203, 237, 278)
[infer_isize] low and high boundaries: 125 and 428 for estimating avg and std
[infer_isize] inferred external isize from 234205 pairs: 240.975 +/- 54.236
[infer_isize] skewness: 0.581; kurtosis: 0.304; ap_prior: 1.08e-04
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
00:18:40.056 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:18:40.402 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[bwa_sai2sam_pe_core] time elapses: 8.49 sec
[bwa_sai2sam_pe_core] changing coordinates of 4314 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7508 out of 8772 Q17 singletons are mated.
[bwa_paired_sw] 164 out of 3204 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 10223616 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241409 pairs: 241.337 +/- 54.067
[infer_isize] skewness: 0.575; kurtosis: 0.292; ap_prior: 7.61e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.07 sec
[bwa_sai2sam_pe_core] changing coordinates of 1593 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6648 out of 7949 Q17 singletons are mated.
[bwa_paired_sw] 86 out of 2921 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.92 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 10485760 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 242318 pairs: 241.163 +/- 54.208
[infer_isize] skewness: 0.565; kurtosis: 0.265; ap_prior: 7.16e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.26 sec
[bwa_sai2sam_pe_core] changing coordinates of 1123 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7132 out of 8387 Q17 singletons are mated.
[bwa_paired_sw] 61 out of 2758 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec
[bwa_sai2sam_pe_core] print alignments... 00:19:41.066 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:19:41.431 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.40 sec
[bwa_sai2sam_pe_core] 10747904 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 232642 pairs: 242.107 +/- 54.538
[infer_isize] skewness: 0.559; kurtosis: 0.272; ap_prior: 8.50e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.37 sec
[bwa_sai2sam_pe_core] changing coordinates of 2939 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8947 out of 10345 Q17 singletons are mated.
[bwa_paired_sw] 470 out of 2878 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.18 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 11010048 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 237944 pairs: 241.449 +/- 54.241
[infer_isize] skewness: 0.566; kurtosis: 0.256; ap_prior: 6.93e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.24 sec
[bwa_sai2sam_pe_core] changing coordinates of 1803 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9422 out of 10715 Q17 singletons are mated.
[bwa_paired_sw] 90 out of 2655 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.11 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 00:20:42.076 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:20:42.463 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.39 sec
[bwa_sai2sam_pe_core] 11272192 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241589 pairs: 241.877 +/- 54.100
[infer_isize] skewness: 0.554; kurtosis: 0.261; ap_prior: 6.48e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.86 sec
[bwa_sai2sam_pe_core] changing coordinates of 1718 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7173 out of 8446 Q17 singletons are mated.
[bwa_paired_sw] 97 out of 2664 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.98 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 11534336 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 280)
[infer_isize] low and high boundaries: 125 and 432 for estimating avg and std
[infer_isize] inferred external isize from 209044 pairs: 241.522 +/- 54.806
[infer_isize] skewness: 0.589; kurtosis: 0.332; ap_prior: 2.16e-04
[infer_isize] inferred maximum insert size: 622 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.25 sec
[bwa_sai2sam_pe_core] changing coordinates of 9141 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7974 out of 9114 Q17 singletons are mated.
[bwa_paired_sw] 2363 out of 5908 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.68 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.99 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 11796480 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 237, 277)
[infer_isize] low and high boundaries: 125 and 423 for estimating avg and std
[infer_isize] inferred external isize from 221239 pairs: 241.071 +/- 53.998
[infer_isize] skewness: 0.549; kurtosis: 0.224; ap_prior: 6.78e-05
[infer_isize] inferred maximum insert size: 616 (6.94 sigma)
00:21:43.087 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:21:43.488 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[bwa_sai2sam_pe_core] time elapses: 7.12 sec
[bwa_sai2sam_pe_core] changing coordinates of 5527 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9036 out of 10330 Q17 singletons are mated.
[bwa_paired_sw] 137 out of 2666 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 12058624 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 218609 pairs: 241.787 +/- 54.166
[infer_isize] skewness: 0.555; kurtosis: 0.252; ap_prior: 7.90e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.84 sec
[bwa_sai2sam_pe_core] changing coordinates of 4611 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10112 out of 11387 Q17 singletons are mated.
[bwa_paired_sw] 126 out of 2491 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.18 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 12320768 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 237, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 242319 pairs: 241.220 +/- 54.138
[infer_isize] skewness: 0.564; kurtosis: 0.266; ap_prior: 7.51e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.75 sec
[bwa_sai2sam_pe_core] changing coordinates of 1436 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6544 out of 7804 Q17 singletons are mated.
[bwa_paired_sw] 86 out of 2933 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.91 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 00:22:44.097 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:22:44.515 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.39 sec
[bwa_sai2sam_pe_core] 12582912 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 232523 pairs: 241.792 +/- 54.116
[infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 6.30e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.38 sec
[bwa_sai2sam_pe_core] changing coordinates of 2633 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9185 out of 10503 Q17 singletons are mated.
[bwa_paired_sw] 129 out of 2574 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.10 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 12845056 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 232904 pairs: 242.020 +/- 54.229
[infer_isize] skewness: 0.549; kurtosis: 0.242; ap_prior: 6.33e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.51 sec
[bwa_sai2sam_pe_core] changing coordinates of 3660 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9223 out of 10590 Q17 singletons are mated.
[bwa_paired_sw] 188 out of 2627 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.15 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 13107200 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:23:45.108 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:23:45.545 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 219802 pairs: 241.772 +/- 54.243
[infer_isize] skewness: 0.566; kurtosis: 0.258; ap_prior: 7.47e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 10.74 sec
[bwa_sai2sam_pe_core] changing coordinates of 3894 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7542 out of 8921 Q17 singletons are mated.
[bwa_paired_sw] 172 out of 2869 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.81 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 13369344 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 217339 pairs: 241.578 +/- 54.285
[infer_isize] skewness: 0.561; kurtosis: 0.269; ap_prior: 7.24e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 9.32 sec
[bwa_sai2sam_pe_core] changing coordinates of 5582 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7345 out of 8649 Q17 singletons are mated.
[bwa_paired_sw] 402 out of 3103 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.04 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.97 sec
[bwa_sai2sam_pe_core] print alignments... 00:24:46.118 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:24:46.576 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.44 sec
[bwa_sai2sam_pe_core] 13631488 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 207599 pairs: 241.946 +/- 54.334
[infer_isize] skewness: 0.557; kurtosis: 0.251; ap_prior: 6.88e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.03 sec
[bwa_sai2sam_pe_core] changing coordinates of 2486 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7069 out of 8259 Q17 singletons are mated.
[bwa_paired_sw] 123 out of 2524 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.29 sec
[bwa_sai2sam_pe_core] 13893632 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 237102 pairs: 241.269 +/- 54.105
[infer_isize] skewness: 0.558; kurtosis: 0.271; ap_prior: 7.43e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.94 sec
[bwa_sai2sam_pe_core] changing coordinates of 1746 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7152 out of 8466 Q17 singletons are mated.
[bwa_paired_sw] 95 out of 2884 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.95 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.86 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 14155776 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
00:25:47.127 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:25:47.602 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241742 pairs: 241.442 +/- 54.195
[infer_isize] skewness: 0.565; kurtosis: 0.269; ap_prior: 7.46e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.97 sec
[bwa_sai2sam_pe_core] changing coordinates of 1357 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6962 out of 8292 Q17 singletons are mated.
[bwa_paired_sw] 91 out of 2910 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 14417920 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 237545 pairs: 242.005 +/- 54.241
[infer_isize] skewness: 0.546; kurtosis: 0.234; ap_prior: 6.70e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.27 sec
[bwa_sai2sam_pe_core] changing coordinates of 1859 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7586 out of 8886 Q17 singletons are mated.
[bwa_paired_sw] 176 out of 2795 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 14680064 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:26:48.136 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:26:48.642 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 165910 pairs: 241.445 +/- 54.164
[infer_isize] skewness: 0.556; kurtosis: 0.255; ap_prior: 6.87e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.99 sec
[bwa_sai2sam_pe_core] changing coordinates of 10492 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6833 out of 7929 Q17 singletons are mated.
[bwa_paired_sw] 575 out of 2957 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 14942208 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239475 pairs: 241.925 +/- 54.169
[infer_isize] skewness: 0.550; kurtosis: 0.242; ap_prior: 6.71e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.42 sec
[bwa_sai2sam_pe_core] changing coordinates of 1769 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7245 out of 8509 Q17 singletons are mated.
[bwa_paired_sw] 57 out of 2667 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.83 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 15204352 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 236985 pairs: 242.755 +/- 54.228
[infer_isize] skewness: 0.538; kurtosis: 0.221; ap_prior: 5.33e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.23 sec
[bwa_sai2sam_pe_core] changing coordinates of 1542 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
00:27:49.147 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:27:49.666 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[bwa_paired_sw] 9598 out of 10961 Q17 singletons are mated.
[bwa_paired_sw] 205 out of 2501 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.17 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 15466496 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 240, 283)
[infer_isize] low and high boundaries: 125 and 439 for estimating avg and std
[infer_isize] inferred external isize from 164815 pairs: 241.293 +/- 54.960
[infer_isize] skewness: 0.609; kurtosis: 0.423; ap_prior: 4.07e-04
[infer_isize] inferred maximum insert size: 623 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.31 sec
[bwa_sai2sam_pe_core] changing coordinates of 11751 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 16477 out of 17913 Q17 singletons are mated.
[bwa_paired_sw] 6646 out of 14896 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 3.94 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.29 sec
[bwa_sai2sam_pe_core] print alignments... 1.31 sec
[bwa_sai2sam_pe_core] 15728640 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 180808 pairs: 241.650 +/- 54.397
[infer_isize] skewness: 0.570; kurtosis: 0.289; ap_prior: 1.18e-04
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.54 sec
[bwa_sai2sam_pe_core] changing coordinates of 8446 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 18848 out of 20965 Q17 singletons are mated.
[bwa_paired_sw] 2413 out of 7478 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 2.75 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 00:28:50.156 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
1.03 sec
[bwa_sai2sam_pe_core] print alignments... 00:28:50.699 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.38 sec
[bwa_sai2sam_pe_core] 15990784 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 237342 pairs: 242.157 +/- 53.980
[infer_isize] skewness: 0.544; kurtosis: 0.236; ap_prior: 5.96e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.93 sec
[bwa_sai2sam_pe_core] changing coordinates of 2125 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8926 out of 10371 Q17 singletons are mated.
[bwa_paired_sw] 83 out of 2468 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 16252928 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 236010 pairs: 242.648 +/- 54.404
[infer_isize] skewness: 0.550; kurtosis: 0.248; ap_prior: 6.07e-05
[infer_isize] inferred maximum insert size: 620 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.92 sec
[bwa_sai2sam_pe_core] changing coordinates of 1412 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8689 out of 10138 Q17 singletons are mated.
[bwa_paired_sw] 146 out of 2542 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 00:29:51.165 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:29:51.802 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.39 sec
[bwa_sai2sam_pe_core] 16515072 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239670 pairs: 241.812 +/- 54.151
[infer_isize] skewness: 0.553; kurtosis: 0.237; ap_prior: 7.06e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.94 sec
[bwa_sai2sam_pe_core] changing coordinates of 1772 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7567 out of 8903 Q17 singletons are mated.
[bwa_paired_sw] 119 out of 2821 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 16777216 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 222796 pairs: 242.972 +/- 54.182
[infer_isize] skewness: 0.540; kurtosis: 0.222; ap_prior: 5.34e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.45 sec
[bwa_sai2sam_pe_core] changing coordinates of 1866 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9087 out of 10416 Q17 singletons are mated.
[bwa_paired_sw] 179 out of 2372 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.11 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 1.35 sec
[bwa_sai2sam_pe_core] 17039360 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:30:52.175 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:30:52.830 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 238431 pairs: 241.573 +/- 54.091
[infer_isize] skewness: 0.561; kurtosis: 0.274; ap_prior: 6.92e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.26 sec
[bwa_sai2sam_pe_core] changing coordinates of 2225 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7661 out of 9041 Q17 singletons are mated.
[bwa_paired_sw] 100 out of 2855 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 17301504 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 238517 pairs: 242.691 +/- 54.200
[infer_isize] skewness: 0.534; kurtosis: 0.215; ap_prior: 5.24e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.15 sec
[bwa_sai2sam_pe_core] changing coordinates of 1554 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9296 out of 10655 Q17 singletons are mated.
[bwa_paired_sw] 75 out of 2253 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 17563648 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239624 pairs: 241.711 +/- 54.205
[infer_isize] skewness: 0.566; kurtosis: 0.267; ap_prior: 7.25e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
00:31:53.186 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:31:53.867 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[bwa_sai2sam_pe_core] time elapses: 6.91 sec
[bwa_sai2sam_pe_core] changing coordinates of 1734 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8306 out of 9642 Q17 singletons are mated.
[bwa_paired_sw] 199 out of 2983 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec
[bwa_sai2sam_pe_core] print alignments... 1.42 sec
[bwa_sai2sam_pe_core] 17825792 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 236157 pairs: 242.325 +/- 54.285
[infer_isize] skewness: 0.543; kurtosis: 0.234; ap_prior: 5.99e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.91 sec
[bwa_sai2sam_pe_core] changing coordinates of 1344 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9037 out of 10480 Q17 singletons are mated.
[bwa_paired_sw] 170 out of 2642 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.11 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.37 sec
[bwa_sai2sam_pe_core] 18087936 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 238149 pairs: 241.347 +/- 54.168
[infer_isize] skewness: 0.565; kurtosis: 0.271; ap_prior: 6.74e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 8.20 sec
[bwa_sai2sam_pe_core] changing coordinates of 1932 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8677 out of 10299 Q17 singletons are mated.
[bwa_paired_sw] 164 out of 2811 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.05 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.93 sec
[bwa_sai2sam_pe_core] print alignments... 00:32:54.197 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:32:54.891 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.38 sec
[bwa_sai2sam_pe_core] 18350080 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241676 pairs: 241.561 +/- 54.104
[infer_isize] skewness: 0.559; kurtosis: 0.266; ap_prior: 6.62e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.32 sec
[bwa_sai2sam_pe_core] changing coordinates of 1170 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7904 out of 9180 Q17 singletons are mated.
[bwa_paired_sw] 65 out of 2708 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 18612224 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 237795 pairs: 242.306 +/- 54.049
[infer_isize] skewness: 0.536; kurtosis: 0.207; ap_prior: 6.24e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.11 sec
[bwa_sai2sam_pe_core] changing coordinates of 1420 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10665 out of 12145 Q17 singletons are mated.
[bwa_paired_sw] 138 out of 2651 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.21 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 00:33:55.207 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:33:55.932 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.40 sec
[bwa_sai2sam_pe_core] 18874368 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 240122 pairs: 241.747 +/- 54.155
[infer_isize] skewness: 0.560; kurtosis: 0.270; ap_prior: 6.81e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.03 sec
[bwa_sai2sam_pe_core] changing coordinates of 1405 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8267 out of 9643 Q17 singletons are mated.
[bwa_paired_sw] 100 out of 2824 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.04 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.01 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 19136512 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 237, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 238939 pairs: 241.117 +/- 54.132
[infer_isize] skewness: 0.572; kurtosis: 0.292; ap_prior: 7.93e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.52 sec
[bwa_sai2sam_pe_core] changing coordinates of 1734 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7713 out of 9032 Q17 singletons are mated.
[bwa_paired_sw] 112 out of 3134 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 19398656 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:34:56.217 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:34:56.970 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (204, 237, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241223 pairs: 241.199 +/- 54.272
[infer_isize] skewness: 0.576; kurtosis: 0.288; ap_prior: 8.00e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.70 sec
[bwa_sai2sam_pe_core] changing coordinates of 1145 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7723 out of 9021 Q17 singletons are mated.
[bwa_paired_sw] 75 out of 3055 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 19660800 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 228855 pairs: 241.991 +/- 54.371
[infer_isize] skewness: 0.560; kurtosis: 0.262; ap_prior: 7.11e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.40 sec
[bwa_sai2sam_pe_core] changing coordinates of 3584 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8220 out of 9625 Q17 singletons are mated.
[bwa_paired_sw] 203 out of 2908 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.07 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.06 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 19922944 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 239673 pairs: 241.343 +/- 54.120
[infer_isize] skewness: 0.559; kurtosis: 0.268; ap_prior: 7.46e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
00:35:57.227 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:35:58.013 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[bwa_sai2sam_pe_core] time elapses: 8.23 sec
[bwa_sai2sam_pe_core] changing coordinates of 1652 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 7887 out of 9252 Q17 singletons are mated.
[bwa_paired_sw] 95 out of 3074 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.03 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.90 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 20185088 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 241111 pairs: 241.994 +/- 53.964
[infer_isize] skewness: 0.550; kurtosis: 0.235; ap_prior: 6.18e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.63 sec
[bwa_sai2sam_pe_core] changing coordinates of 811 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8984 out of 10444 Q17 singletons are mated.
[bwa_paired_sw] 70 out of 2524 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 20447232 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 241787 pairs: 242.718 +/- 54.491
[infer_isize] skewness: 0.548; kurtosis: 0.238; ap_prior: 5.57e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.12 sec
[bwa_sai2sam_pe_core] changing coordinates of 560 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9140 out of 10732 Q17 singletons are mated.
[bwa_paired_sw] 39 out of 2368 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 00:36:58.237 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:36:59.037 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.40 sec
[bwa_sai2sam_pe_core] 20709376 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 211208 pairs: 241.952 +/- 54.254
[infer_isize] skewness: 0.550; kurtosis: 0.245; ap_prior: 7.35e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.26 sec
[bwa_sai2sam_pe_core] changing coordinates of 6941 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9654 out of 11048 Q17 singletons are mated.
[bwa_paired_sw] 713 out of 3672 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.34 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.02 sec
[bwa_sai2sam_pe_core] print alignments... 1.44 sec
[bwa_sai2sam_pe_core] 20971520 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 232720 pairs: 242.181 +/- 54.097
[infer_isize] skewness: 0.537; kurtosis: 0.208; ap_prior: 5.86e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.92 sec
[bwa_sai2sam_pe_core] changing coordinates of 2321 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8616 out of 10046 Q17 singletons are mated.
[bwa_paired_sw] 227 out of 2662 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.08 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.94 sec
[bwa_sai2sam_pe_core] print alignments... 00:37:59.248 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:38:00.064 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.41 sec
[bwa_sai2sam_pe_core] 21233664 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 230618 pairs: 242.563 +/- 54.232
[infer_isize] skewness: 0.542; kurtosis: 0.236; ap_prior: 5.70e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.50 sec
[bwa_sai2sam_pe_core] changing coordinates of 3391 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9369 out of 10877 Q17 singletons are mated.
[bwa_paired_sw] 164 out of 2452 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.13 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 21495808 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 239, 280)
[infer_isize] low and high boundaries: 125 and 432 for estimating avg and std
[infer_isize] inferred external isize from 175886 pairs: 242.093 +/- 54.809
[infer_isize] skewness: 0.575; kurtosis: 0.310; ap_prior: 1.50e-04
[infer_isize] inferred maximum insert size: 622 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.88 sec
[bwa_sai2sam_pe_core] changing coordinates of 14849 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10410 out of 11647 Q17 singletons are mated.
[bwa_paired_sw] 1098 out of 3950 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.53 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec
[bwa_sai2sam_pe_core] print alignments... 1.45 sec
[bwa_sai2sam_pe_core] 21757952 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:39:00.260 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:39:01.108 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 240042 pairs: 242.133 +/- 53.974
[infer_isize] skewness: 0.538; kurtosis: 0.219; ap_prior: 6.07e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.88 sec
[bwa_sai2sam_pe_core] changing coordinates of 1189 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8823 out of 10263 Q17 singletons are mated.
[bwa_paired_sw] 59 out of 2533 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.06 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.88 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 22020096 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 235826 pairs: 243.120 +/- 54.317
[infer_isize] skewness: 0.533; kurtosis: 0.212; ap_prior: 4.75e-05
[infer_isize] inferred maximum insert size: 620 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.85 sec
[bwa_sai2sam_pe_core] changing coordinates of 1184 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 11886 out of 13477 Q17 singletons are mated.
[bwa_paired_sw] 144 out of 2219 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.29 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.00 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 22282240 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 239, 279)
[infer_isize] low and high boundaries: 125 and 429 for estimating avg and std
[infer_isize] inferred external isize from 203989 pairs: 242.361 +/- 54.435
[infer_isize] skewness: 0.557; kurtosis: 0.255; ap_prior: 6.65e-05
[infer_isize] inferred maximum insert size: 620 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.81 sec
[bwa_sai2sam_pe_core] changing coordinates of 5352 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 11501 out of 13005 Q17 singletons are mated.
[bwa_paired_sw] 500 out of 3014 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.39 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 00:40:01.269 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
0.90 sec
[bwa_sai2sam_pe_core] print alignments... 00:40:02.136 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.38 sec
[bwa_sai2sam_pe_core] 22544384 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 234558 pairs: 242.925 +/- 54.183
[infer_isize] skewness: 0.536; kurtosis: 0.228; ap_prior: 4.77e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.40 sec
[bwa_sai2sam_pe_core] changing coordinates of 2309 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10097 out of 11556 Q17 singletons are mated.
[bwa_paired_sw] 77 out of 2200 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.14 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.95 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 22806528 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 238, 278)
[infer_isize] low and high boundaries: 125 and 424 for estimating avg and std
[infer_isize] inferred external isize from 238233 pairs: 242.014 +/- 54.015
[infer_isize] skewness: 0.546; kurtosis: 0.231; ap_prior: 6.17e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.16 sec
[bwa_sai2sam_pe_core] changing coordinates of 1779 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9106 out of 10609 Q17 singletons are mated.
[bwa_paired_sw] 112 out of 2578 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 23068672 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:41:02.279 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:41:03.163 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 232179 pairs: 243.228 +/- 54.536
[infer_isize] skewness: 0.531; kurtosis: 0.197; ap_prior: 4.67e-05
[infer_isize] inferred maximum insert size: 622 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.63 sec
[bwa_sai2sam_pe_core] changing coordinates of 1424 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 12265 out of 13789 Q17 singletons are mated.
[bwa_paired_sw] 233 out of 2436 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.42 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.92 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 23330816 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 221149 pairs: 241.475 +/- 54.270
[infer_isize] skewness: 0.571; kurtosis: 0.276; ap_prior: 7.39e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.19 sec
[bwa_sai2sam_pe_core] changing coordinates of 2589 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9311 out of 10672 Q17 singletons are mated.
[bwa_paired_sw] 223 out of 2908 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.14 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.89 sec
[bwa_sai2sam_pe_core] print alignments... 1.35 sec
[bwa_sai2sam_pe_core] 23592960 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 241875 pairs: 241.740 +/- 54.114
[infer_isize] skewness: 0.550; kurtosis: 0.239; ap_prior: 6.90e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.21 sec
[bwa_sai2sam_pe_core] changing coordinates of 1003 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
00:42:03.289 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:42:04.192 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[bwa_paired_sw] 7307 out of 8701 Q17 singletons are mated.
[bwa_paired_sw] 65 out of 2842 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 0.96 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.89 sec
[bwa_sai2sam_pe_core] print alignments... 1.41 sec
[bwa_sai2sam_pe_core] 23855104 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 240216 pairs: 241.660 +/- 54.105
[infer_isize] skewness: 0.560; kurtosis: 0.269; ap_prior: 7.01e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 7.22 sec
[bwa_sai2sam_pe_core] changing coordinates of 979 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8792 out of 10260 Q17 singletons are mated.
[bwa_paired_sw] 121 out of 2866 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.38 sec
[bwa_sai2sam_pe_core] 24117248 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 234765 pairs: 242.776 +/- 54.312
[infer_isize] skewness: 0.551; kurtosis: 0.245; ap_prior: 5.67e-05
[infer_isize] inferred maximum insert size: 620 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.45 sec
[bwa_sai2sam_pe_core] changing coordinates of 1428 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8458 out of 9917 Q17 singletons are mated.
[bwa_paired_sw] 229 out of 2699 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.85 sec
[bwa_sai2sam_pe_core] print alignments... 00:43:04.300 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:43:05.218 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.38 sec
[bwa_sai2sam_pe_core] 24379392 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 194632 pairs: 242.906 +/- 54.133
[infer_isize] skewness: 0.542; kurtosis: 0.248; ap_prior: 5.47e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.82 sec
[bwa_sai2sam_pe_core] changing coordinates of 1837 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 11734 out of 13338 Q17 singletons are mated.
[bwa_paired_sw] 319 out of 2430 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.34 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.87 sec
[bwa_sai2sam_pe_core] print alignments... 1.25 sec
[bwa_sai2sam_pe_core] 24641536 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (206, 239, 279)
[infer_isize] low and high boundaries: 125 and 425 for estimating avg and std
[infer_isize] inferred external isize from 235487 pairs: 243.090 +/- 54.007
[infer_isize] skewness: 0.518; kurtosis: 0.189; ap_prior: 4.67e-05
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.25 sec
[bwa_sai2sam_pe_core] changing coordinates of 688 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 14407 out of 16066 Q17 singletons are mated.
[bwa_paired_sw] 38 out of 2101 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.42 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.96 sec
[bwa_sai2sam_pe_core] print alignments... 1.39 sec
[bwa_sai2sam_pe_core] 24903680 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
00:44:05.311 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:44:06.242 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 209885 pairs: 242.759 +/- 54.445
[infer_isize] skewness: 0.542; kurtosis: 0.225; ap_prior: 7.64e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.09 sec
[bwa_sai2sam_pe_core] changing coordinates of 2187 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 18103 out of 20206 Q17 singletons are mated.
[bwa_paired_sw] 1580 out of 8401 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 2.68 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.97 sec
[bwa_sai2sam_pe_core] print alignments... 1.37 sec
[bwa_sai2sam_pe_core] 25165824 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 214545 pairs: 242.922 +/- 54.190
[infer_isize] skewness: 0.531; kurtosis: 0.219; ap_prior: 5.74e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.82 sec
[bwa_sai2sam_pe_core] changing coordinates of 7312 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 12477 out of 14025 Q17 singletons are mated.
[bwa_paired_sw] 202 out of 2278 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.33 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.98 sec
[bwa_sai2sam_pe_core] print alignments... 1.40 sec
[bwa_sai2sam_pe_core] 25427968 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 224301 pairs: 242.907 +/- 54.135
[infer_isize] skewness: 0.531; kurtosis: 0.218; ap_prior: 6.02e-05
[infer_isize] inferred maximum insert size: 619 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.06 sec
[bwa_sai2sam_pe_core] changing coordinates of 4498 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 8901 out of 10339 Q17 singletons are mated.
[bwa_paired_sw] 313 out of 2657 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.13 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.91 sec
[bwa_sai2sam_pe_core] print alignments... 00:45:06.323 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:45:07.272 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.41 sec
[bwa_sai2sam_pe_core] 25690112 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (204, 238, 278)
[infer_isize] low and high boundaries: 125 and 426 for estimating avg and std
[infer_isize] inferred external isize from 217409 pairs: 241.736 +/- 54.137
[infer_isize] skewness: 0.557; kurtosis: 0.261; ap_prior: 6.86e-05
[infer_isize] inferred maximum insert size: 617 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 6.65 sec
[bwa_sai2sam_pe_core] changing coordinates of 3923 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 11035 out of 12609 Q17 singletons are mated.
[bwa_paired_sw] 474 out of 3372 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.38 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.16 sec
[bwa_sai2sam_pe_core] print alignments... 1.36 sec
[bwa_sai2sam_pe_core] 25952256 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (205, 239, 279)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 131869 pairs: 242.488 +/- 54.584
[infer_isize] skewness: 0.540; kurtosis: 0.220; ap_prior: 7.70e-05
[infer_isize] inferred maximum insert size: 621 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 5.40 sec
[bwa_sai2sam_pe_core] changing coordinates of 5325 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 14489 out of 15932 Q17 singletons are mated.
[bwa_paired_sw] 1142 out of 3588 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.88 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 1.05 sec
[bwa_sai2sam_pe_core] print alignments... 00:46:07.333 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:46:08.299 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
1.08 sec
[bwa_sai2sam_pe_core] 26214400 sequences have been processed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (199, 234, 275)
[infer_isize] low and high boundaries: 125 and 427 for estimating avg and std
[infer_isize] inferred external isize from 15370 pairs: 237.628 +/- 54.847
[infer_isize] skewness: 0.570; kurtosis: 0.230; ap_prior: 1.33e-04
[infer_isize] inferred maximum insert size: 618 (6.94 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.06 sec
[bwa_sai2sam_pe_core] changing coordinates of 4990 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 10195 out of 12365 Q17 singletons are mated.
[bwa_paired_sw] 1265 out of 2897 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.52 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.57 sec
[bwa_sai2sam_pe_core] print alignments... 0.59 sec
[bwa_sai2sam_pe_core] 26458520 sequences have been processed.
[main] Version: 0.7.13-r1126
[main] CMD: bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.sai ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq
[main] Real time: 2762.464 sec; CPU: 1156.834 sec
00:47:08.341 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:47:09.323 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:48:09.350 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:48:10.347 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:49:10.359 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:49:11.376 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:50:11.367 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:50:12.410 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:51:12.376 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:51:13.435 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:52:13.385 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:52:14.460 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:53:14.394 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:53:15.486 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:54:15.402 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:54:16.513 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:55:16.410 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:55:17.545 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:56:17.418 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:56:18.568 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:57:18.426 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:57:19.608 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:58:19.435 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:58:20.633 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
00:59:20.443 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
00:59:21.656 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:00:21.451 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:00:22.684 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:01:22.459 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:01:23.708 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
[bam_sort_core] merging from 39 files...
01:02:23.467 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:02:24.730 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:03:24.474 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:03:25.752 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:04:25.483 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:04:26.783 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:05:26.491 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:05:27.807 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:06:27.498 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:06:28.832 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:07:28.505 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:07:29.856 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:08:29.513 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:08:30.878 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:09:30.521 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:09:31.899 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:10:31.529 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:10:32.922 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:11:32.537 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:11:33.946 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:12:33.546 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:12:34.972 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:13:34.554 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:13:35.996 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:14:35.562 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:14:37.060 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:15:36.571 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | --------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 15573 | running (RUNNING) | bwa_sam_PE rep1 | | bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re |
01:15:38.087 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:15:48.610 Wait: Task 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished.
01:15:48.615 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: FINISHED
01:15:48.615 Wait: Task 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished.
01:15:48.617 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: FINISHED
01:15:48.617 Wait: Task 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished.
01:15:49.799 ExecutionerLocal 'Local[38]': Queuing task: chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11
01:15:49.799 Waiting for all tasks to finish.
01:15:49.800 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10, state: FINISHED
01:15:49.800 Wait: Task 'chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10' finished.
01:15:49.800 Wait: Waiting for task to finish: chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11, state: SCHEDULED
01:15:50.075 ExecutionerLocal 'Local[38]': Task selected 'chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11' on host 'localhost'
01:16:37.590 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 1 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | ------------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 16002 | running (RUNNING) | dedup_bam_PE_1 rep1 | | if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam |; sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI |
01:16:39.322 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:17:38.614 ExecutionerLocal 'Local[38]': Tasks [Local[38]] Pending: 0 Running: 1 Done: 1 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ----- | ----------------- | ------------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 16002 | running (RUNNING) | dedup_bam_PE_1 rep1 | | if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam |; sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI |
01:17:40.431 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
sambamba-sort: Unable to write to stream
ChIPSeq/chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11.sh: line 21: 19368 Broken pipe samtools view -F 1804 -f 2 -q 30 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam
19369 Segmentation fault (core dumped) | sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam
Task failed:
Program & line : 'tools/TF_chipseq_pipeline/modules/postalign_bam.bds', line 260
Task Name : 'dedup_bam_PE_1 rep1'
Task ID : 'chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11'
Task PID : '16002'
Task hint : 'if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam |; sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI'
Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000'
State : 'ERROR'
Dependency state : 'ERROR'
Retries available : '1'
Input files : '[ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam]'
Output files : '[ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.filt.bam]'
Script file : 'ChIPSeq/chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11.sh'
Exit status : '1'
Program :
# SYS command. line 262
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
# SYS command. line 278
if [[ 0 > 0 ]]; then \
samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam | \
sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam; \
samtools view -h ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam | \
$(which assign_multimappers.py) -k 0 --paired-end | \
samtools fixmate -r /dev/stdin ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam; \
else \
samtools view -F 1804 -f 2 -q 30 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam | \
sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam; \
samtools fixmate -r ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam; \
fi
# SYS command. line 290
samtools view -F 1804 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam | sambamba sort -t 1 /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.filt.bam
# SYS command. line 292
rm -f ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam.fixmate.bam
# SYS command. line 293
rm -f ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam
# SYS command. line 295
TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
StdErr (100000000 lines) :
sambamba-sort: Unable to write to stream
ChIPSeq/chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11.sh: line 21: 19368 Broken pipe samtools view -F 1804 -f 2 -q 30 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam
19369 Segmentation fault (core dumped) | sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.dupmark.bam
01:17:55.737 Wait: Task 'chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11' finished.
Fatal error: tools/TF_chipseq_pipeline/modules/postalign_bam.bds, line 300, pos 3. Task/s failed.
chipseq.bds, line 76 : main()
chipseq.bds, line 79 : void main() { // chipseq pipeline starts here
chipseq.bds, line 87 : align() // align and postalign
chipseq.bds, line 318 : void align() {
chipseq.bds, line 355 : for ( int ctl=0; ctl <= 1; ctl++) { // iterate through inputs (ctl==0 : exp. replicate, ctl==1 : control)
chipseq.bds, line 358 : for ( int rep=1; rep <= get_num_rep( ctl ); rep++) {
chipseq.bds, line 364 : if ( no_par ) align( ctl, rep, nth_rep{group} ) // parallel jobs for align() for each replicate and each control
chipseq.bds, line 374 : void align( int ctl, int rep, int nth_rep ) {
chipseq.bds, line 376 : if ( is_se( ctl, rep ) ) align_SE( ctl, rep, nth_rep )
chipseq.bds, line 377 : else align_PE( ctl, rep, nth_rep )
chipseq.bds, line 550 : void align_PE( int ctl, int rep, int nth_rep ) {
chipseq.bds, line 624 : if ( is_input_bam( ctl, rep ) || is_input_fastq( ctl, rep ) ) {
chipseq.bds, line 633 : if ( no_dup_removal ) {
chipseq.bds, line 637 : else {
chipseq.bds, line 638 : ( filt_bam_, dup_qc_, flagstat_nodup_qc_, pbc_qc_ )
chipseq.bds, line 639 : = dedup_bam_PE( bam_, aln_o_dir, qc_o_dir, group, nth_rep )
postalign_bam.bds, line 233 : string[] dedup_bam_PE( string bam, string o_dir, string log_o_dir, string group, int nth_dedup ) {
postalign_bam.bds, line 249 : if ( out<-in ) {
postalign_bam.bds, line 300 : wait
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
01:17:55.894 Writing report file 'chipseq.bds.20170602_104615_132.report.html'
01:17:55.935 Program 'chipseq.bds.20170602_104615_132' finished, exit value: 1, tasks executed: 2, tasks failed: 1, tasks failed names: dedup_bam_PE_1 rep1.
01:17:55.935 Finished. Exit code: 1
01:17:55.935 ExecutionerLocal 'Local[38]': Killed
from chipseq_pipeline.
rdali
commented on July 21, 2024
################################### STDOUT of ChIPSeq pipeline ###################################
################################### STDOUT of ChIPSeq pipeline ###################################
################################### STDOUT of ChIPSeq pipeline ###################################
== git info
Latest git commit : f26ac96 (Tue May 9 23:50:11 2017)
Reading parameters from section (default) in file(tools/TF_chipseq_pipeline/default.env)...
== configuration file info
Hostname : lm-4r10-n70.guillimin.clumeq.ca
Configuration file :
Environment file : tools/TF_chipseq_pipeline/default.env
Warning: Maximum # threads (-nth) for a pipeline is <= 1. Turning off parallelization... (-no_par)
== parallelization info
No parallel jobs : true
Maximum # threads : 1
== cluster/system info
Walltime (general) : 5h50m
Max. memory (general) : 7G
Force to use a system : local
Process priority (niceness) : 0
Retiral for failed tasks : 0
Submit tasks to a cluster queue :
Unlimited cluster mem./walltime : false
== shell environment info
Conda env. : aquas_chipseq
Conda env. for python3 : aquas_chipseq_py3
Conda bin. directory :
Shell cmd. for init. : if [[ -f
Shell cmd. for init.(py3) : if [[ -f
Shell cmd. for fin. : TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
Cluster task min. len. : 60
Cluster task delay : 0
== output directory/title info
Output dir. : ChIPSeq/160130_CTCF
Title (prefix) : 160130_CTCF
Reading parameters from section (default) in file(tools/TF_chipseq_pipeline/default.env)...
Reading parameters from section (hg19) in file(tools/TF_chipseq_pipeline/Genomes/aquas_chipseq_species.conf)...
== species settings
Species : hg19
Species file : tools/TF_chipseq_pipeline/Genomes/aquas_chipseq_species.conf
Species name (WashU browser) : hg19
Ref. genome seq. fasta : tools/TF_chipseq_pipeline/Genomes/hg19/male.hg19.fa
Chr. sizes file : tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes
Black list bed : tools/TF_chipseq_pipeline/Genomes/hg19/wgEncodeDacMapabilityConsensusExcludable.bed.gz
Ref. genome seq. dir. :
== ENCODE accession settings
ENCODE experiment accession :
ENCODE award RFA :
ENCODE assay category :
ENCODE assay title :
ENCODE award :
ENCODE lab :
ENCODE assembly genome :
ENCODE alias prefix : KLAB_PIPELINE
== report settings
URL root for output directory :
Genome coord. for browser tracks :
== align bwa settings
Param. for bwa : -q 5 -l 32 -k 2
BWA index : tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa
Walltime (bwa) : 47h
Max. memory (bwa) : 12G
== align multimapping settings
alignments reported for multimapping : 0
== postalign bam settings
MAPQ reads rm thresh. : 30
Rm. tag reads with str. :
No dupe removal in filtering raw bam : false
Walltime (bam filter) : 23h
Max. memory (bam filter) : 12G
Dup marker : picard
Use sambamba markdup (instead of picard) : false
== postalign bed/tagalign settings
Max. memory for UNIX shuf : 12G
== postalign cross-corr. analysis settings
Max. memory for UNIX shuf : 12G
User-defined cross-corr. peak strandshift : -1
Extra parameters for cross-corr. analysis :
== callpeak spp settings
Threshold for # peak : 300000
Walltime (spp) : 47h
Max. memory (spp) : 12G
Stack size for run_spp.R :
Use-defined cross-corr. peak strandshift; if -1, use frag. len. :-1
Extra parameters for run_spp.R :
== callpeak gem settings
Threshold for # peak in GEM : 300000
Min. length of k-mers in GEM : 6
Max. length of k-mers in GEM : 13
Q-value threshold for GEM : 0.0
Read distribution txt for GEM : tools/TF_chipseq_pipeline/etc/Read_Distribution_default.txt
Extra parameters for GEM :
Walltime (GEM) : 47h
Max. memory (GEM) : 15G
== callpeak PeakSeq settings
Target FDR for PeakSeq :0.05
Number of simulations for PeakSeq :10
Enrichment mapped frag. len. for PeakSeq :-1
Minimum interpeak distance for PeakSeq :-1
Mappability map file for PeakSeq :
Maximum Q-value for PeakSeq :0.1
Background model for PeakSeq :Simulated
Extra parameters for PeakSeq :
Walltime (PeakSeq) : 47h
Max. memory (PeakSeq) : 12G
== callpeak macs2 settings
Genome size (hs,mm) : hs
Walltime (macs2) : 23h
Max. memory (macs2) : 15G
P-value cutoff (macs2 callpeak) : 0.01
--keep-dup (macs2 callpeak) : all
--extsize (macs2 callpeak); if -1 then use frag. len. : -1
--shift (macs2 callpeak) : 0
Extra parameters for macs2 callpeak :
== callpeak naiver overlap settings
Bedtools intersect -nonamecheck : false
== IDR settings
Append IDR threshold to IDR out_dir : false
== chipseq pipeline settings
replicates : 1
Type of ChIP-Seq pipeline : TF
Final stage for ChIP-Seq : peak
Signal tracks for pooled rep. only : false
Aligner to map raw reads : bwa
reads to subsample for cross-corr. analysis : 15000000
reads to subsample exp. replicates (0: no subsampling): 0
reads to subsample controls (0: no subsampling) : 0
Generate anonymized filt. bam : false
Peak caller for IDR analysis : spp
Control rep. depth ratio : 1.2
Scoring column for IDR : signal.value
IDR threshold : 0.05
Force to use pooled ctl : false
Peak calling for true reps only : false
No peak calling for self pseudo reps : false
Disable cross-correlation analysis : false
Disable g. peak filt. thru. n. peak : false
== checking chipseq parameters ...
== checking input files ...
Rep1 fastq (PE) :
ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq
ChIPSeq/HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq
Control Rep1 fastq (PE) :
ChIPSeq/HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq
ChIPSeq/HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq
Distributing 1 to ...
{rep1=1, ctl1=1}
Distributing 1 to ...
[1, 1]
Task has finished (4516 seconds).
bds -c tools/TF_chipseq_pipeline/bds.config -v tools/TF_chipseq_pipeline/chipseq.bds -title 160130_CTCF -final_stage peak -gensz hs -out_dir ChIPSeq/160130_CTCF -chrsz tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -nth 1 -type TF -species hg19 -bwa_idx tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa -pe1 -fastq1_1:1 HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq -fastq1_2:1 HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq -ctl_pe1 -ctl_fastq1_1:1 HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq -ctl_fastq1_2:1 HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq
################################### chipseq.bds.20170602_104615_132.report.html ###################################
################################### chipseq.bds.20170602_104615_132.report.html ###################################
################################### chipseq.bds.20170602_104615_132.report.html ###################################
chipseq.bds.20170602_104615_132.report.html
<style type="text/css"> pre { width:1200px; overflow: auto; word-wrap: normal; white-space: pre; } </style> <script src="http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js"></script> <script src="http://cytoscape.github.io/cytoscape.js/api/cytoscape.js-latest/cytoscape.min.js"></script> <script src="chipseq.bds.20170602_104615_132.dag.js"></script>BigDataScript report: chipseq.bds
<table class="table table-striped">
<tr> <th> Script file </th><td> tools/TF_chipseq_pipeline/chipseq.bds </td></tr>
<tr> <th> Program ID </th><td> chipseq.bds.20170602_104615_132 </td></tr>
<tr> <th> Start time </th><td> 2017-06-02 10:46:15 </td></tr>
<tr> <th> Run time </th><td> 01:17:42.170 </td></tr>
<tr> <th> Tasks executed </th><td> 2 </td></tr>
<tr> <th> Tasks failed </th><td> 1 </td></tr>
<tr> <th> Tasks failed names </th><td> <pre>dedup_bam_PE_1 rep1</pre> </td></tr>
<tr> <th> Arguments* </th><td> [-title, 160130_CTCF, -final_stage, peak, -gensz, hs, -out_dir, ChIPSeq/160130_CTCF, -chrsz, tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes, -nth, 1, -type, TF, -species, hg19, -bwa_idx, tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa, -pe1, -fastq1_1:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, -fastq1_2:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, -ctl_pe1, -ctl_fastq1_1:1, HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq, -ctl_fastq1_2:1, HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq] </td></tr>
<tr> <th> System* </th><td> local </td></tr>
<tr> <th> Cpus* </th><td> -1 </td></tr>
<tr> <th> Exit value </th><td style="background-color: #ffc0c0"> 1 </td></tr>
</table>
<b>*</b> Values in global scope when program finished execution.
Timeline
<script type="text/javascript" src="https://www.google.com/jsapi?autoload={'modules':[{'name':'visualization','version':'1','packages':['timeline']}]}"></script> <script type="text/javascript"> google.setOnLoadCallback(drawChart);function drawChart() {
var container = document.getElementById('bdsTimeline');
var chart = new google.visualization.Timeline(container);
var dataTable = new google.visualization.DataTable();
dataTable.addColumn({ type: 'string', id: 'TaskName' });
dataTable.addColumn({ type: 'string', id: 'TaskHint' });
dataTable.addColumn({ type: 'date', id: 'Start' });
dataTable.addColumn({ type: 'date', id: 'End' });
dataTable.addRows([
[ 'bwa_sam_PE rep1', 'bwa sampe tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.sai ChIPSeq/160130_CTCF/align/re', new Date(2017,5,02,10,46,23), new Date(2017,5,02,12,01,50) ],
[ 'dedup_bam_PE_1 rep1', 'if [[ 0 > 0 ]]; then; samtools view -F 524 -f 2 -u ChIPSeq/160130_CTCF/align/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.bam |; sambamba sort -t 1 -n /dev/stdin -o ChIPSeq/160130_CTCF/align/rep1/HI', new Date(2017,5,02,12,01,52), new Date(2017,5,02,12,01,52) ],
]);
var options = {
timeline: { groupByRowLabel: false }
};
chart.draw(dataTable, options);
}
</script>
<div id="bdsTimeline" style="width: 900px; height: 168px;"></div>
Task Graph
Parallel (threads) details
| Thread ID | Parent | Tasks |
|---|---|---|
| thread_Root | None | chipseq.bds.20170602_104615_132/task.align_bwa.bwa_sam_PE_rep1.line_181.id_10 chipseq.bds.20170602_104615_132/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_11 |
Task details
| Task | Execution | Time | Dependencies | Task program, Errors, StdOut / StdErr | ||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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|
|
| # SYS command. line 183
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|
|
| # SYS command. line 262
|
Global scope
Note: Global scope when program finished execution.| Type | Name | Value |
|---|---|---|
| string | _ | /home/rdali/.bds/bds |
| string | _LMFILES_ | /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles/perl/5.16:/sb/software/CentOS-6/eb/modules/all/Core/Java/1.8.0_45.lua |
| string | _ModuleTable001_ | 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 |
| string | _ModuleTable002_ | 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 |
| string | _ModuleTable003_ | bC9MaW51eCIsIi9zYi9zb2Z0d2FyZS9DZW50T1MtNi9lYi9tb2R1bGVzL2FsbC9Db3JlIiwiL3NiL2hvbWUvcmRhbGkvbW9kdWxlZmlsZXMiLH0sWyJzeXN0ZW1CYXNlTVBBVEgiXT0iL3NiL3NvZnR3YXJlL0NlbnRPUy02L3Rvb2xzL01vZHVsZXMvMy4yLjkvbW9kdWxlZmlsZXM6L3NiL3NvZnR3YXJlL0NlbnRPUy02L2ViL21vZHVsZXMvYWxsL0xpbnV4Oi9zYi9zb2Z0d2FyZS9DZW50T1MtNi9lYi9tb2R1bGVzL2FsbC9Db3JlOi9zYi9ob21lL3JkYWxpL21vZHVsZWZpbGVzIixbInZlcnNpb24iXT0yLH0= |
| string | _ModuleTable_Sz_ | 3 |
| bool | allowEmpty | false |
| string[] | args | [-title, 160130_CTCF, -final_stage, peak, -gensz, hs, -out_dir, ChIPSeq/160130_CTCF, -chrsz, tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes, -nth, 1, -type, TF, -species, hg19, -bwa_idx, tools/TF_chipseq_pipeline/Genomes/hg19/bwa_index/male.hg19.fa, -pe1, -fastq1_1:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.fastq, -fastq1_2:1, HI.4031.007.Index_2.160130_CTCF_lib_170103_R2.fastq, -ctl_pe1, -ctl_fastq1_1:1, HI.4031.007.Index_3.160130_inp_lib_170103_R1.fastq, -ctl_fastq1_2:1, HI.4031.007.Index_3.160130_inp_lib_170103_R2.fastq] |
| string | BASH_ENV | /software/CentOS-6/tools/lmod/lmod/init/bash |
| string | BASH_FUNC_ml() | () { eval $( |
| string | BASH_FUNC_module() | () { eval $( |
| bool | canFail | false |
| string | CONDA_DEFAULT_ENV | aquas_chipseq |
| string | CONDA_PATH_BACKUP | tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin |
| string | CONDA_PREFIX | tools/miniconda3/envs/aquas_chipseq |
| string | CONDA_PS1_BACKUP | |
| string | CPATH | /software/CentOS-6/eb/software/Core/Java/1.8.0_45/include |
| int | cpus | -1 |
| int | cpusLocal | 16 |
| string | CVS_RSH | ssh |
| int | day | 86400 |
| real | E | 2.718281828459045 |
| string | EBDEVELJAVA | /software/CentOS-6/eb/software/Core/Java/1.8.0_45/easybuild/Core-Java-1.8.0_45-easybuild-devel |
| string | EBROOTJAVA | /software/CentOS-6/eb/software/Core/Java/1.8.0_45 |
| string | EBVERSIONJAVA | 1.8.0_45 |
| string | ENVIRONMENT | BATCH |
| int | G | 1073741824 |
| string | G_BROKEN_FILENAMES | 1 |
| string | HDF5_DIR | tools/hdf5-1.8.14/bin |
| string | HISTCONTROL | ignoreboth:erasedups |
| string | HISTIGNORE | ls:pwd:logout:rm*:mkdir*:rdali:hic:q |
| string | HISTSIZE | 1000000 |
| string | HISTTIMEFORMAT | %F %T |
| string | HOME | /home/rdali |
| string | HOSTNAME | lm-4r10-n70 |
| int | hour | 3600 |
| string | JAVA_HOME | /software/CentOS-6/eb/software/Core/Java/1.8.0_45 |
| int | K | 1024 |
| string | LANG | C |
| string | LD_LIBRARY_PATH | /gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/lib/amd64/server:/gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/lib/amd64:/gs/software/CentOS-6/eb/software/Core/Java/1.8.0_45/jre/../lib/amd64:/software/CentOS-6/eb/software/Core/Java/1.8.0_45/lib:$LD_LIBRARY_PATH:~/software/lib:/home/rdali/software/lib:tools/hdf5-1.8.14/lib/:/home/rdali/tools/ghmm-0.9-rc3/lib:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/bin/glnxa64:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:~/software/lib:/home/rdali/software/lib:tools/hdf5-1.8.14/lib:/home/rdali/tools/ghmm-0.9-rc3/lib:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/runtime/glnxa64:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/bin/glnxa64:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:tools/miniconda3/envs/aquas_chipseq/extra/MATLAB_Compiler_Runtime/v714/sys/java/jre/glnxa64/jre/lib/amd64/server |
| string | LESSOPEN | ||/usr/bin/lesspipe.sh %s |
| string | LIBRARY_PATH | /software/CentOS-6/eb/software/Core/Java/1.8.0_45/lib |
| string | LMOD_arch | x86_64 |
| string | LMOD_CMD | /software/CentOS-6/tools/lmod/lmod/libexec/lmod |
| string | LMOD_COLORIZE | yes |
| string | LMOD_DEFAULT_MODULEPATH | /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles:/sb/software/CentOS-6/eb/modules/all/Linux:/sb/software/CentOS-6/eb/modules/all/Core:/sb/home/rdali/modulefiles |
| string | LMOD_DIR | /software/CentOS-6/tools/lmod/lmod/libexec |
| string | LMOD_FULL_SETTARG_SUPPORT | no |
| string | LMOD_PKG | /software/CentOS-6/tools/lmod/lmod |
| string | LMOD_PREPEND_BLOCK | normal |
| string | LMOD_SETTARG_CMD | : |
| string | LMOD_sys | Linux |
| string | LMOD_VERSION | 6.1 |
| string | LOADEDMODULES | perl/5.16:Java/1.8.0_45 |
| string | LOGNAME | rdali |
| string | LSCRATCH | /localscratch/91503356.gm-1r16-n04.guillimin.clumeq.ca |
| int | M | 1048576 |
| string | /var/spool/mail/rdali | |
| string | MANPATH | /software/CentOS-6/eb/software/Core/Java/1.8.0_45/man:/software/CentOS-6/tools/perl-5.16/man:/software/CentOS-6/tools/lmod/lmod/share/man:: |
| int | mem | -1 |
| int | minute | 60 |
| string | MODULEPATH | /sb/software/CentOS-6/tools/Modules/3.2.9/modulefiles:/sb/software/CentOS-6/eb/modules/all/Linux:/sb/software/CentOS-6/eb/modules/all/Core:/sb/home/rdali/modulefiles |
| string | MODULEPATH_ROOT | /sb/software/CentOS-6/eb/modules/all |
| string | MODULESHOME | /software/CentOS-6/tools/lmod/lmod |
| string | NLSPATH | /usr/dt/lib/nls/msg/%L/%N.cat |
| string | node | |
| int | P | 1125899906842624 |
| string | PATH | /software/CentOS-6/eb/software/Core/Java/1.8.0_45:/software/CentOS-6/eb/software/Core/Java/1.8.0_45/bin:tools/miniconda3/envs/aquas_chipseq/extra/phantompeakqualtools:tools/miniconda3/envs/aquas_chipseq/bin:tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin:tools/miniconda3/envs/aquas_chipseq/extra/align2rawsignal/bin |
| string | PBS_ENVIRONMENT | PBS_BATCH |
| string | PBS_GPUFILE | /var/spool/pbs/aux//91503356.gm-1r16-n04.guillimin.clumeq.cagpu |
| string | PBS_JOBCOOKIE | 9DEB57F6415F639D50503B9C2E3B4F29 |
| string | PBS_JOBID | 91503356.gm-1r16-n04.guillimin.clumeq.ca |
| string | PBS_JOBNAME | AQUAS-160130_CTCF |
| string | PBS_MICFILE | /var/spool/pbs/aux//91503356.gm-1r16-n04.guillimin.clumeq.camic |
| string | PBS_MOMPORT | 15003 |
| string | PBS_NODEFILE | /var/spool/pbs/aux//91503356.gm-1r16-n04.guillimin.clumeq.ca |
| string | PBS_NODENUM | 0 |
| string | PBS_NP | 1 |
| string | PBS_NUM_NODES | 1 |
| string | PBS_NUM_PPN | 1 |
| string | PBS_O_HOME | /home/rdali |
| string | PBS_O_HOST | lg-1r14-n04.guillimin.clumeq.ca |
| string | PBS_O_LANG | en_CA.UTF-8 |
| string | PBS_O_LOGNAME | rdali |
| string | PBS_O_MAIL | /var/spool/mail/rdali |
| string | PBS_O_PATH | tools/miniconda3/bin:tools/perl5/bin:/software/CentOS-6/tools/perl-5.16/bin:/opt/torque/x86_64/bin:/usr/lib64/qt-3.3/bin:/opt/moab/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:/sb/software/tools/scripts:/usr/lpp/mmfs/bin:/usr/lpp/mmfs/bin:tools:tools/cmake-3.4.1/bin:tools/circos-0.68/bin:tools/MACS-1.4.2/bin:tools/bam-readcount/build/bin:tools/HTSeq-0.6.1/scripts:tools/bowtie-1.1.1:tools/hicup_v0.5.3:/usr/bin/gnuplot:tools/hdf5-1.8.14/bin:/home/rdali/tools/pythonPackages/bin:/home/rdali/tools/pythonPackages:/home/rdali/tools/tabix-0.2.6:/home/rdali/tools/vcftools_0.1.12b/perl:/home/rdali/tools/samtools-0.1.19/bcftools:/home/rdali/tools/IGVTools:/home/rdali/tools/novocraft:/home/rdali/tools/bowtie2-2.1.0:/home/rdali/tools/tophat-2.0.11.Linux_x86_64:/home/rdali/tools/samtools-0.1.19:/home/rdali/.aspera/connect/bin:/home/rdali/tools/FastQC:/home/rdali/tools/cutadapt-1.4.1/bin:/home/rdali/tools:/home/rdali/software/bin:/home/rdali/tools/sratoolkit.2.3.5-2-centos_linux64/bin:/home/rdali/tools/bedtools-2.17.0/bin:/home/rdali/tools/bwa-0.7.10:/home/rdali/tools/mySoftwareLibs:/home/rdali/tools/ghostscript-9.15/bin:/home/rdali/tools/weblogo:tools/homer/bin:/sb/home/rdali/.local/lib/python2.7/site-packages:/home/rdali/.bds:/home/rdali/bin |
| string | PBS_O_QUEUE | metaq |
| string | PBS_O_SERVER | gm-schrmat |
| string | PBS_O_SHELL | /bin/bash |
| string | PBS_O_SUBMIT_FILTER | /opt/torque/x86_64/libexec/qsub_filter |
| string | PBS_O_WORKDIR | ChIPSeq |
| string | PBS_QUEUE | xlm2 |
| string | PBS_TASKNUM | 1 |
| string | PBS_VERSION | TORQUE-5.1.3 |
| string | PBS_VNODENUM | 0 |
| string | PBS_WALLTIME | 86400 |
| string | PBSCOREDUMP | 1 |
| string | PERL5LIB | tools/perl5/lib/perl5:/home/rdali/tools/vcftools_0.1.12b/perl |
| string | PERL_LOCAL_LIB_ROOT | tools/perl5 |
| string | PERL_MB_OPT | --install_base \"tools/perl5\" |
| string | PERL_MM_OPT | INSTALL_BASE=tools/perl5 |
| real | PI | 3.141592653589793 |
| string | ppwd | ChIPSeq |
| string | programName | chipseq.bds |
| string | programPath | tools/TF_chipseq_pipeline/chipseq.bds |
| string | PROMPT_COMMAND | history -a |
| string | PWD | ChIPSeq |
| string | QTDIR | /usr/lib64/qt-3.3 |
| string | QTINC | /usr/lib64/qt-3.3/include |
| string | QTLIB | /usr/lib64/qt-3.3/lib |
| string | queue | |
| string | R_LIBS | tools/R_LIBS |
| string | RAMDISK | /dev/shm/91503356.gm-1r16-n04.guillimin.clumeq.ca |
| int | retry | 0 |
| string | SCRATCH | /gs/scratch/rdali |
| string | SHELL | /bin/bash |
| string | SHLVL | 3 |
| string | SSH_ASKPASS | /usr/libexec/openssh/gnome-ssh-askpass |
| string | system | local |
| int | T | 1099511627776 |
| int | timeout | -1 |
| string | USER | rdali |
| string | VDB_PWFILE | keys/prj_6419.ngc |
| int | walltimeout | 8640000 |
| int | week | 604800 |
| string | XAPPLRESDIR | tools/miniconda3/envs/aquas_chipseq/bin/../extra/MATLAB_Compiler_Runtime/v714/X11/app-defaults |
| string | XFILESEARCHPATH | /usr/dt/app-defaults/%L/Dt |
from chipseq_pipeline.
leepc12
commented on July 21, 2024
This looks like sambamba issue (bcbio/bcbio-nextgen#1055). Did you have enough disk space on $TMP?
from chipseq_pipeline.
rdali
commented on July 21, 2024
So disk space on $TMP certainly made a difference. I gave it 1TB and it ran for 4 days. The exit status in the STDOUT is 0 but it seems that macs2 had an error. How do I fix that?
if I do not specify a peak caller, will both spp and macs2 be used?
Also, what is the final output of the pipeline at the "peak" stage to know things are ok. I assume the "nodup.tagAlign.filt.regionPeak.gz" file is a good indication things are complete?
from chipseq_pipeline.
rdali
commented on July 21, 2024
4 days 14:15:59.701 ExecutionerLocal 'Local[41]': Tasks [Local[41]] Pending: 0 Running: 1 Done: 26 Failed: 2
| PID | Task state | Task name | Dependencies | Task definition |
| ---- | ----------------- | ------------------ | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 6644 | running (RUNNING) | macs2 n/s rep1-pr2 | | macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_17 |
Traceback (most recent call last):
File "tools/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in
import('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
File ".local/lib/python2.7/site-packages/pkg_resources/init.py", line 719, in run_script
self.require(requires)[0].run_script(script_name, ns)
File ".local/lib/python2.7/site-packages/pkg_resources/init.py", line 1517, in run_script
exec(script_code, namespace, namespace)
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in bootstrap
File "init.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
ValueError: numpy.dtype has the wrong size, try recompiling
Task failed:
Program & line : 'tools/TF_chipseq_pipeline/modules/callpeak_macs2_chipseq.bds', line 83
Task Name : 'macs2 n/s rep1-pr2'
Task ID : 'chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr2.line_83.id_36'
Task PID : '6644'
Task hint : 'macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_17'
Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000'
State : 'ERROR'
Dependency state : 'ERROR'
Retries available : '1'
Input files : '[project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz, project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz]'
Output files : '[project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.narrowPeak.gz]'
Script file : 'project/ChIPSeq/chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr2.line_83.id_36.sh'
Exit status : '1'
Program :
# SYS command. line 85
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
# SYS command. line 86
export LC_COLLATE=C
# SYS command. line 91
macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz -f BED -n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 230 --keep-dup all -B --SPMR
# SYS command. line 94
sort -k 8gr,8gr "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.narrowPeak.gz
# SYS command. line 97
rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.xls \
"project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.narrowPeak \
"project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_summits.bed
# SYS command. line 101
if [[ false == "false" ]]; then \
rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; \
exit; \
fi
# SYS command. line 111
macs2 bdgcmp -t "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg -c "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg --outdir project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2 -o "HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg -g tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 128
controlReads=$(zcat project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 130
macs2 bdgcmp -t "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg -c "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg --outdir project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2 -o "HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg -g tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 134
rm -rf "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg
# SYS command. line 137
sort -k1,1 -k2,2n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 138
bedGraphToBigWig project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bw
# SYS command. line 139
rm -f project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 141
rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr2/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr2.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 143
TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
StdErr (100000000 lines) :
Traceback (most recent call last):
File "tools/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in <module>
__import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
File ".local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 719, in run_script
self.require(requires)[0].run_script(script_name, ns)
File ".local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script
exec(script_code, namespace, namespace)
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
ValueError: numpy.dtype has the wrong size, try recompiling
4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr2.line_83.id_36' finished.
4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.bedpe_to_tag_ctl1.line_651.id_30, state: FINISHED
4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.bedpe_to_tag_ctl1.line_651.id_30' finished.
4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_sam_PE_rep1.line_181.id_12, state: FINISHED
4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_sam_PE_rep1.line_181.id_12' finished.
4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_13, state: FINISHED
4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_1_rep1.line_260.id_13' finished.
4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_ctl1_2.line_111.id_23, state: FINISHED
4 days 14:16:01.881 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_ctl1_2.line_111.id_23' finished.
4 days 14:16:01.881 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_rep1_2.line_111.id_11, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_rep1_2.line_111.id_11' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.bam_to_bedpe_rep1.line_613.id_17, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.bam_to_bedpe_rep1.line_613.id_17' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bed.spr_PE_rep1.line_180.id_20, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bed.spr_PE_rep1.line_180.id_20' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_2_rep1.line_323.id_15, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_2_rep1.line_323.id_15' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.callpeak_spp.spp_rep1_pr1.line_68.id_33, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.callpeak_spp.spp_rep1_pr1.line_68.id_33' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_2_ctl1.line_323.id_27, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.dedup_bam_PE_2_ctl1.line_323.id_27' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.callpeak_spp.spp_rep1_pr2.line_68.id_34, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.callpeak_spp.spp_rep1_pr2.line_68.id_34' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_ctl1_1.line_111.id_22, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_ctl1_1.line_111.id_22' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_sam_PE_ctl1.line_181.id_24, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_sam_PE_ctl1.line_181.id_24' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_xcor.subsample_bedpe2tag_rep1.line_85.id_19, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_xcor.subsample_bedpe2tag_rep1.line_85.id_19' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_rep1_1.line_111.id_10, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.align_bwa.bwa_aln_rep1_1.line_111.id_10' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.postalign_bam.bedpe_to_tag_rep1.line_651.id_18, state: FINISHED
4 days 14:16:01.882 Wait: Task 'chipseq.bds.20170604_153842_923/task.postalign_bam.bedpe_to_tag_rep1.line_651.id_18' finished.
4 days 14:16:01.882 Wait: Waiting for task to finish: chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_83.id_35, state: ERROR
Task failed:
Program & line : 'tools/TF_chipseq_pipeline/modules/callpeak_macs2_chipseq.bds', line 83
Task Name : 'macs2 n/s rep1-pr1'
Task ID : 'chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_83.id_35'
Task PID : '4610'
Task hint : 'macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_17'
Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000'
State : 'ERROR'
Dependency state : 'ERROR'
Retries available : '1'
Input files : '[project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign.gz, project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz]'
Output files : '[project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.narrowPeak.gz]'
Script file : 'project/ChIPSeq/chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_83.id_35.sh'
Exit status : '1'
Program :
# SYS command. line 85
if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi; export PATH=tools/TF_chipseq_pipeline/.:tools/TF_chipseq_pipeline/modules:tools/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
# SYS command. line 86
export LC_COLLATE=C
# SYS command. line 91
macs2 callpeak -t project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign.gz -c project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz -f BED -n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign -g hs -p 0.01 --nomodel --shift 0 --extsize 230 --keep-dup all -B --SPMR
# SYS command. line 94
sort -k 8gr,8gr "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.narrowPeak | awk 'BEGIN{OFS="\t"}{$4="Peak_"NR ; print $0}' | gzip -nc > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.narrowPeak.gz
# SYS command. line 97
rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.xls \
"project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_peaks.narrowPeak \
"project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_summits.bed
# SYS command. line 101
if [[ false == "false" ]]; then \
rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg; \
TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; \
exit; \
fi
# SYS command. line 111
macs2 bdgcmp -t "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg -c "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg --outdir project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1 -o "HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg -m FE
# SYS command. line 114
slopBed -i "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg -g tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph
# SYS command. line 115
rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_FE.bdg
# SYS command. line 118
sort -k1,1 -k2,2n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 119
bedGraphToBigWig project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bw
# SYS command. line 120
rm -f project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.bedgraph project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.fc.signal.srt.bedgraph
# SYS command. line 126
chipReads=$(zcat project/ChIPSeq/160130_CTCF/align/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}')
# SYS command. line 128
controlReads=$(zcat project/ChIPSeq/160130_CTCF/align/ctl1/HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.gz | wc -l | awk '{printf "%f", $1/1000000}'); sval=$(echo "${chipReads} ${controlReads}" | awk '$1>$2{printf "%f",$2} $1<=$2{printf "%f",$1}')
# SYS command. line 130
macs2 bdgcmp -t "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg -c "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg --outdir project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1 -o "HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg -m ppois -S "${sval}"
# SYS command. line 133
slopBed -i "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg -g tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes -b 0 | awk '{if ($3 != -1) print $0}' | bedClip stdin tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph
# SYS command. line 134
rm -rf "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_ppois.bdg
# SYS command. line 137
sort -k1,1 -k2,2n project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph > project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 138
bedGraphToBigWig project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph tools/TF_chipseq_pipeline/Genomes/hg19/hg19.chrom.sizes project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bw
# SYS command. line 139
rm -f project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.bedgraph project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign.pval.signal.srt.bedgraph
# SYS command. line 141
rm -f "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_treat_pileup.bdg "project/ChIPSeq/160130_CTCF/peak/macs2/pseudo_reps/rep1/pr1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.pr1.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign"_control_lambda.bdg
# SYS command. line 143
TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."
StdErr (100000000 lines) :
Traceback (most recent call last):
File "tools/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in <module>
__import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
File ".local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 719, in run_script
self.require(requires)[0].run_script(script_name, ns)
File ".local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1517, in run_script
exec(script_code, namespace, namespace)
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 55, in main
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 30, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/OptValidator.py", line 27, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 7, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/IO/Parser.py", line 6, in __bootstrap__
File "__init__.pxd", line 155, in init MACS2.IO.Parser (MACS2/IO/Parser.c:24419)
ValueError: numpy.dtype has the wrong size, try recompiling
4 days 14:16:01.883 Wait: Task 'chipseq.bds.20170604_153842_923/task.callpeak_macs2_chipseq.macs2_n_s_rep1_pr1.line_83.id_35' finished.
Fatal error: tools/TF_chipseq_pipeline/chipseq.bds, line 1237, pos 2. Task/s failed.
chipseq.bds, line 76 : main()
chipseq.bds, line 79 : void main() { // chipseq pipeline starts here
chipseq.bds, line 91 : call_peaks() // call peaks in parallel (MACS2,SPP)
chipseq.bds, line 820 : void call_peaks() {
chipseq.bds, line 1237 : wait
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
4 days 14:16:02.500 Writing report file 'chipseq.bds.20170604_153842_923.report.html'
4 days 14:16:02.634 Program 'chipseq.bds.20170604_153842_923' finished, exit value: 1, tasks executed: 27, tasks failed: 3, tasks failed names: macs2 n/s rep1 , macs2 n/s rep1-pr2 , macs2 n/s rep1-pr1.
4 days 14:16:02.635 Finished. Exit code: 1
4 days 14:16:02.635 ExecutionerLocal 'Local[41]': Killed
4 days 14:16:02.702 ExecutionerLocal 'Local[41]': Finished running
from chipseq_pipeline.
leepc12
commented on July 21, 2024
If a peak-caller is not specified, it defaults to spp. In such case, macs2 is used for generating bigwigs. Yes if you got nodup.tagAlign.filt.regionPeak.gz, then that means spp ran successfully.
About macs2 error, it looks like macs2 is combined with wrong numpy version. Please check the following:
$ source activate aquas_chipseq
$ conda list numpy
from chipseq_pipeline.
rdali
commented on July 21, 2024
packages in environment at tools/miniconda3/envs/aquas_chipseq:
numpy 1.10.2 py27_0
from chipseq_pipeline.
leepc12
commented on July 21, 2024
It's a problem related to Conda's virtual environment. conda/conda#448 (comment)
Can you add the following to your ~/.bashrc and re-login?
export PYTHONNOUSERSITE=True
Please let me know if this works.
from chipseq_pipeline.
rdali
commented on July 21, 2024
I get a different error now:
INFO @ Fri, 09 Jun 2017 15:33:37: #3 Write bedGraph files for control lambda (after scaling if necessary)... project/ChIPSeq/160130_CTCF/peak/macs2/rep1/HI.4031.007.Index_2.160130_CTCF_lib_170103_R1.PE2SE.nodup.tagAlign_x_HI.4031.007.Index_3.160130_inp_lib_170103_R1.PE2SE.nodup.tagAlign_control_lambda.bdg
INFO @ Fri, 09 Jun 2017 15:33:37: #3 --SPMR is requested, so pileup will be normalized by sequencing depth in million reads.
INFO @ Fri, 09 Jun 2017 15:33:37: #3 Call peaks for each chromosome...
Traceback (most recent call last):
File "tools/miniconda3/envs/aquas_chipseq/bin/macs2", line 4, in <module>
__import__('pkg_resources').run_script('MACS2==2.1.0.20150731', 'macs2')
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 1506, in run_script
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 614, in <module>
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/EGG-INFO/scripts/macs2", line 56, in main
File "tools/miniconda3/envs/aquas_chipseq/lib/python2.7/site-packages/MACS2-2.1.0.20150731-py2.7-linux-x86_64.egg/MACS2/callpeak_cmd.py", line 261, in run
File "MACS2/PeakDetect.pyx", line 105, in MACS2.PeakDetect.PeakDetect.call_peaks (MACS2/PeakDetect.c:1632)
File "MACS2/PeakDetect.pyx", line 251, in MACS2.PeakDetect.PeakDetect.__call_peaks_w_control (MACS2/PeakDetect.c:3172)
File "MACS2/IO/CallPeakUnit.pyx", line 857, in MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks (MACS2/IO/CallPeakUnit.c:12297)
File "MACS2/IO/CallPeakUnit.pyx", line 911, in MACS2.IO.CallPeakUnit.CallerFromAlignments.call_peaks (MACS2/IO/CallPeakUnit.c:12049)
File "MACS2/IO/CallPeakUnit.pyx", line 966, in MACS2.IO.CallPeakUnit.CallerFromAlignments.__chrom_call_peak_using_certain_criteria (MACS2/IO/CallPeakUnit.c:12455)
File "MACS2/IO/CallPeakUnit.pyx", line 461, in MACS2.IO.CallPeakUnit.CallerFromAlignments.__pileup_treat_ctrl_a_chromosome (MACS2/IO/CallPeakUnit.c:6457)
EOFError
00:38:10.137 Wait: Task 'chipseq.bds.20170609_152437_788/task.callpeak_macs2_chipseq.macs2_n_s_rep1.line_83.id_10' finished.
Fatal error: tools/TF_chipseq_pipeline/chipseq.bds, line 1237, pos 2. Task/s failed.
chipseq.bds, line 76 : main()
chipseq.bds, line 79 : void main() { // chipseq pipeline starts here
chipseq.bds, line 91 : call_peaks() // call peaks in parallel (MACS2,SPP)
chipseq.bds, line 820 : void call_peaks() {
chipseq.bds, line 1237 : wait
Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
00:38:10.377 Writing report file 'chipseq.bds.20170609_152437_788.report.html'
00:38:10.416 Program 'chipseq.bds.20170609_152437_788' finished, exit value: 1, tasks executed: 3, tasks failed: 2, tasks failed names: macs2 n/s rep1-pr1 , macs2 n/s rep1.
00:38:10.417 Finished. Exit code: 1
00:38:10.417 ExecutionerLocal 'Local[38]': Killed
from chipseq_pipeline.
leepc12
commented on July 21, 2024
macs3-project/MACS#105
Can you check your disk space on $TMP?
$ echo $TMP
$ df -h $TMP
from chipseq_pipeline.
rdali
commented on July 21, 2024
$echo $TMP
$ df -h $TMP
Filesystem Size Used Avail Use% Mounted on
/dev/sda6 193G 42G 141G 23% /
tmpfs 32G 149M 32G 1% /dev/shm
/dev/sda2 477M 116M 337M 26% /boot
/dev/sda1 200M 260K 200M 1% /boot/efi
/dev/sda3 30G 20G 8.1G 72% /cvmfs-cache
/dev/gs 3.1P 2.9P 221T 93% /gs
/dev/lb 1.3P 1.1P 145T 89% /lb
/dev/sb 456T 405T 52T 89% /sb
/dev/sf1 349T 229T 120T 66% /sf1
I had set $TMPDIR to the extra 1TB not $TMP:
$echo $TMPDIR
/gs/scratch/
$ df -h $TMPDIR
Filesystem Size Used Avail Use% Mounted on
/dev/gs 1.0T 2.0M 1.0T 1% /gs
from chipseq_pipeline.
leepc12
commented on July 21, 2024
Sorry. MACS2 does not use $TMP or $TMPDIR. It always writes temporary files on /tmp. Can you check your /tmp too?
from chipseq_pipeline.
rdali
commented on July 21, 2024
df -h /tmp
Filesystem Size Used Avail Use% Mounted on
/dev/sda6 217G 19G 188G 9% /
from chipseq_pipeline.
leepc12
commented on July 21, 2024
I guess that your /tmp was running out of space at the moment you ran the pipeline. Can you try running pipelines again?
from chipseq_pipeline.
rdali
commented on July 21, 2024
Looks like it ran to completion. Thanks!
from chipseq_pipeline.
Related Issues (20)
- aquas_chipseq pipline SPP error HOT 6
- Trimmed data-sets HOT 1
- Read length HOT 2
- shuf: end of file HOT 8
- "-q [SLURM_ACCOUNT_NAME]" interpreted as file HOT 1
- ERROR:root:--extsize must >= 1! HOT 2
- Fatal error: chipseq.bds, line 1354, pos 2. Task/s failed. HOT 4
- [fread] Unexpected end of file (bwa_sai2sam_pe_core) HOT 6
- dead loop HOT 18
- job submission command HOT 2
- [Error] two same tag align file in (z)cat and shuf in pipe HOT 1
- Missing `-c` for `macs2 peakcall` ? HOT 1
- pipeline deprecated? HOT 2
- Can't download hg19 genome data HOT 2
- Some reps get ERROR:root:--extsize must >= 1! HOT 2
- Documentation for macs2? HOT 2
- Citing the AQUAS Pipeline HOT 1
- ERROR:root:--extsize must >= 1! and chipseq.bds can not get all replicates go through HOT 25
- mm10 HOT 1
- JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa" HOT 1
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