Comments (18)
leepc12
commented on July 21, 2024
Looks like it's still running.
…On Fri, May 18, 2018 at 11:41 AM, Liang Ma ***@***.***> wrote:
Hi Jin,
I've updated the pipeline on SCG, and ran the pipeline again using the
same sample files. It took 8h to run successfully last time. However, it's
almost 2 days, the pipeline is still do the alignment, no error pop up
though. I attached the two logs, could you let me know what is wrong?
Thanks.
h3k27ac_noncellcycle_dmso.BDS20180129.log
<https://github.com/kundajelab/chipseq_pipeline/files/2018217/h3k27ac_noncellcycle_dmso.BDS20180129.log>
h3k27ac_noncellcycle_dmso20180516.BDS.log
<https://github.com/kundajelab/chipseq_pipeline/files/2018218/h3k27ac_noncellcycle_dmso20180516.BDS.log>
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LiangMa2017
commented on July 21, 2024
Thank you so much, Jin. Yes, it is still running. I thought it gets into a dead loop because it takes so long this time. I will keep looking how it goes and let you know. Cheers!
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nteran
commented on July 21, 2024
I've had the same issue. I've let it spin for 3 days before to no avail.
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leepc12
commented on July 21, 2024
Check your job status with sacct -j 1610998 and squeue -j 1610998. Also check your output directory.
$ ls -l out/qc/*/*
$ ls -l out/align/*/*
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LiangMa2017
commented on July 21, 2024
$ ls -l out20180516/qc//
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 390 May 18 04:49 out20180516/qc/rep1/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.flagstat.qc
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 391 May 18 04:51 out20180516/qc/rep2/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.flagstat.qc
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 322 May 18 05:05 out20180516/qc/rep3/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.dup.qc
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 390 May 17 07:20 out20180516/qc/rep3/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.flagstat.qc
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 322 May 18 05:06 out20180516/qc/rep4/Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.dup.qc
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 391 May 17 07:22 out20180516/qc/rep4/Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.flagstat.qc
$ ls -l out20180516/align//
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 736038176 May 18 04:49 out20180516/align/rep1/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 3481536 May 18 04:49 out20180516/align/rep1/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.bam.bai
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 511004826 May 18 05:07 out20180516/align/rep1/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.filt.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 6000520 May 18 05:07 out20180516/align/rep1/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.filt.bam.bai
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 559273988 May 18 04:50 out20180516/align/rep2/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 3979872 May 18 04:51 out20180516/align/rep2/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.bam.bai
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 354197738 May 18 05:07 out20180516/align/rep2/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.filt.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 5869784 May 18 05:07 out20180516/align/rep2/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.filt.bam.bai
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 428556883 May 17 07:20 out20180516/align/rep3/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 4201584 May 17 07:20 out20180516/align/rep3/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.bam.bai
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 250005527 May 18 05:05 out20180516/align/rep3/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.dupmark.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 248908658 May 18 04:44 out20180516/align/rep3/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.filt.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 5807680 May 18 04:44 out20180516/align/rep3/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.filt.bam.bai
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 400974621 May 17 07:21 out20180516/align/rep4/Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 4311208 May 17 07:22 out20180516/align/rep4/Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.bam.bai
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 241749196 May 18 05:06 out20180516/align/rep4/Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.dupmark.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 240300507 May 18 04:44 out20180516/align/rep4/Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.filt.bam
-rw-r--r-- 1 liangma1 scgpm-informatics_chetty 5804072 May 18 04:44 out20180516/align/rep4/Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.filt.bam.bai
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leepc12
commented on July 21, 2024
Check job status, exit code or fail reason first. Please learn about some SLURM command for this (sacct, sinfo, squeue).
If your FASTQS are huge, check if you gave enough memory for mapping tasks (bwa and dedup). Try with higher memory settings (-mem_bwa 30G or -mem_dedup 30G according to the stage where pipeline failed). They are 12G by default.
SLURM is very strict about memory usage.
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LiangMa2017
commented on July 21, 2024
$ sacct -j 1611181
JobID JobName Partition Account AllocCPUS State ExitCode
1611181 sbatch batch chettys 2 COMPLETED 0:0
1611181.bat+ batch chettys 2 COMPLETED 0:0
1611181.ext+ extern chettys 2 COMPLETED 0:0
$ squeue -j 1611181
slurm_load_jobs error: Invalid job id specified
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LiangMa2017
commented on July 21, 2024
Thank you, Jin. I've killed current job and run it with increased memory setting:
bds_scr h3k27ac_noncellcycle_dmso20180518 ~/TF_chipseq_pipeline/chipseq.bds -se -species hg19 -dup_marker sambamba -nth 4 -type histone -mem_bwa 30G -mem_dedup 30G -mem_macs2 30G -out_dir out20180516 -fastq1 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.fastq.gz -fastq2 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.fastq.gz -fastq3 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.fastq.gz -fastq4 Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.fastq.gz -ctl_fastq1 /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso2.gz -ctl_fastq2 /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso3.gz
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LiangMa2017
commented on July 21, 2024
Hi Jin,
I have 2 jobs is running. but I guess the jobs get into dead loop again, could you take a look?
h3k27ac_noncellcycle_dmso20180518.BDS.log
SRR3554631.BDS.log
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leepc12
commented on July 21, 2024
Please use some SLURM commands to get status of jobs. You can Job IDs in
the log.
…On Fri, May 18, 2018 at 10:39 PM, Liang Ma ***@***.***> wrote:
Hi Jin,
I have 2 jobs is running. but I guess the jobs get into dead loop again,
could you take a look?
h3k27ac_noncellcycle_dmso20180518.BDS.log
<https://github.com/kundajelab/chipseq_pipeline/files/2019177/h3k27ac_noncellcycle_dmso20180518.BDS.log>
SRR3554631.BDS.log
<https://github.com/kundajelab/chipseq_pipeline/files/2019178/SRR3554631.BDS.log>
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LiangMa2017
commented on July 21, 2024
Thanks, Jin.
The status below shows all of them are pending, but they are actually keep printing on screen. So what to do to get it normal?
For job h3k27ac_noncellcycle_dmso
##############
21:53:03.741 ExecutionerClusterGeneric 'ClusterGeneric[33]': Tasks [ClusterGeneric[33]] Pending: 0 Running: 4 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ------- | ----------------- | ------------------------- | ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| 1658231 | running (RUNNING) | markdup_bam_sambamba rep2 | | sambamba markdup -t 1 --hash-table-size=17592186044416; --overflow-list-size=20000000 --io-buffer-size=256 /labs/chettys/liangma1/test/chipseq/h3k27ac_noncellcycle_dmso/out20180516/align/rep2/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.filt.bam /labs/chettys/liangma1/test/chipseq/h3k27ac_noncel |
| 1658233 | running (RUNNING) | bwa_aln ctl2 | | bwa aln -q 5 -l 32 -k 2 -t 1 /ifs/scratch/leepc12/pipeline_genome_data/hg19/bwa_index/male.hg19.fa /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso3.gz > /labs/chettys/liangma1/test/chipseq/h3k27ac_noncellcycle_dmso/out20180516/align/ctl2/wce_for_dmso3.sai; TASKTIME=$[$(date +%s)-${STARTTIME}]; |
| 1658230 | running (RUNNING) | markdup_bam_sambamba rep1 | | sambamba markdup -t 1 --hash-table-size=17592186044416; --overflow-list-size=20000000 --io-buffer-size=256 /labs/chettys/liangma1/test/chipseq/h3k27ac_noncellcycle_dmso/out20180516/align/rep1/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.filt.bam /labs/chettys/liangma1/test/chipseq/h3k27ac_noncel |
| 1658232 | running (RUNNING) | bwa_aln ctl1 | | bwa aln -q 5 -l 32 -k 2 -t 1 /ifs/scratch/leepc12/pipeline_genome_data/hg19/bwa_index/male.hg19.fa /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso2.gz > /labs/chettys/liangma1/test/chipseq/h3k27ac_noncellcycle_dmso/out20180516/align/ctl1/wce_for_dmso2.sai; TASKTIME=$[$(date +%s)-${STARTTIME}]; |
^C
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$ sacct -j 1658231
JobID JobName Partition Account AllocCPUS State ExitCode
1658231 sbatch batch default 1 PENDING 0:0
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$ sacct -j 1658233
JobID JobName Partition Account AllocCPUS State ExitCode
1658233 sbatch batch default 1 PENDING 0:0
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$ sacct -j 1658230
JobID JobName Partition Account AllocCPUS State ExitCode
1658230 sbatch batch default 1 PENDING 0:0
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$ sacct -j 1658232
JobID JobName Partition Account AllocCPUS State ExitCode
1658232 sbatch batch default 1 PENDING 0:0
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$ squeue -j 1658231
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1658231 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$ squeue -j 1658233
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1658233 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$ squeue -j 1658230
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1658230 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
[liangma1@sgiuv20-rcf-111-32 h3k27ac_noncellcycle_dmso]$ squeue -j 1658232
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1658232 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
For job SRR3554631
##########
[liangma1@sgiuv20-rcf-111-32 test]$ sacct -j 1659097
JobID JobName Partition Account AllocCPUS State ExitCode
1659097 sbatch batch default 1 PENDING 0:0
[liangma1@sgiuv20-rcf-111-32 test]$ squeue -j 1659097
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1659097 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
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leepc12
commented on July 21, 2024
Please see the error `AccountNotAllowed`. It looks like you don't have an
account on SCG or didn't specify it in the command line?
Did you try with `-q [YOUR_ACCOUNT_ON_SCG]`?
…On Sat, May 19, 2018 at 11:27 AM, Liang Ma ***@***.***> wrote:
Thanks, Jin.
The status below shows all of them are pending, but they are actually keep
printing on screen. So what to do to get it normal?
For job h3k27ac_noncellcycle_dmso
##############
21:53:03.741 ExecutionerClusterGeneric 'ClusterGeneric[33]': Tasks
[ClusterGeneric[33]] Pending: 0 Running: 4 Done: 0 Failed: 0
| PID | Task state | Task name | Dependencies | Task definition |
| ------- | ----------------- | ------------------------- | ------------ |
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------ |
| 1658231 | running (RUNNING) | markdup_bam_sambamba rep2 | | sambamba
markdup -t 1 --hash-table-size=17592186044416;
--overflow-list-size=20000000 --io-buffer-size=256
/labs/chettys/liangma1/test/chipseq/h3k27ac_noncellcycle_
dmso/out20180516/align/rep2/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.filt.bam
/labs/chettys/liangma1/test/chipseq/h3k27ac_noncel |
| 1658233 | running (RUNNING) | bwa_aln ctl2 | | bwa aln -q 5 -l 32 -k 2
-t 1 /ifs/scratch/leepc12/pipeline_genome_data/hg19/bwa_index/male.hg19.fa
/labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso3.gz >
/labs/chettys/liangma1/test/chipseq/h3k27ac_noncellcycle_
dmso/out20180516/align/ctl2/wce_for_dmso3.sai; TASKTIME=$[$(date
+%s)-${STARTTIME}]; |
| 1658230 | running (RUNNING) | markdup_bam_sambamba rep1 | | sambamba
markdup -t 1 --hash-table-size=17592186044416;
--overflow-list-size=20000000 --io-buffer-size=256
/labs/chettys/liangma1/test/chipseq/h3k27ac_noncellcycle_
dmso/out20180516/align/rep1/Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.filt.bam
/labs/chettys/liangma1/test/chipseq/h3k27ac_noncel |
| 1658232 | running (RUNNING) | bwa_aln ctl1 | | bwa aln -q 5 -l 32 -k 2
-t 1 /ifs/scratch/leepc12/pipeline_genome_data/hg19/bwa_index/male.hg19.fa
/labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso2.gz >
/labs/chettys/liangma1/test/chipseq/h3k27ac_noncellcycle_
dmso/out20180516/align/ctl1/wce_for_dmso2.sai; TASKTIME=$[$(date
+%s)-${STARTTIME}]; |
^C
***@***.*** h3k27ac_noncellcycle_dmso]$ sacct -j 1658231
JobID JobName Partition Account AllocCPUS State ExitCode
------------------------------
1658231 sbatch batch default 1 PENDING 0:0
***@***.*** h3k27ac_noncellcycle_dmso]$ sacct -j 1658233
JobID JobName Partition Account AllocCPUS State ExitCode
------------------------------
1658233 sbatch batch default 1 PENDING 0:0
***@***.*** h3k27ac_noncellcycle_dmso]$ sacct -j 1658230
JobID JobName Partition Account AllocCPUS State ExitCode
------------------------------
1658230 sbatch batch default 1 PENDING 0:0
***@***.*** h3k27ac_noncellcycle_dmso]$ sacct -j 1658232
JobID JobName Partition Account AllocCPUS State ExitCode
------------------------------
1658232 sbatch batch default 1 PENDING 0:0
***@***.*** h3k27ac_noncellcycle_dmso]$
***@***.*** h3k27ac_noncellcycle_dmso]$ squeue -j 1658231
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1658231 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
***@***.*** h3k27ac_noncellcycle_dmso]$ squeue -j 1658233
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1658233 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
***@***.*** h3k27ac_noncellcycle_dmso]$ squeue -j 1658230
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1658230 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
***@***.*** h3k27ac_noncellcycle_dmso]$ squeue -j 1658232
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1658232 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
For job SRR3554631
##########
***@***.*** test]$ sacct -j 1659097
JobID JobName Partition Account AllocCPUS State ExitCode
------------------------------
1659097 sbatch batch default 1 PENDING 0:0
***@***.*** test]$ squeue -j 1659097
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1659097 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
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LiangMa2017
commented on July 21, 2024
Thanks. Yes, I tried to add '--account=chettys', but still having this error. Maybe the position I added is not right?
bds_scr SRR3554631 ~/TF_chipseq_pipeline/chipseq.bds --account=chettys -pe -species hg19 -dup_marker sambamba -nth 4 -type histone -mem_bwa 30G -mem_dedup 30G -mem_macs2 30G -out_dir out -fastq1_1 SRR3554631_1.fastq.gz -fastq1_2 SRR3554631_2.fastq.gz
$ sacct -j 1687688
JobID JobName Partition Account AllocCPUS State ExitCode
1687688 sbatch batch default 1 PENDING 0:0
[liangma1@sgiuv20-rcf-111-32 test]$ squeue -j 1687688
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1687688 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
from chipseq_pipeline.
leepc12
commented on July 21, 2024
Pipeline does not recognize double-dash parameters.
Use `-q chettys` instead of `--account=chettys`
…On Sat, May 19, 2018 at 6:39 PM, Liang Ma ***@***.***> wrote:
Thanks. Yes, I tried to add '--account=chettys', but still having this
error. Maybe the position I added is not right?
bds_scr SRR3554631 ~/TF_chipseq_pipeline/chipseq.bds --account=chettys
-pe -species hg19 -dup_marker sambamba -nth 4 -type histone -mem_bwa 30G
-mem_dedup 30G -mem_macs2 30G -out_dir out -fastq1_1 SRR3554631_1.fastq.gz
-fastq1_2 SRR3554631_2.fastq.gz
$ sacct -j 1687688
JobID JobName Partition Account AllocCPUS State ExitCode
------------------------------
1687688 sbatch batch default 1 PENDING 0:0
***@***.*** test]$ squeue -j 1687688
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1687688 batch sbatch liangma1 PD 0:00 1 (AccountNotAllowed)
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LiangMa2017
commented on July 21, 2024
Got you. I will change it to '-q' and try it again.
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LiangMa2017
commented on July 21, 2024
Hi Jin, where should I put -q chettys in the command? I used the command below but a fetal error popped up, said "Error message : 'sbatch: error: Unable to open file chettys", I've attached the log.
$ bds_scr h3k27ac_noncellcycle_dmso20180519.2 ~/TF_chipseq_pipeline/chipseq.bds -q chettys -se -species hg19 -dup_marker sambamba -nth 4 -type histone -mem_bwa 30G -mem_dedup 30G -mem_macs2 30G -out_dir out20180519.2 -fastq1 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.fastq.gz -fastq2 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.fastq.gz -fastq3 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.fastq.gz -fastq4 Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.fastq.gz -ctl_fastq1 /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso2.gz -ctl_fastq2 /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso3.gz
$ bds_scr h3k27ac_noncellcycle_dmso20180519.2 -q chettys ~/TF_chipseq_pipeline/chipseq.bds -se -species hg19 -dup_marker sambamba -nth 4 -type histone -mem_bwa 30G -mem_dedup 30G -mem_macs2 30G -out_dir out20180519.2 -fastq1 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.fastq.gz -fastq2 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.fastq.gz -fastq3 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.fastq.gz -fastq4 Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.fastq.gz -ctl_fastq1 /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso2.gz -ctl_fastq2 /labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso3.gz
h3k27ac_noncellcycle_dmso20180519.2.BDS.log
from chipseq_pipeline.
leepc12
commented on July 21, 2024
Use the top one.
```
$ bds_scr h3k27ac_noncellcycle_dmso20180519.2 ~/TF_chipseq_pipeline/chipseq.bds
-q chettys ...
```
I looks like you didn't update your BDS.
Remove your old BDS (`rm -rf ~/.bds`) and update it.
https://github.com/kundajelab/atac_dnase_pipelines#bigdatascript
Thanks,
Jin
…On Sat, May 19, 2018 at 7:28 PM, Liang Ma ***@***.***> wrote:
Hi Jin, where should I put -q chettys in the command? I used the command
below but a fetal error popped up, said "Error message : 'sbatch: error:
Unable to open file chettys", I've attached the log.
$ bds_scr h3k27ac_noncellcycle_dmso20180519.2
~/TF_chipseq_pipeline/chipseq.bds -q chettys -se -species hg19
-dup_marker sambamba -nth 4 -type histone -mem_bwa 30G -mem_dedup 30G
-mem_macs2 30G -out_dir out20180519.2 -fastq1 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.fastq.gz
-fastq2 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.fastq.gz -fastq3
Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.fastq.gz -fastq4
Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.fastq.gz -ctl_fastq1
/labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso2.gz -ctl_fastq2
/labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso3.gz
$ bds_scr h3k27ac_noncellcycle_dmso20180519.2 -q chettys
~/TF_chipseq_pipeline/chipseq.bds -se -species hg19 -dup_marker sambamba
-nth 4 -type histone -mem_bwa 30G -mem_dedup 30G -mem_macs2 30G -out_dir
out20180519.2 -fastq1 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.2.fastq.gz
-fastq2 Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.3.fastq.gz -fastq3
Sample_Hues6_P35_DMSO_H3K27ac_R1_2_TGTCGGAT.R1.fastq.gz -fastq4
Sample_Hues6_P37_DMSO_H3K27ac_GACCGTTG.R1.fastq.gz -ctl_fastq1
/labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso2.gz -ctl_fastq2
/labs/chettys/liangma1/test/chipseq/wce/wce_for_dmso3.gz
h3k27ac_noncellcycle_dmso20180519.2.BDS.log
<https://github.com/kundajelab/chipseq_pipeline/files/2019950/h3k27ac_noncellcycle_dmso20180519.2.BDS.log>
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LiangMa2017
commented on July 21, 2024
Thank you, Jin. I've updated BDS and use '-q' as you suggested, and the job status looks good
$ squeue -j 1688140
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
1688140 batch sbatch liangma1 R 1:58 1 sgisummit-rcf-111-08
from chipseq_pipeline.
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