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HS-BLAST output required!

When running NanoVar I get the following error:
HS-BLAST output required!

I installed with ./configure --disable-bowtie2 because I do not need short reads. Everything passed when make && make check was ran. I have attached NanoVar.log. Any ideas on how to resolve this issue would be appreciated?
Thanks,
Scott

24-Oct~22-02-49_NanoVar.log

python3 ?

Hi, Python2 is only supported till 2020 - that's six months. Any plans for a python3 version ?

cheers,
Colin

***** WARNING: File bed2.sort has inconsistent naming convention for record

Why chromosome name starting with 'chr' exist in the bed file?
I just used the reference genome with chromosome name without 'chr'.

the command

$ nanovar -r  Homo_sapiens.GRCh38.dna.primary_assembly.fa -l M625-0_test.fastq -t 20 -o Project/nanoVar 


NanoVar initiated --- Thu Jun 20 08:53:12 CST 2019
<WARNING: Long read sequencing depth is below recommended depth of more than 4x, output may not be comprehensive>
Traceback (most recent call last):  (32%)
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/scripts/nv_lcov_outlier.py", line 186, in <module>
    print main()
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/scripts/nv_lcov_outlier.py", line 177, in main
    curve(data2, n, round((medad*6) + med, 0))
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/scripts/nv_lcov_outlier.py", line 136, in curve
    smooth = spline(c,y,xnew)
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/nv_virtualenv/lib/python2.7/site-packages/numpy/lib/utils.py", line 101, in newfunc
    return func(*args, **kwds)
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/nv_virtualenv/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 2918, in spline
    return spleval(splmake(xk, yk, order=order, kind=kind, conds=conds), xnew)
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/nv_virtualenv/lib/python2.7/site-packages/numpy/lib/utils.py", line 101, in newfunc
    return func(*args, **kwds)
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/nv_virtualenv/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 2827, in splmake
    coefs = func(xk, yk, order, conds, B)
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/nv_virtualenv/lib/python2.7/site-packages/scipy/interpolate/interpolate.py", line 2743, in _find_smoothest
    J = _fitpack._bspldismat(order, xk)
ValueError: too few samples (0)
awk: cmd. line:1: {if (>$11+$13 && $11+$13>=1) print $0}
awk: cmd. line:1:      ^ syntax error
awk: cmd. line:1: {if (>$11+$13 && $11+$13>=1) print $0}
awk: cmd. line:1:                            ^ syntax error
***** WARNING: File bed2.sort has inconsistent naming convention for record:
chr1	8695050	8695150	8eba26d1-af9a-41f8-b59d-7c178244812e~D9JRT-l	Inter

***** WARNING: File bed2.sort has inconsistent naming convention for record:
chr1	8695050	8695150	8eba26d1-af9a-41f8-b59d-7c178244812e~D9JRT-l	Inter

***** WARNING: File bed4.sort has inconsistent naming convention for record:
chr1	8695100	8695101	8eba26d1-af9a-41f8-b59d-7c178244812e~D9JRT

***** WARNING: File bed4.sort has inconsistent naming convention for record:
chr1	8695100	8695101	8eba26d1-af9a-41f8-b59d-7c178244812e~D9JRT

Traceback (most recent call last):
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/scripts/nv_lr_overlap.py", line 468, in <module>
    main()
  File "/home/wuzhikun/anaconda3/envs/NanoSV/bin/NanoVar/scripts/nv_lr_overlap.py", line 465, in main
    print ''.join(output)
IOError: [Errno 32] Broken pipe
***SV Overlap file required***

some outputs of bed file

1       114008484       114008485       004b9ad2-7d29-4551-810d-3eea8f4d6fba~W7G81-l    Inv
1       114017276       114017277       004b9ad2-7d29-4551-810d-3eea8f4d6fba~W7G81-r    Inv
2       207066285       207066286       005415d7-eb64-4066-81a8-8f56dbde7072~Z74K9-l    Del
2       207066420       207066421       005415d7-eb64-4066-81a8-8f56dbde7072~Z74K9-r    Del
chr19   8737550 8737551 00615688-1316-49f4-a5ba-0509160fb232~QHKRD-l    Inter
chr8    1180748 1180749 00615688-1316-49f4-a5ba-0509160fb232~QHKRD-r    Inter
8       1186230 1186231 00615688-1316-49f4-a5ba-0509160fb232~Q03T9-l    Del
8       1186420 1186421 00615688-1316-49f4-a5ba-0509160fb232~Q03T9-r    Del
8       1203368 1203369 00615688-1316-49f4-a5ba-0509160fb232~7UH6N-l    bp_Nov_Ins
18      21323540        21323541        007f8067-7c62-4740-ac25-ce22408e023d~FS3E5-l    Del
18      21323859        21323860        007f8067-7c62-4740-ac25-ce22408e023d~FS3E5-r    Del
chr20   29401544        29401545        00a122de-0fc7-4d59-8a28-2ecb740e1e38~YSCE3-l    Inter
chr3    75678747        75678748        00a122de-0fc7-4d59-8a28-2ecb740e1e38~YSCE3-r    Inter
9       10966651        10966652        00bc5252-7494-4d94-8d17-31636a5cd979~Y8ZAN-l    bp_Nov_Ins
chr13   54314747        54314748        00bc5252-7494-4d94-8d17-31636a5cd979~J05OC-l    Inter
chr9    10965652        10965653        00bc5252-7494-4d94-8d17-31636a5cd979~J05OC-r    Inter

Long read sequencing depth is below recommended depth of more than 4x, output may not be comprehensive

I used nanovar wrapped with docker to run, and had the error WARNING: Long read sequencing depth is below recommended depth of more than 4x, output may not be comprehensive,but the input fastq file is at least 15 X.

This is the log file:

Log file for NanoVar-1.0.
Thu Jun 20 12:17:42 UTC 2019
Command /usr/local/bin/nanovar -r /root/database/genome/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa -l /root/Project/NanoTrio/clean/M625-0.fastq.gz -t 20 -o /root/Test/nanovar
<Long read fasta file contains no spaces> --- PASSED
<Long read fasta file contains no wraped lines> --- PASSED
nanovar_run directory already present
nanovar_results directory already present
figures directory already present
bowtie2_shortreads directory already present
hsblast_longreads directory already present

Inputs and parameters:
main=/home/NanoVar
refgenome=/root/database/genome/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa
longread=/root/Project/NanoTrio/clean/M625-0.fastq.gz
shortread1=NIL
shortread2=NIL
Short paired-end reads not provided, only long reads will be used for SV characterization
output_dir=/root/Test/nanovar
no_of_threads=20
Genomic_region_excluded_file=0
Neural_network_threshold=0
SV_threshold_score=2.6
SV_alignment_threshold=0.95
Buffered_SV_length_threshold=50
minimum_short_cov=NA
maximum_short_cov=NA
Total_long_reads=2468218

Starting run...
SKIPPING - Build BLAST DB
[Thu-20-Jun 12:17:42] Generate freq counts file
SKIPPING - Convert frequency counts file to obinary
SKIPPING - Build FMD index
SKIPPING - HS-BLAST read alignment search
[Thu-20-Jun 12:43:21] HS-BLAST Parse
<WARNING: Long read sequencing depth is below recommended depth of more than 4x, output may not be comprehensive>

Longread_overlap_upper_limit=
Genome_size=3099750718 bases
Mapped_bases=0 bases
Seq_depth=<1 x
Number_of_splits=1
Splitted_coverage=0.0

***HS-BLAST parsed file required!***

But the input fastq file is at least 15X, I don't why has this error.

-rw-rw-r--  39G Mar 29 02:37 Project/NanoTrio/clean/M625-0.fastq.gz

can not install NanoVar

Hi,

We missed a problem when install NanoVar:

~/tools/NanoVar-master$ make
Dependency error: bedtools required to be version 2.26.0 or greater
make: *** [checkversions] Error 1
~/tools/NanoVar-master$ bedtools --version
bedtools v2.27.1

Could you please help us to solve this problem?

Error: SV Overlap file required

Error encountered: SV Overlap file required

Error - SV Parse file required

When running NanoVar I get the following error:

Traceback (most recent call last): (32%)
File "/home/dnd/NanoVar/scripts/nv_breakpoint_parser.py", line 177, in
coord1 = int(breakpointfile[i].split('\t')[6].split(' ')[1].split(',')[int(del_count - del_counter)].split(':')[1].split('-')[0])
IndexError: list index out of range
SV Parse file required---- ] (35%)

NanoVar was installed with ./configure --disable-bowtie2 and everything passed when make && make check was ran. NanoVar finished without error on 3 other data sets. I have attached NanoVar.log and NanoVar.commandlog. Any ideas on how to resolve this issue would be appreciated?

Thanks,
Scott

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