nccl-jmli / varben Goto Github PK

Dear Prof. Li,
I got some error message when running the example command 03-spikein_snv_and_indel_Illumina.sh, could you please help me ? The attachment is the complete log file.
log.txt

step3: modify the reads in total_chosen_reads itself
[E::bam_read1] CIGAR and query sequence lengths differ for FCHV3N7BCXY:1:2115:4208:45056#TCACCTCA
samtools sort: truncated file. Aborting
step4: write edited reads to edited file and exclude reads to exclude file ,than remap edited file to reference
remap start .......................................
samtools sort start................................
samtools sort -n -o ../output/illumina/tempDir/edit.sortByName.bam ../output/illumina/tempDir/edit.bam
Traceback (most recent call last):
File "../../bin/muteditor.py", line 122, in
run()
File "../../bin/muteditor.py", line 118, in run
main(run_args)
File "../../bin/muteditor.py", line 60, in main
run_args.alignerIndex, run_args.single)
File "/home/lierhan/VarBen-master/bin/../varben/deal_mut/readsReplace.py", line 65, in reads_replace
remap(aligner_index, edit_bam_file, edit_remap_bam_file, aligner, is_single, header=head)
File "/home/lierhan/VarBen-master/bin/../varben/common/bamconvert.py", line 98, in remap
bamSort(inBamFile, inPrefix + ".sortByName", sort_key="name")
File "/home/lierhan/VarBen-master/bin/../varben/common/bamconvert.py", line 78, in bamSort
_call(bamSort_cmd)
File "/home/lierhan/VarBen-master/bin/../varben/common/bamconvert.py", line 14, in _call
raise Exception("Cmd Error: %s" % cmd)
Exception: Cmd Error: samtools sort -n -o ../output/illumina/tempDir/edit.sortByName.bam ../output/illumina/tempDir/edit.bam

Thanks a lot!
Best,
lierhan

Hi,

When I use your software to add cnv variants, there have error ：'could not convert string to float: cnv'.
Counld I use the software to add cnv variants ?

Looking forward to your reply!
Thanks

hi ，liliya:

when I run "muteditor.py" , the following error is reported :

Exception: Cmd Error: samtools sort -n -o /bioinfo/home/tempDir/edit.sortByName.bam /bioinfo/home/tempDir/edit.bam

Then I run this command line , the error is :
[E::bam_read1] CIGAR and query sequence lengths differ for A00821:395:H7Y5MDSXY:3:2170:22788:14497 samtools sort: truncated file. Aborting

I extracted this reads, when it is a hardclip reads , the reads will be trimed by BWA , So led to the error .
I'm not sure if this is the reason, or is my script problem?

Thank you !

why i usually get invalid mutation 'All reads is filtered in this scope, total & filtered reads num 3716'

hi,
When I was running sveditor.py script to add CNV to BAM files, it had an error"Failed to open file ./sv_out/tempDir/edit.remap.bam".I checkd every script in VarBen , i didn't find which step can generate this edit.remap.bam. so can you help me?

Hi Lijia Yu,
When I was runningmuteditor.py script, the error CIGAR and query sequence lengths differ happen

python2 bin/muteditor.py -m /data/project/varben_model_20230209/test_l4/varben.tsv -b /data/project/varben_model_20230209/test_l4/n5TRUE.mem_pe.sort.bam -r /data/Homo_sapiens/Homo_sapiens_38/Homo_sapiens_assembly38.fasta -p 4 --aligner bwa --alignerIndex /data/Homo_sapiens/Homo_sapiens_38/Homo_sapiens_assembly38.fasta --seqer illumina --haplosize 10 --mindepth 500 --minmutreads 5 --snpfrac 0.1 --outdir /data/project/varben_model_20230209/test_l4/n5.50.sort.varben.snv_out

the error is
samtools sort start................................
samtools sort -n -o /data/project/varben_model_20230209/test_l4/n5.50.sort.varben.snv_out/tempDir/edit.sortByName.bam /data/project/varben_model_20230209/test_l4/n5.50.sort.varben.snv_out/tempDir/edit.bam
[E::bam_read1] CIGAR and query sequence lengths differ for A00265:734:HK2CTDSX2:2:2424:27968:16360
samtools sort: truncated file. Aborting
Traceback (most recent call last):
File "bin/muteditor.py", line 122, in
run()
File "bin/muteditor.py", line 118, in run
main(run_args)
File "bin/muteditor.py", line 60, in main
run_args.alignerIndex, run_args.single)
File "/root/software/varben/VarBen-master/bin/../varben/deal_mut/readsReplace.py", line 65, in reads_replace
remap(aligner_index, edit_bam_file, edit_remap_bam_file, aligner, is_single, header=head)
File "/root/software/varben/VarBen-master/bin/../varben/common/bamconvert.py", line 98, in remap
bamSort(inBamFile, inPrefix + ".sortByName", sort_key="name")
File "/root/software/varben/VarBen-master/bin/../varben/common/bamconvert.py", line 78, in bamSort
_call(bamSort_cmd)
File "/root/software/varben/VarBen-master/bin/../varben/common/bamconvert.py", line 14, in _call
raise Exception("Cmd Error: %s" % cmd)
Exception: Cmd Error: samtools sort -n -o /data/project/varben_model_20230209/test_l4/n5.50.sort.varben.snv_out/tempDir/edit.sortByName.bam /data/project/varben_model_20230209/test_l4/n5.50.sort.varben.snv_out/tempDir/edit.bam

I have use picard.jar ValidateSamFile to find where the error is ,but the software say "No errors found"

Could you help me fix it ?

Hi Lijia Yu,
When I was running sveditor.py script with an inversion variant as an input, the job was killed when the step of mapping by bwa starts

File "/home/asmmahmoud/ctg/varben/VarBen-master/bin/../varben/common/bamconvert.py", line 14, in _call
raise Exception("Cmd Error: %s" % cmd)
Exception: Cmd Error: bwa mem -R "@rg\tID:A4-NA24143-WEST_L1\tLB:RGLB\tPU:1\tSM:A4-NA24143-WEST" -t 1 /home/asmmahmoud/ctg/ref/GRCh38_full_analysis_set_plus_decoy_hla.fa /home/asmmahmoud/ctg/varben/inv_test/tempDir/edit.remap.to_1.fq /home/asmmahmoud/ctg/varben/inv_test/tempDir/edit.remap.to_2.fq >/home/asmmahmoud/ctg/varben/inv_test/tempDir/edit.remap.sam

Could you help me fix it ?

Hi,

default version of pysam installed on TorrentServer was 0.7.7, while VarBen require pysam>=0.9.4.
We failed to update pysam on TS5.4/5.6/5.10 since default library had been set to 'ion-updates' and cannot be changed.
Any suggestion?

Regards
Tang

Hi,
when '\t' are included in bam header (for example, read group header line such as '@rg\tID:foo\tSM:bar'), VarBen will report errors and stop at the remapping stage. It seems that the python script cannot resolve the bam header correctly because '\t' is a non-literal characters.
Here are some related issues:
tseemann/snippy#100
CPTR-ReSeqTB/UVP#18

Dear Prof. Li,
I got some error message when simulating CNV use VarBen, could you please help me ?
the command:
python VarBen-master/bin/sveditor.py --svfile mut.list --bamfile mybam.bam --reffasta hg19.fasta --readlength 150 -o varben_out --alignerIndex hg19.fasta --seqer illumina --aligner bwa
the input sv file:
chr1 110883028 110884090 cnv 2.5 gain
chr1 16258586 16259761 cnv 2 loss
and I got these error:
['chr1', '110883028', '110884090', 'cnv', '2.5', 'gain']
['chr1', '16258586', '16259761', 'cnv', '2', 'loss']
Traceback (most recent call last): File "/mnt/cfs/project/test_freshman/liaoxinhui/3.20190624_bio_performance/software/VarBen-master/bin/../varben/deal_sv/checkSVInput.py", line 40, in check_sv raise Exception("cnv is not in correct format") Exception: cnv is not in correct format
('cnv is not in correct format',) ('chr1\t16258586\t16259761\tcnv\t2\tloss', 'cnv is not in correct format')
It seems that the 'AF' column in input file is uncorrected, so how to set 'AF' column ? Was the 'AF' column mean copies of gain/loss ?
Thanks a lot!
Best,
Gerde Liao