Empty output file

[Addicted-to-coding]

Hi,
When I run the tool wham using the command
toolPath -e $EXCLUDE -f $reference -t $alignments | perl ${utilsPath}/filtWhamG.pl
The tool runs without any error with a non-zero runtime. However, it produces an output file with only a header, and no structural variants predictions. When I run a different tool on the same bam file, many structural variants are predicted. What is wrong here?

Thanks

[zeeev]

Hello @Addicted-to-coding,

I'd be happy to help you trouble shoot. First, what happens if you don't pipe the whamg stdout to the filtering script? Do you get any SV calls? What type of data are you working with?

Best,

Zev

[Addicted-to-coding]

Hi zeeev,
Even when I remove the pipe to the whamg stdout to the filtering script, I get an empty output with only a header. I am using mouse data in the form of a .bam file and a mm10 reference .fa file

[zeeev]

What is printed to STDERR and STDOUT?

[Addicted-to-coding]

when I run /u/home/a/angelakl/project-zarlab/sv-project/install/wham/bin/wham -e $EXCLUDE -f ~/reference.genome/mm10.fa -t ~/A_J.bam A , the output is
INFO: WHAM-BAM will only score within bed coordiates provided: GL000207.1,GL000226.1,GL000229.1,GL000231.1,GL000210.1,GL000239.1,GL000235.1,GL000201.1,GL000247.1,GL000245.1,GL000197.1,GL000203.1,GL000246.1,GL000249.1,GL000196.1,GL000248.1,GL000244.1,GL000238.1,GL000202.1,GL000234.1,GL000232.1,GL000206.1,GL000240.1,GL000236.1,GL000241.1,GL000243.1,GL000242.1,GL000230.1,GL0002371,GL000233.1,GL000204.1,GL000198.1,GL000208.1,GL000191.1,GL000227.1,GL000228.1,GL000214.1,GL000221.1,GL000209.1,GL000218.1,GL000220.1,GL000213.1,GL000211.1,GL000199.1,GL000217.1,GL000216.1,GL000215.1,GL000205.1,GL000219.1,GL000224.1,GL000223.1,GL000195.1,GL000212.1,GL000222.1,GL000200.1,GL000193.1,GL000194.1,GL000225.1,GL000192.1,NC_007605
INFO: WHAM-BAM will using the following fasta: ~/reference.genome/mm10.fa
INFO: target bams:
/A_J.bam
INFO: gathering stats for each bam file.
INFO: for file:/A_J.bam
~/A_J.bam: mean depth: ......... 46.3324
~/A_J.bam: sd depth: ......... 15.365
~/A_J.bam: mean insert length: . 362.121
~/A_J.bam: sd insert length: . 90.0449
~/A_J.bam: lower insert length: 137.008
~/A_J.bam: upper insert length: 587.233
~/A_J.bam: average base quality: 36.6236 366738173 10013700
~/A_J.bam: number of reads used: 100137

##fileformat=VCFv4.1
##INFO=<ID=LRT,Number=1,Type=Float,Description="Likelihood Ratio Test statistic">
##INFO=<ID=WAF,Number=3,Type=Float,Description="Allele frequency of: background,target,combined">
##INFO=<ID=GC,Number=2,Type=Integer,Description="Number of called genotypes in: background,target">
##INFO=<ID=AT,Number=15,Type=Float,Description="Pileup attributes">
##INFO=<ID=CF,Number=1,Type=Float,Description="Fraction of reads with more than three cigar operations">
##INFO=<ID=CISTART,Number=2,Type=Integer,Description="PE confidence interval around POS">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">
##INFO=<ID=PU,Number=1,Type=Integer,Description="Number of reads supporting position">
##INFO=<ID=SU,Number=1,Type=Integer,Description="Number of supplemental reads supporting position">
##INFO=<ID=CU,Number=1,Type=Integer,Description="Number of neighboring all soft clip clusters across all individuals at pileup position">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Number of reads at pileup position across individuals passing filters">
##INFO=<ID=NC,Number=1,Type=Float,Description="Number of soft clipped sequences collapsed into consensus">
##INFO=<ID=MQ,Number=1,Type=Float,Description="Average mapping quality">
##INFO=<ID=MQF,Number=1,Type=Float,Description="Fraction of reads with MQ less than 50">
##INFO=<ID=SP,Number=3,Type=Integer,Description="Number of reads supporting endpoint: mate-position,split-read,alternative-mapping">
##INFO=<ID=CHR2,Number=3,Type=String,Description="Other seqid">
##INFO=<ID=DI,Number=1,Type=Character,Description="Consensus is from front or back of pileup: f,b">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between POS and END">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GL,Number=A,Type=Float,Description="Genotype Likelihood">
##FORMAT=<ID=NR,Number=1,Type=Integer,Description="Number of reads that do not support a SV">
##FORMAT=<ID=NA,Number=1,Type=Integer,Description="Number of reads supporting a SV">
##FORMAT=<ID=NS,Number=1,Type=Integer,Description="Number of reads with a softclip at POS for individual">
##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Number of reads passing filters">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
~/A_J.bam
INFO: WHAM-BAM finished normally.

[zeeev]

What aligner did you use? Is this exome or whole genome data? I'd expect at least a couple SVs for WGS data.