Open Addicted-to-coding opened 6 years ago
zeeev
commented
6 years ago 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
commented
6 years ago 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
commented
6 years ago What is printed to STDERR and STDOUT?
Addicted-to-coding
commented
6 years ago 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
~/A_J.bam INFO: WHAM-BAM finished normally.
zeeev
commented
6 years ago What aligner did you use? Is this exome or whole genome data? I'd expect at least a couple SVs for WGS data.
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