keiranmraine
commented
5 years ago Likely this would be caused in your cent-telo file had a mismatch in chromosome naming to that of the data you are processing:
https://github.com/cancerit/BRASS/wiki/Centromere-Telomere-locations
I was running brass.pl but the process was quit with error like:
"/usr/bin/time teem/tmpBrass/logs/Sanger_CGP_Brass_Implement_input.1.sh 1> teem/tmpBrass/logs/Sanger_CGP_Brass_Implement_input.1.out 2> teem/tmpBrass/logs/Sanger_CGP_Brass_Implement_input.1.err" unexpectedly returned exit value 1 at /opt/wtsi-cgp/lib/perl5/PCAP/Threaded.pm line 270. at /opt/wtsi-cgp/lib/perl5/PCAP/Threaded.pm line 268
my command line is like:
brass.pl -o teem -t Tumor.realigned.md.bam -n Normal.realigned.md.bam -d depth_final.bed -g chr_genome.fa -s human -as GRCh37 -pr WGS -gc vagrent.human.GRCh37.homo_sapiens_91_37.cache.gz -vi viral.genomic.fa -mi all_bacteria.fa -b gcBins.bed -cb cytoband.txt -ct centTelo.tsv
for the sh file generated, seems it added option like -p T -i:
!/bin/bash
set -eux bash -c 'set -o pipefail; /opt/wtsi-cgp/bin/samtools view -F 3854 -q 6 -u Tumor.realigned.md.bam | /opt/wtsi-cgp/bin/bedtools intersect -ubam -v -abam stdin -b depth_final.bed | /opt/wtsi-cgp/biobambam2/bin/bamcollate2 outputformat=sam exclude= classes=F,F2 T=/teem/tmpBrass/bamcollate2_1 | /usr/bin/perl /opt/wtsi-cgp/bin/brassI_prep_bam.pl -b Tumor.realigned.md.bam.bas -p T -i | /opt/wtsi-cgp/biobambam2/bin/bamsort tmpfile=/teem/tmpBrass/bamsort_1 inputformat=sam verbose=0 index=1 md5=1 md5filename=/teem/tmpBrass/Tumor.brm.bam.md5 indexfilename=/teem/tmpBrass/Tumor.brm.bam.bai O=/scratch/wangyong/all/teem/tmpBrass/Tumor.brm.bam'
The error file is:
/opt/wtsi-cgp/biobambam2/bin/../lib/libmaus2.so.2(libmaus2::util::StackTrace::StackTrace()+0x4c)[0x2aaaaadb2e3c] /opt/wtsi-cgp/biobambam2/bin/bamsort(libmaus2::exception::LibMausException::LibMausException()+0x20)[0x420410] /opt/wtsi-cgp/biobambam2/bin/bamsort()[0x448f53] /opt/wtsi-cgp/biobambam2/bin/bamsort()[0x4191a1] /opt/wtsi-cgp/biobambam2/bin/bamsort()[0x4124d5] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x2aaaae52e830] /opt/wtsi-cgp/biobambam2/bin/bamsort()[0x412be2]
WARNING: SAM header designates more than one PG tree root by PP tags. Command exited with non-zero status 1 1.72user 0.26system 0:01.43elapsed 138%CPU (0avgtext+0avgdata 45492maxresident)k 11440inputs+32outputs (88major+12763minor)pagefaults 0swaps
It shows "Option i requires an argument". Not sure how this option gets into the command line and also how to solve the problem. Thanks for your help. By the way, in order to make the files less crowded, I have manually removed the absolute long path of most of my input files (if not all) in the content above.
regards Yonghong