I got the following error (after about 4 h after starting the whole thing):
STDERR: + bash -c 'set -o pipefail; /opt/wtsi-cgp/bin/brass-group -I /bam_files/depth_calculations/depth_mask.bed.gz -n 2 /bam_files/brass/tmpBrass/AS-226583-LR-34284_R1.brm.bam /bam_files/brass/tmpBrass/AS-226595-LR-34290_R1.brm.bam | /usr/bin/perl /opt/wtsi-cgp/bin/brassI_pre_filter.pl -i - -t AS-226583-LR-34284_R1 -o /bam_files/brass/AS-226583-LR-34284_R1_vs_AS-226595-LR-34290_R1.groups'
STDERR: brass-group: No read groups listed (-s/-m/etc options required)
STDERR: ERROR: Specified tumour 'AS-226583-LR-34284_R1' not found in input
STDERR: Command exited with non-zero status 255
I checked the bam files (both have their corresponding name as read group (SM) set. I found a nearly identical issue in the closed ones, where the .bas file was the problem, but my .bas file has the read group set. At least all files I checked (centro/telo, cache, cytobands) have the same notation as my bam files for chromosome.
I got the following error (after about 4 h after starting the whole thing):
STDERR: + bash -c 'set -o pipefail; /opt/wtsi-cgp/bin/brass-group -I /bam_files/depth_calculations/depth_mask.bed.gz -n 2 /bam_files/brass/tmpBrass/AS-226583-LR-34284_R1.brm.bam /bam_files/brass/tmpBrass/AS-226595-LR-34290_R1.brm.bam | /usr/bin/perl /opt/wtsi-cgp/bin/brassI_pre_filter.pl -i - -t AS-226583-LR-34284_R1 -o /bam_files/brass/AS-226583-LR-34284_R1_vs_AS-226595-LR-34290_R1.groups' STDERR: brass-group: No read groups listed (-s/-m/etc options required) STDERR: ERROR: Specified tumour 'AS-226583-LR-34284_R1' not found in input STDERR: Command exited with non-zero status 255
I checked the bam files (both have their corresponding name as read group (SM) set. I found a nearly identical issue in the closed ones, where the .bas file was the problem, but my .bas file has the read group set. At least all files I checked (centro/telo, cache, cytobands) have the same notation as my bam files for chromosome.