search

cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
57 stars 20 forks source link

Error: Sanger_CGP_Brass_Implement_group.0.err" unexpectedly returned exit value 1 #81

Closed Dorical closed 5 years ago

Dorical commented 5 years ago

Hi,

I am getting this error and I do not know how to get around it:

"/usr/bin/time /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO10900/tmpBrass/logs/Sanger_CGP_Brass_Implement_group.0.sh 1> /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO10900/tmpBrass/logs/Sanger_CGP_Brass_Implement_group.0.out 2> /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO10900/tmpBrass/logs/Sanger_CGP_Brass_Implement_group.0.err" unexpectedly returned exit value 1 at /services/tools/pcap-core/3.5.0/lib/perl5/PCAP/Threaded.pm line 230.
 at /services/tools/pcap-core/3.5.0/lib/perl5/PCAP/Threaded.pm line 228
"

looking at similar previous error reported here I looked into: grep -v 'Combinatorial surprise' Sanger_CGP_Brass_Implement_group.*.err

And I got this (below) but still I do not know what it means or how to solve it

+ bash -c 'set -o pipefail; /services/tools/brass/6.0.0/bin/brass-group -I /home/projects/pr_46630/data/references/BRASS_references_grch37/depth_1k_noexones.bed -n 2 /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO10900/tmpBrass/96ef40c3-8d4c-4fe1-a33a-99f5b205a0bb.brm.bam /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO10900/tmpBrass/e8114ae7-e076-44ca-b2bb-b6c3629b53b0.brm.bam | /services/tools/perl/5.20.2/bin/perl /services/tools/brass/6.0.0/bin/brassI_pre_filter.pl -i - -t 96ef40c3-8d4c-4fe1-a33a-99f5b205a0bb -o /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO10900/96ef40c3-8d4c-4fe1-a33a-99f5b205a0bb_vs_e8114ae7-e076-44ca-b2bb-b6c3629b53b0.groups'
brass-group: basic_ios::clear
49.04user 1.57system 1:46.30elapsed 47%CPU (0avgtext+0avgdata 39692maxresident)k
4137720inputs+25448outputs (0major+26849minor)pagefaults 0swaps

Thanks for any help

keiranmraine commented 5 years ago

Hi,

There are only a couple of things I can suggest here as the error is very minimal.

  1. Try sorting, bgzip'ing and tabix indexing the /home/projects/pr_46630/data/references/BRASS_references_grch37/depth_1k_noexones.bed file
    • If this resolves please let me know so I can update the wiki page.
  2. Are the chromosome names in your bed file matched to the BAM file headers?
Dorical commented 5 years ago

Thanks for the timely reply.

I have checked the .bam files and they were starting with:

@SQ    SN:1    LN:249250621
@SQ    SN:2    LN:243199373
@SQ    SN:3    LN:198022430

while the .bed file header was

chr1    564467    564846
chr1    566721    568181
chr1    569717    570088

I have removed the "chr" rom the elements of the first row. Testing right now, hopefully it will solve the issue

Dorical commented 5 years ago

bgzip and tabix helped, however now the error is:

+ bash -c 'set -o pipefail; /services/tools/brass/6.0.0/bin/brass-group -I /home/projects/pr_46630/data/references/BRASS_references_grch37/depth_1k_noexones_noChrTRY.bed.gz.tbi -n 2 /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO13144/tmpBrass/65723119-bdfe-46f0-b629-c171023abd71.brm.bam /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO13144/tmpBrass/5b9d2db6-f2b7-47b8-8105-ba44ff3274b7.brm.bam | /services/tools/perl/5.20.2/bin/perl /services/tools/brass/6.0.0/bin/brassI_pre_filter.pl -i - -t 65723119-bdfe-46f0-b629-c171023abd71 -o /home/projects/pr_46630/data/TCGA/DNA/WGS/GBM-US/BRASSresults/DO13144/65723119-bdfe-46f0-b629-c171023abd71_vs_5b9d2db6-f2b7-47b8-8105-ba44ff3274b7.groups'
brass-group: too few BED fields for "/home/projects/pr_46630/data/references/BRASS_references_grch37/depth_1k_noexones_noChrTRY.bed.gz.tbi" at record 1
ERROR: Specified tumour '65723119-bdfe-46f0-b629-c171023abd71' not found in input
0.25user 0.04system 0:00.31elapsed 92%CPU (0avgtext+0avgdata 39708maxresident)k
1344inputs+16outputs (0major+11763minor)pagefaults 0swaps

I am not really sure from where this comes from:

Specified tumour '65723119-bdfe-46f0-b629-c171023abd71' not found in input

As there is no file with such name.

Previously some colleagues used the same .bed file successfully for BRASS 5.4, and I was trying to update the protocol to BRASS 6.0.0. It is the first time I doing this so any tip would really be a massive help

keiranmraine commented 5 years ago

See here:

https://github.com/cancerit/BRASS/wiki/Generating-brass-filter-file#c-convert-pre-v541-brass_npgroupsgz-to-v600-format

keiranmraine commented 5 years ago

File can be converted by following directions linked from previous comment.