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

Iterations must be a positive integer: 0 at /opt/wtsi-cgp/bin/brass.pl line 83. #117

Open DingTin opened 1 year ago

DingTin commented 1 year ago

Sorry when I use brass I met the problem as the title suggested. I'm using the lated version, and I could not found the solution. Here is my script and the results printed. script: brass.pl -o /data/brass_sv/test/ -t /data/all_bam/1/1_T.aligned.duplicates_marked.recalibrated.bam -n /data/all_bam/1/1_P.aligned.duplicates_marked.recalibrated.bam -d /data/brass_sv/hg38depth.bed -g /data/brass_sv/fa/GRCh38.primary_assembly.genome.fa -vi /data/brass_sv/2bit/viral.genomic.merged.fa.2bit -ct /data/brass_sv/hg38_centelo.txt -gc /data/brass_sv/homo_sapiens_vep_109_GRCh38.tar.gz -cb /data/brass_sv/hg38_cytoband.txt -ss /data/brass_sv/sampstat1/1_T.txt -mi /data/brass_sv/2bit/all_ncbi_bacteria -s human -as hg38 -pr WXS -c 2 results: Skipping Sanger_CGP_Brass_Implement_input.1 as previously successful Skipping Sanger_CGP_Brass_Implement_input.2 as previously successful Iterations must be a positive integer: 0 at /opt/wtsi-cgp/bin/brass.pl line 83.

davidrajones commented 1 year ago

Hi @DingTin

What are the contents of your /data/brass_sv/fa/GRCh38.primary_assembly.genome.fa.fai and /data/brass_sv/hg38_centelo.txt files. Do the naming conventions align?

Ajburdett commented 1 year ago

Closing issue due to lack of response