Closed Leehyeonjin93 closed 5 years ago
tobiasrausch
commented
5 years ago Is this happening with the latest version of delly v0.8.1 ? Previously delly created more I/O which apparently on very busy filesystems in cluster environments created these bus errors in rare occasions. I haven't seen this anymore in v0.8.1.
Leehyeonjin93
commented
5 years ago yes. These are my tool's version. Delly version: v0.8.1 using Boost: v1.58.0 using HTSlib: v1.6
tobiasrausch
commented
5 years ago Sorry for the long delay. We recently used Delly on >3,000 WGS samples and I couldn't reproduce this error. You didn't edit the Delly Makefile I suppose? The "-O3 -fno-tree-vectorize" is crucial because of htslib cigar memory alignment. I also bumped now the htslib version to the latest release 1.9. Maybe that helps in your case, I am not sure. I am using now htslib v1.9 and boost v1.65.
Leehyeonjin93
commented
5 years ago It works now, thank you.
Hi, I ran 15 samples to use delly2. but only 2 samples stoped and I got error message like this;
[2019-Apr-29 19:19:53] SV annotation
0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| ****./0.run.delly.sh: line 24: 40933 Bus error (core dumped) $delly_sv call -x ~/Programs/delly/excludeTemplates/human.hg19.excl.exChr.tsv -o $output_path/$samplename.bcf -g $ref_gen $input_path/$samplename/$samplename.sorted.RGfixed.Rmdup.realign.recal.bam
2 bam files were used for varscan, mosaichunter, haplotypecaller, cnvnator. I tried again 3 times but got same message.
thank you.