Bus error during detect_gaps_search

[rozaimirazali]

Hi. I am getting a Bus error message during the Detect stage.

[Wed Mar 6 07:23:10 2019] Finished job 16. 16 of 72 steps (22%) done

[Wed Mar 6 07:23:10 2019] rule detect_gaps_search: input: align/bam/4.bam, reference/ref.fasta, reference/ref.fasta.fai output: detect/gaps/batch/4_all.bed log: detect/gaps/batch/log/4.log jobid: 62 wildcards: batch_id=4

/usr/bin/bash: line 1: 219513 Broken pipe samtools view -F 0x4 -q 30 align/bam/4.bam 219514 Bus error | python2 /gpfs/software/genomics/smrtsv2/smrtsv2/scripts/PrintGaps.py reference/ref.fasta /dev/stdin --condense 20 > detect/gaps/batch/4_all.bed 2> detect/gaps/batch/log/4.log /gpfs/home/rmohamadrazali/.lsbatch/1551709440.220922: line 8: 284704 Bus error smrtsv.py --tempdir tmp --verbose --log log.txt run --batches 10 --threads 32 GRCh37.fa multi_runs.fofn

When I look at the log inside detect/gaps/batch/log/ , the file size are all 0 bytes.

-rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 0 Mar 5 19:36 7.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 0 Mar 5 21:37 6.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 0 Mar 5 23:45 8.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 0 Mar 6 01:27 2.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 0 Mar 6 03:27 1.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 0 Mar 6 05:34 5.log -rw-rw-r-- 1 rmohamadrazali SDR_gref_ymokrab 0 Mar 6 07:23 4.log

[paudano]

I have only seen "Bus error" when the system kills one process in a command pipeline (cmd1 | cmd2 | cmd3 ...). If you are running it through a cluster system, check the job history to see what the runtime and memory usage was and if it was killed. If you are running it on a standalone host, check memory utilization, temp space, etc.