Prachi Kothiyal - 2018-04-12

Hello, we are using Scalpel to call indels on DREAM dataset 4 as a test and parallelized it by chromosome. While jobs for majority of the chromosomes run fine, few give errors and do no produce an output VCF. I've tried rerunning the jobs multiple times and it's not the same set of chromosomes that produce errors. I was hoping to get some suggestions on figuring out what the issue is.

Here's the command:
scalpel-discovery --somatic --normal synthetic.challenge.set4.normal.bam --tumor synthetic.challenge.set4.tumour.bam --ref human_g1k_v37_no_decoy.fasta --dir chr$SGE_TASK_ID --bed $region --window 600 --numprocs 10

where $region is defined to span each chromosome.

Here's a sample error log:

Local date and time: Fri Mar 23 09:08:03 2018

Program: scalpel-discovery (micro-assembly variant detection)
Version: 0.5.4 (beta), January 11 2018
Contact: Giuseppe Narzisi <gnarzisi@nygenome.org>

***MAIN ANALYSIS***
-- Print parameters to chr1/main/parameters.txt
-- Detect mutations on normal
-- Print parameters to chr1/main/normal/parameters.txt
Loading targets region: 1:1-249250621
Loading genome from FASTA file...85 sequences.
Assembly Exons
start assembly of 2492503 regions.
stepSize: 249251
** 0 started, pid: 59749
1. [0..249250]
** 249251 started, pid: 59751
2. [249251..498501]
** 498502 started, pid: 59753
3. [498502..747752]
** 747753 started, pid: 59756
4. [747753..997003]
** 997004 started, pid: 59759
5. [997004..1246254]
** 1246255 started, pid: 59762
6. [1246255..1495505]
** 1495506 started, pid: 59765
7. [1495506..1744756]
** 1744757 started, pid: 59768
8. [1744757..1994007]
** 1994008 started, pid: 59770
9. [1994008..2243258]
** 2243259 started, pid: 59772
10. [2243259..2492502]
Command failure: delete file (rm scalpel/chr1/main/normal/logs/regions-747753-997003.fa.log.gz)...
Command failure: delete file (rm scalpel/chr1/main/normal/logs/regions-249251-498501.fa.log.gz)...
Command failure: delete file (rm scalpel/chr1/main/normal/logs/regions-1495506-1744756.fa.log.gz)...
Command failure: delete file (rm scalpel/chr1/main/normal/regions-997004-1246254.fa)...
Command failure: delete file (rm scalpel/chr1/main/normal/logs/regions-1246255-1495505.fa.log.gz)...
** 249251 just got out of the pool [PID: 59751 | exit code: 0 | exit signal: 9 | core dump: 0]
** 747753 just got out of the pool [PID: 59756 | exit code: 0 | exit signal: 9 | core dump: 0]
Command failure: delete file (rm scalpel/chr1/main/normal/regions-1246255-1495505.fa)...
Command failure: delete file (rm scalpel/chr1/main/normal/logs/regions-1994008-2243258.fa.log.gz)...
** 997004 just got out of the pool [PID: 59759 | exit code: 0 | exit signal: 9 | core dump: 0]
Command failure: delete file (rm scalpel/chr1/main/normal/regions-2243259-2492502.fa)...
Command failure: delete file (rm scalpel/chr1/main/normal/regions-1994008-2243258.fa)...
Command failure: delete file (rm scalpel/chr1/main/normal/regions-0-249250.fa)...
** 1994008 just got out of the pool [PID: 59770 | exit code: 24 | exit signal: 0 | core dump: 0]
** 2243259 just got out of the pool [PID: 59772 | exit code: 187 | exit signal: 0 | core dump: 0]
** 0 just got out of the pool [PID: 59749 | exit code: 0 | exit signal: 0 | core dump: 0]
** 1246255 just got out of the pool [PID: 59762 | exit code: 47 | exit signal: 0 | core dump: 0]
** 1744757 just got out of the pool [PID: 59768 | exit code: 117 | exit signal: 0 | core dump: 0]
** 1495506 just got out of the pool [PID: 59765 | exit code: 210 | exit signal: 0 | core dump: 0]
** 498502 just got out of the pool [PID: 59753 | exit code: 70 | exit signal: 0 | core dump: 0]
Merge DBs...
Load reference coverage...
Argument "" isn't numeric in numeric lt (<) at scalpel/scalpel-0.5.4/HashesIO.pm line 146, <FILE> line 96648269.
Load loc2keys DB...
Can't open scalpel/chr1/main/normal/loc2keys.2.txt (No such file or directory)
Command failure: findVariants (scalpel/scalpel-0.5.4/FindVariants.pl --bam synthetic.challenge.set4.normal.bam --bed 1:1-249250621 --ref human_g1k_v37_no_decoy.fasta --kmer 25 --mincov 5 --covthr 5 --lowcov 2 --covratio 0.01 --radius 100 --window 600 --maxregcov 10000 --step 100 --mapscore 1 --mismatches 3 --pathlimit 1000000 --dir scalpel/chr1/main/normal --sample ALL --numprocs 10 --coords null --format vcf --seed 0 --cov2file)...
Discovery: elapsed time: 0 day(s) 11 hour(s) 31 minute(s) 55 second(s)

Thanks,
Prachi