"exit status 2" error

[yanlolo]

Hey,

It's really a exciting variant calling tool. I would like to use for aligners benchmark. But I ran it on SSD and always got an error "exit status 2". I attached the log and the commands. Thanks.

Log:

2021/12/10 12:47:43 Splitting...
2021/12/10 12:54:06 Filtering (phase 1)...
2021/12/10 13:05:51 Filtering (phase 2) and variant calling...
2021/12/10 13:05:51 exit status 2

Command:

#1.	ref 
elprep fasta-to-elfasta /ssd-path-to-folder/data/hg37.fna \
/ssd-path-to-folder/data/elprep/hg37.elfasta
 
#2.	sites 
elprep vcf-to-elsites /ssd-path-to-folder/yan/variant-call/v2.19-out/truth_snp.recode.vcf \
/ssd-path-to-folder/data/elprep/hg37_snp.elsites
 
elprep vcf-to-elsites /ssd-path-to-folder/yan/variant-call/v2.19-out/truth_indels.recode.vcf \
/ssd-path-to-folder/data/elprep/hg37_indels.elsites
 
#3.	variant calling
elprep sfm /ssd-path-to-folder/yan/NA12878/accalign.mason.bam \
/ssd-path-to-folder/yan/NA12878/NA12878.output.bam \
--mark-duplicates --mark-optical-duplicates /ssd-path-to-folder/yan/NA12878/NA12878.output.metrics \
--sorting-order coordinate \
--bqsr /ssd-path-to-folder/yan/NA12878/NA12878.output.recal \
--known-sites /ssd-path-to-folder/data/elprep/hg37_indels.elsites,/ssd-path-to-folder/data/elprep/hg37_snp.elsites \
--reference /ssd-path-to-folder/data/elprep/hg37.elfasta \
--haplotypecaller accalign.gatk.vcf.gz

[caherzee]

Hi,

The first line of the log should mention a path where other logs are written. Without these, it is hard to figure out what may be going wrong.

Thanks.

Charlotte

[desmodus1984]

Hi,
I ran into the same problem.
I mapped my reads to my reference, and then used the following code:

#!/bin/bash
#SBATCH --time=120:00:00
#SBATCH --ntasks=48
#SBATCH --mem=650G
#SBATCH --job-name=PA_113.vcf
#SBATCH --account=PHS0338

module load python
source activate vcf

elprep sfm PA_113.sam PA_113.sorted.bam --nr-of-threads 48 --tmp-path $TMPDIR
--mark-duplicates --mark-optical-duplicates PA_113.metrics
--sorting-order coordinate
--bqsr PA_113.recal
--reference /users/PHS0338/jpac1984/data/myse-hapog.elfasta
--haplotypecaller PA_113.vcf.gz

I have used the same code for other and it worked fine. But this time I got error, and I got the following error log:
elprep version 5.1.1 compiled with go1.16.7 - see http://github.com/exascience/elprep for more information.

2022/03/22 15:02:15 Created log file at /users/PHS0338/jpac1984/logs/elprep/elprep-2022-03-22-15-02-15-385126188-EDT.log
2022/03/22 15:02:15 Command line: [elprep sfm PA_113.sam PA_113.sorted.bam --nr-of-threads 48 --tmp-path /tmp/slurmtmp.9732793 --mark-duplicates --mark-optical-duplicates PA_113.metrics --sorting-order coordinate --bqsr PA_113.recal --reference /users/PHS0338/jpac1984/data/myse-hapog.elfasta --haplotypecaller PA_113.vcf.gz]
2022/03/22 15:02:15 Executing command:
elprep sfm PA_113.sam PA_113.sorted.bam --mark-duplicates --mark-optical-duplicates PA_113.metrics --optical-duplicates-pixel-distance 100 --bqsr PA_113.recal --reference /users/PHS0338/jpac1984/data/myse-hapog.elfasta --quantize-levels 0 --max-cycle 500 --haplotypecaller PA_113.vcf.gz --sorting-order coordinate --nr-of-threads 48 --tmp-path /tmp/slurmtmp.9732793 --intermediate-files-output-prefix PA_113 --intermediate-files-output-type sam
2022/03/22 15:02:15 Splitting...
2022/03/22 16:49:01 Filtering (phase 1)...
2022/03/22 19:26:56 exit status 2

Other file:
elprep version 5.1.1 compiled with go1.16.7 - see http://github.com/exascience/elprep for more information.

2022/02/20 18:51:20 Created log file at /users/PHS0338/jpac1984/logs/elprep/elprep-2022-02-20-18-51-20-470694768-EST.log
2022/02/20 18:51:20 Command line: [elprep sfm IN33.bam IN33.sorted.bam --nr-of-threads 28 --tmp-path /tmp/slurmtmp.17821988 --mark-duplicates --mark-optical-duplicates IN33.metrics --sorting-order coordinate --bqsr IN33.recal --reference /users/PHS0338/jpac1984/data/myse-hapog.elfasta --haplotypecaller IN33.vcf.gz]
2022/02/20 18:51:20 Executing command:
elprep sfm IN33.bam IN33.sorted.bam --mark-duplicates --mark-optical-duplicates IN33.metrics --optical-duplicates-pixel-distance 100 --bqsr IN33.recal --reference /users/PHS0338/jpac1984/data/myse-hapog.elfasta --quantize-levels 0 --max-cycle 500 --haplotypecaller IN33.vcf.gz --sorting-order coordinate --nr-of-threads 28 --tmp-path /tmp/slurmtmp.17821988 --intermediate-files-output-prefix IN33 --intermediate-files-output-type bam
2022/02/20 18:51:20 Splitting...
2022/02/20 18:57:28 Filtering (phase 1)...
2022/02/20 19:17:21 Filtering (phase 2) and variant calling...
2022/02/23 14:53:29 Merging sam/bam...
2022/02/23 14:58:56 Merging metrics...
2022/02/23 14:58:56 Merge vcf...

Any reason why the failure?

Thanks;

Juan