Segmenation fault

[wcarre]

Hi,

Trying to use Pamir.
/ngs/programs/pamir/pamir.sh --configfile config.yaml -j 16

I end up with a seg fault :
"/bin/bash: line 1: 45911 Segmentation fault (core dumped) /ngs/programs/pamir/pamir/pamir partition /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/005-pamir-oea-processing/17-05-GL-P.bwa.sorted.rd.bam/17-05-GL-P.bwa.sorted.rd.bam.anchor.sorted.sam /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/006-pamir-partition/17-05-GL-P.bwa.sorted.rd.bam/partition 1000 /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/004-length-filtering/17-05-GL-P.bwa.sorted.rd.bam.reads.contigs.filtered.clean.fa /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/005-pamir-oea-processing/17-05-GL-P.bwa.sorted.rd.bam/17-05-GL-P.bwa.sorted.rd.bam.oea2orphan.recalib.sam /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/001-pamir-remove-concordants/17-05-GL-P.bwa.sorted.rd.bam/17-05-GL-P.bwa.sorted.rd.bam.oea.unmapped.fq.gz
[Tue Jul 27 10:16:50 2021]
Error in rule pamir_partition:
jobid: 81
output: /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/006-pamir-partition/17-05-GL-P.bwa.sorted.rd.bam/partition, /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/006-pamir-partition/17-05-GL-P.bwa.sorted.rd.bam/partition.count
shell:
/ngs/programs/pamir/pamir/pamir partition /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/005-pamir-oea-processing/17-05-GL-P.bwa.sorted.rd.bam/17-05-GL-P.bwa.sorted.rd.bam.anchor.sorted.sam /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/006-pamir-partition/17-05-GL-P.bwa.sorted.rd.bam/partition 1000 /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/004-length-filtering/17-05-GL-P.bwa.sorted.rd.bam.reads.contigs.filtered.clean.fa /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/005-pamir-oea-processing/17-05-GL-P.bwa.sorted.rd.bam/17-05-GL-P.bwa.sorted.rd.bam.oea2orphan.recalib.sam /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/001-pamir-remove-concordants/17-05-GL-P.bwa.sorted.rd.bam/17-05-GL-P.bwa.sorted.rd.bam.oea.unmapped.fq.gz
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job pamir_partition since they might be corrupted:
/ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/006-pamir-partition/17-05-GL-P.bwa.sorted.rd.bam/partition, /ngs/datagen/genetique/dev/TEST_pamir/analysis/Fam17-05-GL/006-pamir-partition/17-05-GL-P.bwa.sorted.rd.bam/partition.count"

My config file is 👍
path:
/ngs/datagen/genetique/dev/TEST_pamir
raw-data:
bam
reference:
/ngs/bio-databases/hg19_UCSC/mrsfast_index/ucsc.hg19.fasta
population:
Fam17-05-GL
input:
"17-05-GL-E.bwa.sorted.rd.bam":

• 17-05-GL-E.bwa.sorted.rd.bam
  "17-05-GL-P.bwa.sorted.rd.bam":
• 17-05-GL-P.bwa.sorted.rd.bam
  "17-05-GL-M.bwa.sorted.rd.bam":
• 17-05-GL-M.bwa.sorted.rd.bam
  assembly_threads:
  16