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vpc-ccg / pamir

Discovery and Genotyping of Novel Sequence Insertions in Many Sequenced Individuals
BSD 3-Clause "New" or "Revised" License
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Segmenation fault #55

Open wcarre opened 3 years ago

wcarre commented 3 years ago

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":