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Can't analyze simultaneously

I have trouble about analyzing of BAM file with Picard FixMateInformation(Version: 2.20.1-SNAPSHOT)
I tried to analyze 30 samples simultaneously with supercomputer , but some samples are not successfully analyzed but about one third samples can’t be well processed.

shell scripts are as follows:
#BATCH --partition=shared
#SBATCH -c 6
#SBATCH -t 0-04:00
#SBATCH --job-name=testing_job_4
#SBATCH -o out_
#SBATCH -e err_

# Sort the Japanese bam file with Samtools (Version: 1.9)
samtools sort [email protected] 6 -m 4G /oasis/projects/nsf/ddp195/h1kimura/exon/NC532.bam -o /oasis/projects/nsf/ddp195/h1kimura/exon/NC532.sorted.bam

samtools index /oasis/projects/nsf/ddp195/h1kimura/exon/NC532.sorted.bam /oasis/projects/nsf/ddp195/h1kimura/exon/NC532.sorted.bai

#FixmateInformation with Picard (Version: 2.20.1-SNAPSHOT)
java -jar /home/h1kimura/lib/picard.jar FixMateInformation I=/oasis/projects/nsf/ddp195/h1kimura/exon/NC532.sorted.bam O=/oasis/projects/nsf/ddp195/h1kimura/exon/NC532.fixmate.sorted.bam SO=coordinate AS=true CREATE_INDEX=true

Not successfully analyzed sample' log is as attached files.

Sorry for the long question.

②.png 769.2K
①.png 829.9K

Best Answer


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