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Core Dump Error running masurca #334

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ankush290307 opened this issue Nov 17, 2023 · 0 comments
Open

Core Dump Error running masurca #334

ankush290307 opened this issue Nov 17, 2023 · 0 comments

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@ankush290307
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The error : ./assemble.sh
[Fri Nov 17 00:00:12 EST 2023] Processing pe library reads
[Fri Nov 17 00:00:42 EST 2023] Average PE read length 197
[Fri Nov 17 00:00:42 EST 2023] MIN_Q_CHAR: 33
[Fri Nov 17 00:00:42 EST 2023] Creating mer database for Quorum
./assemble.sh: line 96: 3640278 Broken pipe awk '{print substr($0,1,200)}' p1.renamed.fastq p2.renamed.fastq p3.renamed.fastq p4.renamed.fastq p5.renamed.fastq
3640279 Killed | quorum_create_database -t 128 -s $JF_SIZE -b 7 -m 24 -q $((MIN_Q_CHAR + 5)) -o quorum_mer_db.jf.tmp /dev/stdin
[Fri Nov 17 00:00:52 EST 2023] Error correct PE
./assemble.sh: line 103: 3640286 Aborted (core dumped) quorum_error_correct_reads -q $(($MIN_Q_CHAR + 40)) --contaminant=/apps/eb/MaSuRCA/4.1.0-GCC-11.3.0/bin/../share/adapter.jf -m 3 -s 1 -g 1 -a 9 -t 128 -w 10 -e 3 -M quorum_mer_db.jf p1.renamed.fastq p2.renamed.fastq p3.renamed.fastq p4.renamed.fastq p5.renamed.fastq --no-discard -o pe.cor.tmp --verbose > quorum.err 2>&1
[Fri Nov 17 00:00:54 EST 2023] Error correction of PE reads failed. Check pe.cor.log.
The config file: DATA
PE = p1 180 20 /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND1.paired.1.fq /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND1.paired.2.fq
PE = p2 180 20 /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND2.paired.1.fq /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND2.paired.2.fq
PE = p3 180 20 /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND3.paired.1.fq /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND3.paired.2.fq
PE = p4 180 20 /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND4.paired.1.fq /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND4.paired.2.fq
PE = p5 180 20 /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND5.paired.1.fq /scratch/minliu/IND/IND_sep_fastq/qcfastq/IND5.paired.2.fq
END

PARAMETERS
GRAPH_KMER_SIZE = 127
USE_LINKING_MATES = 1
LIMIT_JUMP_COVERAGE = 550
CA_PARAMETERS = cgwErrorRate=0
KMER_COUNT_THRESHOLD = 3
NUM_THREADS = 128
JF_SIZE = 29854115132
SOAP_ASSEMBLY = 0
END

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