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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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lumpy core dump #20

Open seenvs opened 10 years ago

seenvs commented 10 years ago

Hello,

When attempting to run lumpy on NA12878 processing stops and it appears as though a core dump occurs. Any suggestions?

samtools view -f 97 -F 28 /analysis/projects/myseq/gatk/v4/NA12878/bam//NA12878.bam | tail -n+1000000 | awk '$9>=1000 && $9<=3000'|/home/user/tools/CNV/genome/mixed/lumpy/lumpy-sv/scripts//pairend_distro.pl -rl 150 -X 4 -N 100000 -o /home/user/tools/CNV/genome/mixed/lumpy//NA12878_lumpy.histo > /home/user/tools/CNV/genome/mixed/lumpy//NA12878_lumpy.histo.mean.stddev /home/user/tools/CNV/genome/mixed/lumpy/lumpy-sv/bin//lumpy -mw 4 -tt 1e-3 -pe bam_file:/analysis/projects/myseq/gatk/v4/NA12878/bam//NA12878.bam,histo_file:/home/user/tools/CNV/genome/mixed/lumpy//NA12878_lumpy.histo,mean:1879.67125748503,stdev:569.273940066035,read_length:150,min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1 > /home/user/tools/CNV/genome/mixed/lumpy//NA12878_lumpy.bed 1 1000000 2 1000000 3 1000000 4 1000000 5 1000000 6 1000000 Error removing element:6,149059831,149059783,+ 6,149059852,149059804,- 1 /bin/sh: line 1: 7562 Aborted (core dumped) /home/user/tools/CNV/genome/mixed/lumpy/lumpy-sv/bin//lumpy -mw 4 -tt 1e-3 -pe bam_file:/analysis/projects/myseq/gatk/v4/NA12878/bam//NA12878.bam,histo_file:/home/user/tools/CNV/genome/mixed/lumpy//NA12878_lumpy.histo,mean:1879.67125748503,stdev:569.273940066035,read_length:150,min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1

/home/user/tools/CNV/genome/mixed/lumpy//NA12878_lumpy.bed

genecao commented 10 years ago

I was wondering if there is any fix for this, got the same error on v0.2.6