ryanlayer
commented
7 years ago Can you try vcf output to see if that is the issue?
On Nov 14, 2016, at 3:02 PM, awacs notifications@github.com wrote:
I have bwa mem mapped reads, de-duplication & discordant read/split read extraction by samblaster and coordinate sorted via sambamba. When I try to run lumpy it aborted and core dumped producing the following error message: 443 0 terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check The core dump file is given here. core.zip
The mean/stv/histo files are generated using the example code with the full bam data, and using the full bam file as "-pe" input can run lumpy with no problem.
The command is as follows lumpy -b -mw 4 -tt 0 -t tmp -pe bam_file:/data/talkowski/hw878/Twins/wdl_scripts/cromwell-executions/JointSV/967d1fd0-ed0c-429c-9662-a6b488c8b0b2/call-Get_pesr/shard-0/execution/PM13-02652.sort.disc.bam,histo_file:./PM13-02652.sort.disc.histo,mean:277.459045905,stdev:68.6063129788,read_length:100,min_non_overlap:100,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:10 > ./lumpy_output.bedpe
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awacs
I have bwa mem mapped reads, de-duplication & discordant read/split read extraction by samblaster and coordinate sorted via sambamba. When I try to run lumpy it aborted and core dumped producing the following error message:
443 0 terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_checkThe core dump file is given here. core.zipThe mean/stv/histo files are generated using the example code with the full bam data, and using the full bam file as "-pe" input can run lumpy with no problem.
The command is as follows
lumpy -b -mw 4 -tt 0 -t tmp -pe bam_file:/data/talkowski/hw878/Twins/wdl_scripts/cromwell-executions/JointSV/967d1fd0-ed0c-429c-9662-a6b488c8b0b2/call-Get_pesr/shard-0/execution/PM13-02652.sort.disc.bam,histo_file:./PM13-02652.sort.disc.histo,mean:277.459045905,stdev:68.6063129788,read_length:100,min_non_overlap:100,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:10 > ./lumpy_output.bedpeAny idea of what could be the problem would be greatly appreciated.