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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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bamstats05 ERROR : error msg : Exited with failure (-1) #113

Closed Vithyanatarajan closed 5 years ago

Vithyanatarajan commented 5 years ago

Verify

Subject of the issue

Error on running bamstats05 Getting the error as bamstats05 Exited with failure (-1)

Your environment

Steps to reproduce

Command used

_java -jar dist/bamstats05.jar --bed ~/Documents/Variant_caller/freebayes/TruSeq_exome_targeted_regions.hg19.4col.bed ~/Documents/Variant_caller/freebayes/Santhifastq.bam --strandmost opposite -o output.txt

Actual behaviour

obtained error result

[SEVERE][BamStats05]overlapping region: chr11 64008603 64008710 FKBP2 and chr11:64008413-64008604 + . java.io.IOException: overlapping region: chr11 64008603 64008710 FKBP2 and chr11:64008413-64008604 + . at com.github.lindenb.jvarkit.tools.bamstats04.BamStats05.readBedFile(BamStats05.java:161) at com.github.lindenb.jvarkit.tools.bamstats04.BamStats05.doWork(BamStats05.java:329) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:1145) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:1303) at com.github.lindenb.jvarkit.tools.bamstats04.BamStats05.main(BamStats05.java:406) [INFO][Launcher]bamstats05 Exited with failure (-1)

lindenb commented 5 years ago

as the message said your bed file contains two overlapping regions which is forbidden to compute the coverage for one gene.

Vithyanatarajan commented 5 years ago

Hi @lindenb

as the message said your bed file contains two overlapping regions which is forbidden to compute the coverage for one gene. Thank you for your explanation. I removed the overlapping region and ran,analysis got completed successfully.

      And one query 
           May I know how to use more than one bam file. As I want to run for normal and tumor bam in a single command.
lindenb commented 5 years ago

May I know how to use more than one bam file. As I want to run for normal and tumor bam in a single command.

yes there will be one line per bam/segment

closing