Unspecified error killing verifyBamID process

[Matthew Skirvin]

Hello,

The team I am working with has been exploring options for identifying contamination in sequences of non-model organisms and I have had some success using verifyBamID on in silico contaminated sequences. I've moved on to testing some of our real data but when attempting to analyze using verifyBamID the process runs for a bit then exits with the message "killed". There is nothing written to the log and nothing output to the command line.

Is there a way I can determine what the issue is that I am having? In the past I've seen similar behavior when the process ran out of memory. I ran it on a machine with 240 Gigs of memory, however, and still encountered the issue. Any insight would be much appreciated.

Thanks,

Matthew

[Hyun Min Kang]

Hello Matthew,

I believe that your issue was solved with comminication with Mary Kate in libStatGen thread. Please let me know if there are additional problems persisting.

Hyun

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[huilei xu]

Hi Matthew, 

Browsing through the threads as I have similar 'unspecific error' issue, basically for some bam files, it keeps processing 'Extracting read information in xxxxxx markers from BAM file' and then suddenly stopped without creating output. Any idea? Thanks.

[kiran girdhar]

are your chromosomes in bam file and vcf files are same as in chr or without chr?

KG

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[huilei xu]

Found another thread and replied there, merge the two threads here: https://groups.google.com/d/msg/verifybamid/9CQYHlrqBpk/zHqjh6A7DQAJ

Best,

Huilei