Bob Handsaker
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Activity overview
Latest activity by Bob Handsaker-
Bob Handsaker commented,
You should consult the documentation here: https://software.broadinstitute.org/software/genomestrip/index.html and especially here https://software.broadinstitute.org/software/genomestrip/node_Refe...
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Bob Handsaker commented,
https://www.broadinstitute.org/directory
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Bob Handsaker commented,
Hi, Jason, You seem to be mostly on the right path. To help, I created a public workspace with 1000 Genomes data and some sample workflows that you can use as templates: https://app.terra.bio/#work...
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Bob Handsaker commented,
Send me your terra (google) ID or email address. The workflows are all public in Terra, but it can be helpful to have an example usage to work from. I don't have an example currently that is locked...
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Bob Handsaker commented,
Glad you were able to get it to work. I was also able to recreate this behavior, so I will look to see if there is a problem with the dependencies and try to fix it. A similar option to what you ar...
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Bob Handsaker commented,
I see. Yes, you can try just running it again. Let me know if it runs the second time through. It is possible there is a dependency that is not correct (so it is running some things out of order).
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Bob Handsaker commented,
My best guess would be that either it was a transient error or somehow Queue could not access the job completion status (which is a failure mode I have seen on some clusters) or for some reason thi...
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Bob Handsaker commented,
You need to look at the referenced log files to see what failed in the individual jobs. E.g. /kimlab_wd/yuo1996/C4_analysis/2.Genomestrip_preprocessing_reference/metadata/batch1_ref2021_headn2/log/...
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Bob Handsaker commented,
You need to look for the log files for the failed jobs and provide information about what went wrong for me to be able to help you.
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Bob Handsaker commented,
The CNV pipeline has nested log files, so it can be a little hard for me to tell which log file I am looking at. Can you zip/tar the log file above and also /home/output_CNVDiscoveryPipeline/cnv_st...