Bob Handsaker
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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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https://www.broadinstitute.org/directory
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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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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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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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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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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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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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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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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...