Issues running pbsmrtpipe and confirmation dialogue
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5.4 years ago

I am trying to perform de novo assembly using HGAP on PacBio SMRT sequencing using the smrttools package.

I am currently running this command:

pbsmrtpipe pipeline-id pbsmrtpipe.pipelines.polished_falcon_fat -e eid_subread:prefix.subreadset.xml --preset-xml preset.xml

However we have discovered one of the internal jobs locks up requiring user input and we have no method of attaching to the internal process; the following line is where the program locked up:

[INFO] 2018-06-22 17:33:19,770Z [falcon_polish.sys lg 22] RUN: 'bash /scratch/mtblab/DYLAN/180621_Pacbio/tasks/falcon_ns.tasks.task_falcon0_build_rdb-0/'
You are about to overwrite the current partition settings.  This
will invalidate any tracks, overlaps, and other derivative files.
Are you sure you want to proceed? [Y/N]

Has anyone run into a similar problem? This is on our cluster which does not have GUI support so we can't use the SMRT View front end.

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