I am trying to perform de novo assembly using HGAP on PacBio SMRT sequencing using the
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/prepare_rdb.sh' PBFALCON_ERRFILE=/scratch/mtblab/DYLAN/180621_Pacbio/tasks/falcon_ns.tasks.task_falcon0_build_rdb-0/pbfalcon.run_cmd.err 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.