#267 reenter PBcR pipeline


Dear WGS-developer,

I started the PBcR to selfcorrect PB-reads from 62 SMRTcells.
As its quite time-consuming, i run it with -pbCNS and started the overlap jobs myself by executing:

 qsub -A assembly -pe smp 31 -l mem=2GB -cwd -N "pBcR_ovl_asm" -t 1-9579 -j y -o /dev/null /data/users/mmoser/PBcR//temppbcns/1-overlapper/overlap.sh

It all finished and i now try reentering the pipeline by starting the inital command:

pacBioToCA -length 100 -s /data/users/mmoser/PBcR/peaxiPBcR.spec1 -t 20 -partitions 300 -pbCNS -l pbcns -fastq /data/users/mmoser/Petunia_correct/allReads/data/filtered_subreads.fastq maxCoverage=30

This terminated becasue of a wrongly set qsub paramter after removing all ovls-files:

Unable to run job: job rejected: the requested parallel environment "threads" does not exist.

When i corrected the qsub parameter it continous terminating because all the .ovls-files are already removed. So i am stuck.

rm 000001.ovls
rm: cannot remove `000001.ovls': No such file or directory
                  END Mon Feb 10 11:36:50 2014 (0 seconds)
Failed to execute rm 000001.ovls

Can i somehow prevent this from happening by skipping this command and reenter the PBcR pipeline afterwards (i couldnt find the script)?

Or would it be quicker to just gather all the correct_reads_part-files (assuming these are already error-corrected, which i dont know) in the temp/1-overlapper/-directory, merge them and use them for the assembly?

Any help would be appreciated!
Thank you,


  • Sergey Koren

    Sergey Koren - 2014-02-11


    The pipeline current can't resume in the middle of a step and overlap store construction (including computing overlaps and building the store) is considered one step the way it is written. What you need to do is construct the overlap store yourself and relaunch the pipeline and it should move onto the next step. As long as you have your 1-overlapper/001/*ovb files, you do not need to re-run anything. Running the commands:

    find -L /data/users/mmoser/PBcR//temppbcns/1-overlapper ( -name *ovb ) -print > /data/users/mmoser/PBcR//temppbcns/asm.ovlStore.list
    /data/users/mmoser/Celera/wgs-#8.1/Linux-amd64/bin/overlapStoreBuild -o /data/users/mmoser/PBcR//temppbcns/asm.ovlStore -g /data/users/mmoser/PBcR//temppbcns/asm.gkpStore -M 8192 -L /data/users/mmoser/PBcR//temppbcns/asm.ovlStore.list > /data/users/mmoser/PBcR//temppbcns/asm.ovlStore.err 2>&1
    should let you build the store. After this, you can re-launch pacBioToCA. In future versions, it should be OK resuming the pipeline in the middle of this step.


  • Michel Moser

    Michel Moser - 2014-02-11


    Thank you very much!
    Exactly what i needed to know.


  • Sergey Koren

    Sergey Koren - 2014-07-30
    • status: open --> closed

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