#254 asm.layout: partition error

overlapper
closed-out-of-date
nobody
5
2014-04-04
2013-08-26
No

Best,

I am trying to correct PacBio data with a large HiSeq dataset using pacBioToCA.
Unfortunately pacBioToCA crashes during the overlapper stage. Here are the details:

runCorrection.sh
exited with exit code 1

Failed to execute qsub
runCorrection.sh
Process ended

More useful info in the asm.layout file:

Picking cutoff as 7 mean would be 16.160603
Loaded 2399994 overlaps
ERROR: Could not find appropriate partition for 279415251 though it was either 2 or 3 (279293536-279335216) and (279418576-279460256) but it was neither

In the temp directory I can see all .olaps files are finished. The .rank files are all empty. Im running the latest stable release of Celera Assembler on our computer cluster using SGE. I patched CA to fix runCorrection.sh as described here:
https://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Error_in_runCorrection.sh_Step
Restarting the correction does not help.

I could not find any information about this error, so I hope you can help me figure this one out!

Thanks in advance,

Jeroen

1 Attachments

Related

Bugs: #254

Discussion

  • JeroenF@lumc

    JeroenF@lumc - 2013-08-26

    Best,
    I am trying to correct PacBio data with a large HiSeq dataset using pacBioToCA.
    Unfortunately pacBioToCA crashes during the overlapper stage. Here are the details:

    runCorrection.sh
    exited with exit code 1
    Failed to execute qsub

    runCorrection.sh
    Process ended

    More useful info in the asm.layout file:

    Picking cutoff as 7 mean would be 16.160603
    Loaded 2399994 overlaps
    ERROR: Could not find appropriate partition for 279415251 though it was either 2 or 3 (279293536-279335216) and (279418576-279460256) but it was neither

    In the temp directory I can see all .olaps files are finished. The .rank files are all empty. Im running the latest stable release of Celera Assembler on our computer cluster using SGE. I patched CA to fix runCorrection.sh as described here: https://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Error_in_runCorrection.sh_Step
    Restarting the correction does not help.

    I could not find any information about this error, so I hope you can help me figure this one out!

    Thanks in advance,
    Jeroen

     
  • Sergey Koren

    Sergey Koren - 2013-08-28

    Hi,

    This is a bug in CA 7.0. You can either try the latest version from source which fixes this error following the instructions here: The new code is not compatible with the old code so you will need to restart from scratch.
    http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Check_out_and_Compile
    Alternatively, you could lower the number of partitions to be the same as the number of threads. That is, if you are using 16 threads, set -partitions to be 16 as well. You can edit the runCorrection.sh script to modify the partitions parameter and run just runCorrection.sh to see if it is successful.

    Sergey

    On Aug 26, 2013, at 4:23 AM, JeroenF@lumc jfrank-lumc@users.sf.net wrote:

    Best,
    I am trying to correct PacBio data with a large HiSeq dataset using pacBioToCA.
    Unfortunately pacBioToCA crashes during the overlapper stage. Here are the details:

    runCorrection.sh
    exited with exit code 1
    Failed to execute qsub

    runCorrection.sh
    Process ended

    More useful info in the asm.layout file:

    Picking cutoff as 7 mean would be 16.160603
    Loaded 2399994 overlaps
    ERROR: Could not find appropriate partition for 279415251 though it was either 2 or 3 (279293536-279335216) and (279418576-279460256) but it was neither

    In the temp directory I can see all .olaps files are finished. The .rank files are all empty. Im running the latest stable release of Celera Assembler on our computer cluster using SGE. I patched CA to fix runCorrection.sh as described here: https://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Error_in_runCorrection.sh_Step
    Restarting the correction does not help.

    I could not find any information about this error, so I hope you can help me figure this one out!

    Thanks in advance,
    Jeroen

    [bugs:#254] asm.layout: partition error

    Status: open
    Labels: pacBioToCA partition layout
    Created: Mon Aug 26, 2013 08:20 AM UTC by JeroenF@lumc
    Last Updated: Mon Aug 26, 2013 08:21 AM UTC
    Owner: nobody

    Best,

    I am trying to correct PacBio data with a large HiSeq dataset using pacBioToCA.
    Unfortunately pacBioToCA crashes during the overlapper stage. Here are the details:

    runCorrection.sh
    exited with exit code 1

    Failed to execute qsub
    runCorrection.sh
    Process ended

    More useful info in the asm.layout file:

    Picking cutoff as 7 mean would be 16.160603
    Loaded 2399994 overlaps
    ERROR: Could not find appropriate partition for 279415251 though it was either 2 or 3 (279293536-279335216) and (279418576-279460256) but it was neither

    In the temp directory I can see all .olaps files are finished. The .rank files are all empty. Im running the latest stable release of Celera Assembler on our computer cluster using SGE. I patched CA to fix runCorrection.sh as described here:
    https://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Error_in_runCorrection.sh_Step
    Restarting the correction does not help.

    I could not find any information about this error, so I hope you can help me figure this one out!

    Thanks in advance,

    Jeroen

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    Related

    Bugs: #254

  • Sergey Koren

    Sergey Koren - 2014-04-04
    • status: open --> closed-out-of-date
     

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