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#73 Issue with latest development version on SLURM cluster

New
MOCAT
SLURM (1) development (1) assembly (4)
Medium
Defect
2017-11-11
2017-11-10
Joshua Gray
No

Hi,

I'm running the latest development MOCAT2 version from GitHub on a SLURM cluster and am encountering an error when running the line "-sf my.samples -s hg19 -screened_files" in my runMOCAT.sh file. The relevant portion of the .out file is

MOCAT MODULE MODE ACTIVATED
MODULE = s
ERROR & EXIT: Tried to launch module 's', but could not find expected file /nas/longleaf/home/joshg/mocat2-master/dev/public/mod/s/s.sh at /nas/longleaf/home/joshg/mocat2-master/dev/public/src/MOCAT.pl line 1072.

I've attached the SUMMARIES and logs directories along with the .out and my.samples file. Thanks for the help!

Josh

4 Attachments
SUMMARIES-10-nov-2017-jgray.tar.gz
logs-10-nov-2017-jgray.tar.gz
my.samples
slurm-13217092.out

Related

Tickets: #73

Discussion

  • Joshua Gray

    Joshua Gray - 2017-11-10

    Also, here are the tryMOCAT.sh file and the MOCAT.cfg file.

     
    MOCAT.cfg
    tryMOCAT.sh

    • MOCAT

      MOCAT - 2017-11-10

      Please read the MOCAT documentation. The -s option is deprecated for the
      github version. Use -screen.
      On Fri, Nov 10, 2017 at 10:55 Joshua Gray jgray@users.sf.net wrote:

      Also, here are the tryMOCAT.sh file and the MOCAT.cfg file.

      Attachments:

      ** [tickets:#73] Issue with latest development version on SLURM cluster**

      Status: New
      Labels: SLURM development assembly
      Created: Fri Nov 10, 2017 03:53 PM UTC by Joshua Gray
      Last Updated: Fri Nov 10, 2017 03:53 PM UTC
      Owner: MOCAT
      Attachments:

      Hi,

      I'm running the latest development MOCAT2 version from GitHub on a SLURM
      cluster and am encountering an error when running the line "-sf my.samples
      -s hg19 -screened_files" in my runMOCAT.sh file. The relevant portion of
      the .out file is

      MOCAT MODULE MODE ACTIVATED
      MODULE = s
      ERROR & EXIT: Tried to launch module 's', but could not find expected file
      /nas/longleaf/home/joshg/mocat2-master/dev/public/mod/s/s.sh at
      /nas/longleaf/home/joshg/mocat2-master/dev/public/src/MOCAT.pl line 1072.

      I've attached the SUMMARIES and logs directories along with the .out and
      my.samples file. Thanks for the help!

      Josh

      Sent from sourceforge.net because you indicated interest in <
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      Tickets: #73

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  • Joshua Gray

    Joshua Gray - 2017-11-11

    Unfortunately, this gave the same error.

    MOCAT MODULE MODE ACTIVATED
    MODULE = screen
    ERROR & EXIT: Tried to launch module 'screen', but could not find expected file /nas/longleaf/home/joshg/mocat2-master/dev/public/mod/screen/screen.sh at /nas/longleaf/home/joshg/mocat2-master/dev/public/src/MOCAT.pl line 1072.

    Using your suggestion, I edited the appropriate line of the runMOCAT.sh file to read:

    -sf my.samples -screen hg19 -screened_files

    Josh

     

    • MOCAT

      MOCAT - 2017-11-11

      Again, Please read the documentation. I can't remember he command by heart.
      It's -soap.
      On Fri, Nov 10, 2017 at 20:08 Joshua Gray jgray@users.sf.net wrote:

      Unfortunately, this gave the same error.

      MOCAT MODULE MODE ACTIVATED
      MODULE = screen
      ERROR & EXIT: Tried to launch module 'screen', but could not find expected
      file /nas/longleaf/home/joshg/mocat2-master/dev/public/mod/screen/screen.sh
      at /nas/longleaf/home/joshg/mocat2-master/dev/public/src/MOCAT.pl line 1072.

      Using your suggestion, I edited the appropriate line of the runMOCAT.sh
      file to read:

      -sf my.samples -screen hg19 -screened_files

      Josh

      ** [tickets:#73] Issue with latest development version on SLURM cluster**

      Status: New
      Labels: SLURM development assembly
      Created: Fri Nov 10, 2017 03:53 PM UTC by Joshua Gray
      Last Updated: Sat Nov 11, 2017 12:14 AM UTC
      Owner: MOCAT
      Attachments:

      Hi,

      I'm running the latest development MOCAT2 version from GitHub on a SLURM
      cluster and am encountering an error when running the line "-sf my.samples
      -s hg19 -screened_files" in my runMOCAT.sh file. The relevant portion of
      the .out file is

      MOCAT MODULE MODE ACTIVATED
      MODULE = s
      ERROR & EXIT: Tried to launch module 's', but could not find expected file
      /nas/longleaf/home/joshg/mocat2-master/dev/public/mod/s/s.sh at
      /nas/longleaf/home/joshg/mocat2-master/dev/public/src/MOCAT.pl line 1072.

      I've attached the SUMMARIES and logs directories along with the .out and
      my.samples file. Thanks for the help!

      Josh

      Sent from sourceforge.net because you indicated interest in <
      https://sourceforge.net/p/mocat/tickets/73/>

      To unsubscribe from further messages, please visit <
      https://sourceforge.net/auth/subscriptions/>

      --
      Sent from my iPhone - apologies for any iCorrect mistakes.

       

      Related

      Tickets: #73

      alternate

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