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problem with mapping

PBJelly Tickets
Edi Sudianto
2017-03-06
2017-03-06

  • Edi Sudianto

    Edi Sudianto - 2017-03-06

    Dear PBJelly users,

    I am encountering a problem with the mapping process of PBJelly.
    It seems that the blasr step failed after the .m4 file was created.
    Here I attached the error file output:

    2017-03-04 07:21:22,739 [INFO] Running /home/edi/PBSuite_15.8.24/bin/m4pie.py /home/edi/SpB/6mt_PBJelly/mapping/PB16011_B.fastq.m4 /home/edi/SpB/PB16011_B.fastq /home/edi/SpB/Bsp_LINKS_6mt_contigs.fasta --nproc 20 -i
    2017-03-04 07:22:26,848 [INFO] Extracting tails
    2017-03-04 07:22:29,773 [INFO] Parsed 133247 reads
    2017-03-04 07:22:29,774 [INFO] Found 121888 tails
    2017-03-04 07:22:29,774 [INFO] 40430 reads had double tails
    2017-03-04 07:22:29,774 [INFO] Mapping Tails
    2017-03-04 07:22:30,328 [ERROR] blasr mapping failed!
    2017-03-04 07:22:30,329 [ERROR] RETCODE 1
    2017-03-04 07:22:30,329 [ERROR] STDOUT Could not open FASTA file /home/edi/SpB/Bsp_LINKS_6mt_contigs.fasta

    2017-03-04 07:22:30,329 [ERROR] STDERR None
    2017-03-04 07:22:30,329 [ERROR] Exiting

    I am not too sure what went wrong, and how to fix it.
    FYI, the blasr version that I use is ver 1.3.1

    Thanks for the help,
    Edi

     

  • Cristina Osuna

    Cristina Osuna - 2017-03-08

    Hi Edi,

    How much memory are you using? What is the size of your input read files?

    To me, it seems as a memory issue while running m4pie.py. Please, try to give more memory and see what happens.

    Kind Regards,

    Cristina

     

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