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assembly problem with 6800 seq

sghignone
2007-03-09
2013-04-18
  • sghignone
    sghignone
    2007-03-09

    Hi all.
    I'm not so new with Staden Package (integrated with
    phred/phrap/repeatmasker), but recently I'm facing assembly problems
    never found before. At the moment, I'm using Staden v.1.
    7 on a FedoraCore3 machine (2GB RAM, 2x 80GB HD). When trying to assemble about 6800 seqs
    (mixed .ab1 and .SCF), stored on a new 80GB HD (97% free space), I'm getting
    the following error messages:

    Mon 15 Jan 16:15:44 2007 sequence_vector_clip::run: couldn't open "/mnt/data2/assembly/pregap.tmp": no space left on device
    Mon 15 Jan 16:15:44 2007 cross_match_svec::run: couldn't open "/mnt/data2/assembly/pregap.fasta": no space left on device
    Mon 15 Jan 16:15:44 2007 cloning_vector_clip::run: couldn't open "/mnt/data2/assembly/pregap.tmp": no space left on device
    Mon 15 Jan 16:15:44 2007 repeat_masker::run: couldn't open "/mnt/data2/assembly/pregap.fasta": no space left on device
    Mon 15 Jan 16:15:44 2007 phrap_assemble::run: couldn't open "/mnt/data2/assembly/pregap.tmp": no space left on device
    Mon 15 Jan 16:15:46 2007 Error creating busy file

    Mon 15 Jan 16:15:46 2007 No space left on device [28]
    Mon 15 Jan 16:15:46 2007 cannot create file [5]
    Mon 15 Jan 16:15:46 2007 cannot create database
    Mon 15 Jan 16:15:46 2007 gap-create.c:112
    Mon 15 Jan 16:15:46 2007 Success [0]
    Mon 15 Jan 16:15:46 2007 no error [1000]
    Mon 15 Jan 16:15:46 2007 cannot create database
    Mon 15 Jan 16:15:46 2007 IO.c:1348
    Mon 15 Jan 16:15:46 2007 Continue at own risk!
    Mon 15 Jan 16:15:46 2007 open_db:
    Mon 15 Jan 16:15:46 2007 shutdown::shutdown: couldn't open "/mnt/data2/assembly/pregap.log": no space left on device

    [...]
    - Report from 'Phrap assembly' -
    ERR: Failed to execute phrap.
    ERR: "
    gcphrap -minmatch 12 -minscore 30 -exp /mnt/data2/Candidatus_genome/pregap.assembly /mnt/data2/Candidatus_genome/pregap.tmp
    gcphrap version 0.990329
    Reading parameters ... 0.504 Mbytes allocated -- total 0.504 Mbytes
    Run date:time  070309:141334
    Done
    Total space allocated: 0.504 Mbytes; currently free: 0.499 Mbytes in 2 blocks

    ERROR: FILE /mnt/data2/Candidatus_genome/pregap.tmp.log NOT AVAILABLE FOR WRITING "
    ERR: Aborting assembly.

    - Report from 'Enter assembly (into Gap4)' -
    ERR: Failed to open database cand02.0.
    ERR: ""
    ERR: Aborting.

    This happens only with sequence number higher than 4000, more or less.
    I repeat, the sequences are on a new HD, 97% free....
    How can I solve the problem?

    Thanks in advance

    stefano