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  • SOAPdenovo2 Ambiguous output redirect.

    Currently using SOAPdenovo2 and used submission form below:

    Code:
    #!/bin/bash
    #$ -cwd
    #$ -N SOAPdenovo2
    #$ -e /ibers/ernie/groups/rumenISPG/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/SOAPdenovo2.error
    #$ -o /ibers/ernie/groups/rumenISPG/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/SOApdenovo2.output
    #$ -M [email protected]
    #$ -q intel.q
    
    #step1
    /cm/shared/apps/soapdenovo2/r240 sparse_pregraph -s /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed_trimmed5P_files_.fastq/SOAPdenovo2_config_file -K 35 -R -o graph_prefix 1>pregraph.log 2>pregraph.err
    #step2
    /cm/shared/apps/soapdenovo2/r240 contig -g graph_prefix -R 1>contig.log 2>contig.err
    #step3
    /cm/shared/apps/soapdenovo2/r240 map -s config_file -g graph_prefix 1>map.log 2>map.err
    #step4
    /cm/shared/apps/soapdenovo2/r240 scaff -g graph_prefix -F 1>scaff.log 2>scaff.err
    However this failed instantly and produced a .error and .output file, the .error file contained "Ambiguous output redirect." and the .output file contained "Warning: no access to tty (Bad file descriptor).
    Thus no job control in this shell."

    Anyone know why?

  • #2
    I think you are using the redirects incorrectly in your command lines above: http://forums.fedoraforum.org/showthread.php?t=219335

    Comment

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