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  • NaS (Nanopore Synthetic-long) help

    I compiled NaS but the return message in linux.
    Code:
    root@midox-VGN-NS11S-S:/home/midox/Bureau/NaS-master# $(pwd)/NaS_v2/NaS --fq1 NaS_example_acineto/AWK_DOSF_1_1_A5KR6.IND3_clean.10prc.fastq --fq2 NaS_example_acineto/AWK_DOSF_1_2_A5KR6.IND3_clean.10prc.fastq --nano NaS_example_acineto/MinION_reads_Acinetobacter_baylyi.fa --out NaS_example --nb_proc 5
    Number of parallel task : 5
    [lundi 8 juin 2015, 14:14:24 (UTC+0200)] Create output directory : NaS_example
    [lundi 8 juin 2015, 14:14:24 (UTC+0200)] Create fasta file from fastq...
    /home/midox/Bureau/NaS-master/NaS_v2/FastaToTbl: 60: /home/midox/Bureau/NaS-master/NaS_v2/FastaToTbl: gawk: not found
    /home/midox/Bureau/NaS-master/NaS_v2/TblToFasta: 60: /home/midox/Bureau/NaS-master/NaS_v2/TblToFasta: gawk: not found
    paste: NaS_example_acineto/AWK_DOSF_1_2_A5KR6.IND3_clean.10prc.fastq: No such file or directory
    [lundi 8 juin 2015, 14:14:24 (UTC+0200)] Alignement step in fast mode...
    [lundi 8 juin 2015, 14:14:24 (UTC+0200)] Select reads...
    [lundi 8 juin 2015, 14:14:24 (UTC+0200)] Retrieve similar reads...
    [lundi 8 juin 2015, 14:14:25 (UTC+0200)] Generate NaS reads...
    cat: NaS_example/assemblies/*/NaS_hqctg_reads_final.fa: No such file or directory
    /home/midox/Bureau/NaS-master/NaS_v2/TblToFasta: 60: /home/midox/Bureau/NaS-master/NaS_v2/TblToFasta: gawk: not found
    /home/midox/Bureau/NaS-master/NaS_v2/FastaToTbl: 60: /home/midox/Bureau/NaS-master/NaS_v2/FastaToTbl: gawk: not found
    [lundi 8 juin 2015, 14:14:25 (UTC+0200)] Generate statistics...
    fastalength: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
    fastacomposition: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
    /home/midox/Bureau/NaS-master/NaS_v2/assemblyMetrics: 108: /home/midox/Bureau/NaS-master/NaS_v2/assemblyMetrics: gawk: not found
    fastalength: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
    fastacomposition: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
    /home/midox/Bureau/NaS-master/NaS_v2/assemblyMetrics: 108: /home/midox/Bureau/NaS-master/NaS_v2/assemblyMetrics: gawk: not found
    NbReads=  -1  CumulativeSize=  number=  N50size=    minSize=  -1  maxSize=  -nan  avgSize=    =>  NaS_example/NANO_reads.stats
    NbReads=  -1  CumulativeSize=  number=  N50size=    minSize=  -1  maxSize=  -nan  avgSize=    =>  NaS_example/NaS_hqctg_reads.stats
    do you have an idea on what kind of errors?
    thankyou

  • #2
    If you look through the error messages you generally get a hint of what is missing/in error. In this case looks like you need the gawk package.

    Code:
    $ sudo apt-get install gawk
    You also may need to install glib.

    Comment


    • #3
      new PROBLEMS NaS

      i installed gawd and I recompiled
      there a new problems.

      Code:
      root@midox-VGN-NS11S-S:/home/midox/Bureau/NaS-master# $(pwd)/NaS_v2/NaS --fq1 /home/midox/Bureau/NaS_example_acineto/AWK_DOSF_1_1_A5KR6.IND3_clean.10prc.fastq --fq2 /home/midox/Bureau/NaS_example_acineto/AWK_DOSF_1_2_A5KR6.IND3_clean.10prc.fastq --nano /home/midox/Bureau/NaS_example_acineto/MinION_reads_Acinetobacter_baylyi.fa --out NaS_example --nb_proc 5
      Number of parallel task : 5
      [lundi 8 juin 2015, 14:56:09 (UTC+0200)] Create output directory : NaS_example
      [lundi 8 juin 2015, 14:56:09 (UTC+0200)] Create fasta file from fastq...
      [lundi 8 juin 2015, 14:58:16 (UTC+0200)] Alignement step in fast mode...
      [lundi 8 juin 2015, 14:58:23 (UTC+0200)] Select reads...
      [lundi 8 juin 2015, 14:58:23 (UTC+0200)] Retrieve similar reads...
      [lundi 8 juin 2015, 14:58:24 (UTC+0200)] Generate NaS reads...
      cat: NaS_example/assemblies/*/NaS_hqctg_reads_final.fa: No such file or directory
      [lundi 8 juin 2015, 14:58:25 (UTC+0200)] Generate statistics...
      fastalength: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
      fastacomposition: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
      awk: cmd. line:1: fatal: division by zero attempted
      awk: cmd. line:1: fatal: division by zero attempted
      gawk: cmd. line:1: fatal: division by zero attempted
      fastalength: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
      fastacomposition: error while loading shared libraries: libglib-1.2.so.0: cannot open shared object file: No such file or directory
      awk: cmd. line:1: fatal: division by zero attempted
      awk: cmd. line:1: fatal: division by zero attempted
      gawk: cmd. line:1: fatal: division by zero attempted
      NbReads=    CumulativeSize=    N50size=    minSize=    maxSize=    avgSize=    =>  NaS_example/NANO_reads.stats
      NbReads=    CumulativeSize=    N50size=    minSize=    maxSize=    avgSize=    =>  NaS_example/NaS_hqctg_reads.stats
      have any ideasa about this errors?
      Thankyou

      Comment


      • #4
        Please only post your issues in SeqAnswers OR BioStars - it's a waste of people's time to respond to things that have already been answered elsewhere.

        I was about to reply in BioStars, but I see GenoMax has already said it - you need to install glib.

        Comment


        • #5
          In addition there are other problems. It appears that this directory/file is not there.

          NaS_example/assemblies/*/NaS_hqctg_reads_final.fa

          Comment


          • #6
            Originally posted by A.N.Other View Post
            Please only post your issues in SeqAnswers OR BioStars - it's a waste of people's time to respond to things that have already been answered elsewhere.
            That's your opinion, A.N.

            I say post to as many sites as you like. If more than one person answers a question in 2 different forums--well that gives the answer additional weight, doesn't it?

            --
            Phillip

            Comment

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