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  • BFAST- specifying tmpDir parameters

    Hi,

    I am trying to use the (-T) option in the bfast "match" command to specify the directory to which temporary files will be written instead of the default directory (current directory), but not yet able to do so!

    I am trying to use the following command:
    bfast match -f phi.x.174.fa -r reads.phi.x.174.fastq -T '/home/student/bfast/tmpDir' > bfast.matches.file.phi.x.174.bmf

    and I get this error:
    In function "BfastMatchValidateInputs": Fatal Error[IllegalPath]. Variable/Value: tmpDir.
    Message: Command line argument.
    ***** Exiting due to errors *****

    Could anyone please advise on how to specify the "path" in the (-T) option?

    Thanks in advance.

  • #2
    Get rid of the apostrophes.

    Comment


    • #3
      I tried removing the apostrophes, but still getting the same error!

      Could you please advise on another solution?

      Thanks.

      Comment


      • #4
        Fix the path to your tmpDir. It's wrong if you're getting that error.

        Just did this today with "-T tmp/" and it worked fine.
        Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
        Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
        Projects: U87MG whole genome sequence [Website] [Paper]

        Comment


        • #5
          Thanks Michael.

          I tried with double quotations as you did and added the "/" character at the end of my path and it worked.

          I have another problem now. I get the following error [at the end of the code below]:

          Checking input parameters supplied by the user ...
          Validating fastaFileName phi.x.174.fa.
          Validating readsFileName reads.phi.x.174.fastq.
          Validating tmpDir path home/student/bfast-0.6.4f/output/.
          **** Input arguments look good!
          ************************************************************
          ************************************************************
          Printing Program Parameters:
          programMode: [ExecuteProgram]
          fastaFileName: phi.x.174.fa
          mainIndexes [Auto-recognizing]
          secondaryIndexes [Not Using]
          readsFileName: reads.phi.x.174.fastq
          offsets: [Using All]
          loadAllIndexes: [Not Using]
          compression: [Not Using]
          space: [NT Space]
          startReadNum: 1
          endReadNum: 2147483647
          keySize: [Not Using]
          maxKeyMatches: 8
          maxNumMatches: 384
          whichStrand: [Both Strands]
          numThreads: 1
          queueLength: 250000
          tmpDir: home/student/bfast-0.6.4f/output/
          timing: [Not Using]
          ************************************************************
          Searching for main indexes...
          Found 5 index (5 total files).
          Not using secondary indexes.
          ************************************************************
          Reading in reference genome from phi.x.174.fa.nt.brg.
          In total read 1 contigs for a total of 5386 bases
          ************************************************************
          Reading reads.phi.x.174.fastq into a temp file.
          ************************************************************
          In function "OpenTmpGZFile": Fatal Error[IllegalFileName]. Variable/Value: home/student/bfast-0.6.4f/output/.bfast.tmp.5OL5Ka.
          Message: Could not create a tmp file name.
          ***** Exiting due to errors *****


          Any suggestions?

          Thanks.

          Comment


          • #6
            home/student/bfast-0.6.4f/output should be /home/student/bfast-0.6.4f/output (leading slash!)

            Comment


            • #7
              Hello,

              I have the same problem and I am unable to solve them. Checking through various threads, I have done all that I can

              1. Make install bfast from github

              2. Re-indexed reference file with depth '0'

              And the script used is the following;
              bsub -I /tools/bfast/bfast/bfast match -A 1 -t -n 8 -f /solid-v2/Homo_sapiens_assembly19.fasta -T $HOME/tmp/ -r /data/fastq/test.fastq > test.matches.bmf

              The Error is:

              Validating tmpDir path /PHShome/us024/tmp/*.
              ************************************************************
              In function "BfastMatchValidateInputs": Fatal Error[IllegalPath]. Variable/Value: tmpDir.
              Message: Command line argument.
              ***** Exiting due to errors *****

              Any suggestion to resolve this will be very helpful. The tmp dir is my home dir will the requisite permissions.

              Many thanks

              Uma

              Comment

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