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  • CONTRA error messages (need urgent help!)

    Hi,

    I am using the tool CONTRA, and getting some error messages as below:
    ---------
    Process Process-1:
    Process Process-2:
    Traceback (most recent call last):
    Traceback (most recent call last):
    File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
    File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
    self.run()
    self.run()
    File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
    File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
    self._target(*self._args, **self._kwargs)
    self._target(*self._args, **self._kwargs)
    File "/mnt/gfsusr/files/data/bin/CONTRA.v2.0.6/contra.py", line 371, in convertBam
    File "/mnt/gfsusr/files/data/bin/CONTRA.v2.0.6/contra.py", line 371, in convertBam
    output = subprocess.Popen(args, stdout = iOutFile).wait()
    File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
    errread, errwrite)
    File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
    output = subprocess.Popen(args, stdout = iOutFile).wait()
    raise child_exception
    File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
    OSError: [Errno 2] No such file or directory
    errread, errwrite)
    File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
    raise child_exception
    OSError: [Errno 2] No such file or directory
    Traceback (most recent call last):
    File "/mnt/gfsusr/files/data/bin/CONTRA.v2.0.6/contra.py", line 613, in <module>
    main()
    File "/mnt/gfsusr/files/data/bin/CONTRA.v2.0.6/contra.py", line 583, in main
    t1 = int(file.readlines(open(folder+"temp.txt"))[0].strip("\n"))
    IOError: [Errno 2] No such file or directory: '/mnt/gfsusr/files/data/test/seqdata/All_Cases/project_TD_QC_test1/test1_20150728/project_TD_QC_test1_TD/calls/contra/buf/testData/temp.txt'

    ---------------------------------

    Does this seem a python process/subprocess issue? I have also downloaded python version 2.7, but I have got the same error messages.


    Thanks,

    -J

  • #2
    Can anyone help on this?

    Comment


    • #3
      Are you using this with a job scheduler/on a cluster? Is this (/mnt/gfsusr/files/data/test/seqdata/All_Cases/project_TD_QC_test1/test1_20150728/project_TD_QC_test1_TD/calls/contra/buf/testData/temp.txt) path available on execution node, if it is the latter.

      Comment


      • #4
        Did you reinstall before trying with python2.7?

        Comment


        • #5
          Originally posted by GenoMax View Post
          Are you using this with a job scheduler/on a cluster? Is this (/mnt/gfsusr/files/data/test/seqdata/All_Cases/project_TD_QC_test1/test1_20150728/project_TD_QC_test1_TD/calls/contra/buf/testData/temp.txt) path available on execution node, if it is the latter.
          Hi,thanks for the reply.
          I was running this on a cluster (using condor). So, this is the path/file that CONTRA would generate during the run. It seems to me that, because of some issues with either the contra script or with python, that this file was not successfully generated. That's why I got such message, and I am trying to figure out why exactly this file was not generated..

          Comment


          • #6
            Originally posted by Zaag View Post
            Did you reinstall before trying with python2.7?
            Hi, thanks for the input.

            I am currently using python 2.6.6.
            Someone was suggesting these error messages were due to python version issue, and after they switched to python 2.7, the issues were fixed. However, I have tried python 2.7, and I just got the same error messages.......

            Thanks,

            Comment


            • #7
              Originally posted by DNAmethylome View Post
              Hi, thanks for the input.

              I am currently using python 2.6.6.
              Someone was suggesting these error messages were due to python version issue, and after they switched to python 2.7, the issues were fixed. However, I have tried python 2.7, and I just got the same error messages.......

              Thanks,
              Sorry if you already understood but you need to install contra again with python2.7 for it to work.

              Comment


              • #8
                Originally posted by Zaag View Post
                Sorry if you already understood but you need to install contra again with python2.7 for it to work.
                Hi Zaag, thanks for the input. As you suggested, I just re-installed python2.7.10, and ran contra with python 2.7.10, and I still got similar error messages.

                Command line:
                --------------------------------------
                /home/files/test/bin/Python-2.7.10/python /home/files/test/bin/CONTRA.v2.0.6/contra.py --target /home/files/test/test/scripts/Panels/project/ref_files/panel_target_latest1.bed --test /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_TD/calls/ok.bam --control /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_ND/calls/ok.bam --fasta /usr/local/mrgstorage/refseq/build.hg19.GRCh37.p13/hg19_GRCh37_p13_full.fasta --outFolder /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_ND/calls/contra1
                ----------------------------------------

                Log/Error
                ----------------------------------------
                target : /home/files/test/test/scripts/Panels/project/ref_files/panel_target_latest1.bed
                test : /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_TD/calls/ok.bam
                control : /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_ND/calls/ok.bam
                fasta : /usr/local/mrgstorage/refseq/build.hg19.GRCh37.p13/hg19_GRCh37_p13_full.fasta
                outfolder : /home/files/test/test/Cases/project_TD_QC_test1/test1_20150817/project_TD_QC_test1_ND/calls/contra1
                numBin : [20]
                minreaddepth : 10
                minNBases : 10
                sam : False
                pval : 0.05
                sampleName : No-SampleName
                nomultimapped : False
                plot : False
                bedInput : False
                minExon : 2000
                largeDeletion : False
                removeDups : False
                Creating Output Folder : Done.
                Traceback (most recent call last):
                File "/home/files/test/bin/CONTRA.v2.0.6/contra.py", line 613, in <module>
                main()
                File "/home/files/test/bin/CONTRA.v2.0.6/contra.py", line 558, in main
                get_genome(params.TEST, genomeFile)
                File "/home/files/test/bin/CONTRA.v2.0.6/scripts/get_chr_length.py", line 31, in get_genome
                raw_header = subprocess.Popen(args, stdout = subprocess.PIPE).communicate()[0]
                File "/home/files/test/bin/Python-2.7.10/Lib/subprocess.py", line 710, in __init__
                errread, errwrite)
                File "/home/files/test/bin/Python-2.7.10/Lib/subprocess.py", line 1335, in _execute_child
                raise child_exception
                OSError: [Errno 2] No such file or directory
                ----------------------------------------


                Do you think I was missing something here?...

                Thanks!

                -J

                Comment

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