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  • iAssembler running error

    I am trying to run iAssembler on a small fasta file.

    perl iAssembler.pl -i mutated_Iva_short_1.fasta

    iAssembler starts at: Thu Jun 20 14:17:42 2013

    I get the following error which seems to be related to mira:

    running MIRA assembly cycle 1
    Error at mira -project=mira1 -fasta=mira1.fa -job=denovo,est,accurate,454 -notraceinfo -noclipping -GE:not=1 454_SETTINGS -LR:wqf=no:ft=fasta -AS:epoq=no:mrl=30 COMMON_SETTINGS -AS:nop=4 -SK:not=1r=97 -CLec=no 454_SETTINGS -CL:cpat=novlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no -AL:mo=39:mrs=97 > report 2> error
    Error at command: mira_pipeline 1#mutated_Iva_short_1.fasta 2#/groups/itay_mayrose/naamakop/iAssembler-v1.3.2.x64/mutated_Iva_short_1.fasta_Assembly/mira.uniseq#/groups/itay_mayrose/naamakop/iAssembler-v1.3.2.x64/mutated_Iva_short_1.fasta_Assembly/mira.cmf 1 4#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1r=97_-CLec=no_454ZZZSETTINGS_-CL:cpat=novlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1r=97_-CLec=no_454ZZZSETTINGS_-CL:cpat=novlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1r=97_-CLec=no_454ZZZSETTINGS_-CL:cpat=novlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1r=97_-CLec=no_454ZZZSETTINGS_-CL:cpat=novlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97

    Anyone encountered this problem? Thank you !

  • #2
    Can you add "code" tags around the error message (when editing the message use "Go Advanced" button. In the window that opens up next, highlight the error message by using mouse and then click on "#" button in the top edit tools row). It is hard to make sense of it now (seeing a bunch of emoticons in the error message you have posted).

    Comment


    • #3
      sorry, error message once again

      OK, now I got it right, thank you -

      Code:
      iAssembler starts at: Thu Jun 20 14:17:42 2013
      
      running MIRA assembly cycle 1
      Error at mira -project=mira1 -fasta=mira1.fa -job=denovo,est,accurate,454 -notraceinfo -noclipping -GE:not=1 454_SETTINGS -LR:wqf=no:ft=fasta -AS:epoq=no:mrl=30 COMMON_SETTINGS -AS:nop=4 -SK:not=1:pr=97 -CL:pec=no 454_SETTINGS -CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no -AL:mo=39:mrs=97 > report 2> error
      Error at command: mira_pipeline 1#mutated_Iva_short_1.fasta 2#/groups/itay_mayrose/naamakop/iAssembler-v1.3.2.x64/mutated_Iva_short_1.fasta_Assembly/mira.uniseq#/groups/itay_mayrose/naamakop/iAssembler-v1.3.2.x64/mutated_Iva_short_1.fasta_Assembly/mira.cmf 1 4#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1:pr=97_-CL:pec=no_454ZZZSETTINGS_-CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1:pr=97_-CL:pec=no_454ZZZSETTINGS_-CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1:pr=97_-CL:pec=no_454ZZZSETTINGS_-CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1:pr=97_-CL:pec=no_454ZZZSETTINGS_-CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97
      Thank you!
      Last edited by nako; 06-20-2013, 04:16 AM. Reason: I had a problem with the quotes again -

      Comment


      • #4
        Someone? Anyone?

        Any experience with iAssembler?
        Thank you

        Comment


        • #5
          Originally posted by nako View Post
          Any experience with iAssembler?
          Thank you
          From the code you post. The mira does not work on you server. First, check the mira program. Make sure it could be run.

          Comment


          • #6
            I'm having the same problem,
            mira is installed on my server, but as i read the manual of iAssembler v1.3.2, it says mira is also provided, could it be that this what might cause the error?
            thnx.

            Comment


            • #7
              the same error or look like.

              I guess that it is the same error or look like. When I built the Biopearl, some test was fallen. Then, somebody has a pre-conceived notion how a "script-buddy" (ubunu-mint user like me) could to get it.

              Thanks in advance.

              Code:
              sudo  perl iAssembler.pl -i all_Sf_sequences.fas                                                                                
              
              iAssembler starts at: Tue Feb 11 14:12:38 2014
              Replacement list is longer than search list at /usr/local/share/perl/5.18.2/Bio/Range.pm line 238.
              
              running MIRA assembly cycle 1
              Error at mira -project=mira1 -fasta=mira1.fa -job=denovo,est,accurate,454 -notraceinfo -noclipping -GE:not=1 454_SETTINGS -LR:wqf=no:ft=fasta -AS:epoq=no:mrl=30 COMMON_SETTINGS -AS:nop=4 -SK:not=1:pr=97 -CL:pec=no 454_SETTINGS -CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no -AL:mo=39:mrs=97 > report 2> error
              Error at command: mira_pipeline 1#all_Sf_sequences.fas 2#/home/soba/Documentos/Ensambladores/iAssembler-v1.3.2.x64/all_Sf_sequences.fas_Assembly/mira.uniseq#/home/soba/Documentos/Ensambladores/iAssembler-v1.3.2.x64/all_Sf_sequences.fas_Assembly/mira.cmf 1 4#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1:pr=97_-CL:pec=no_454ZZZSETTINGS_-CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1:pr=97_-CL:pec=no_454ZZZSETTINGS_-CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1:pr=97_-CL:pec=no_454ZZZSETTINGS_-CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97#-job=denovo,est,accurate,454_-notraceinfo_-noclipping_-GE:not=1_454ZZZSETTINGS_-LR:wqf=no:ft=fasta_-AS:epoq=no:mrl=30_COMMONZZZSETTINGS_-AS:nop=4_-SK:not=1:pr=97_-CL:pec=no_454ZZZSETTINGS_-CL:cpat=no:pvlc=no:qc=no:bsqc=no:mbc=no:emlc=no:emrc=no:msvs=no_-AL:mo=39:mrs=97

              Comment


              • #8
                I ran into similar problems and was able to diagnose them by turning on the log file output with parameter -d. It turned out to be that my fasta file had names that were too long as well as having a problem with megahubs in MIRA.

                Comment


                • #9
                  Hi Nako,
                  Have you solved the problem?
                  I met the same error in my HPC server, but it works in my Ubuntu machine.
                  It's so weird.
                  Any help will be appreciatded.

                  Best,
                  Bryan

                  Comment

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