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  • CEGMA error

    Hi,

    I've been trying to run CEGMA on my 280MB genome. It does run fine on all other genomes I've got, but it refuses to run on my genome. It keeps giving the following error:
    Code:
    RUNNING: local_map -n local -f -h /opt/cus/CEGMA/2.3--GCC-4.1.2/data/hmm_profile
    s -i KOG -v  genome.chunks.fa 2>sample.cegma.errors
    FATAL ERROR! 6400: "No such file or directory"
    
    In sample.cegma.errors
    Warning Error
            In GeneLoop6 matrix special read off - out of bounds on matrix [i,j
    is 193,-1 state 0 in standard matrix]
    Warning Error
            Problem - hit bad read off system, exiting now
    Can't use an undefined value as an ARRAY reference at /opt/cus/CEGMA/2.3--GCC-4.
    1.2/bin/parsewise line 217.
    Can't run parsewise
    It is weird that this problem occurs with only my genome. I've tried removing all the non-canonical characters and changing all masked sequences to upper case. However, it does not work.

    I wonder if anyone has encountered anything like this? If yes, how did you solve it, if at all?

    Thanks

  • #2
    CEGMA Errors. GitHub Gist: instantly share code, notes, and snippets.

    Comment


    • #3
      Actually, CEGMA's most recent version did just fine. My problem was resolved thanks to the deft bug-fixing by the CEGMA group.

      Comment


      • #4
        Problem when using CEGMA

        Originally posted by flobpf View Post
        Actually, CEGMA's most recent version did just fine. My problem was resolved thanks to the deft bug-fixing by the CEGMA group.
        Hi flobpf,
        I encountered the same problem as you when using CEGMA. The error is as follows:

        Warning Error
        Major problem (!) - in GeneLoop6 matrix to special read off, position
        0,0 state 0 no source found!
        Warning Error
        In GeneLoop6 read off ending at 0 ... got a bad matrix to special
        read off... returning partial alignment
        Can't use an undefined value as an ARRAY reference at /state/partition1/home/xuchao/software/cegma_v2.3.190711/bin/parsewise line 217.
        Can't run parsewise

        You seem to have solved this problem! Could you tell me how?

        Comment


        • #5
          Originally posted by flobpf View Post
          Actually, CEGMA's most recent version did just fine. My problem was resolved thanks to the deft bug-fixing by the CEGMA group.
          Bold is solution.

          Comment


          • #6
            Hi all,

            This is an old thread, but I'm getting a similar error with CEGMA v2.5. It's not happening all the time - I ran the test data just fine, the test proteins against my data ok, and my data against the Anopholes data ok. But my data against the Core proteins (instead of the 248 Anopholes ones) crashes.

            Is anyone else having this problem?

            Here are the last few lines:
            ********************************************************************************
            ** ACCURATE LOCAL MAPPING **
            ********************************************************************************

            RUNNING: local_map -n local_self -g local.genewise.gff -d geneid_params/self.param -h /media/data/programs/CEGMA_v2.5/data/hmm_profiles -i KOG genome.chunks.fa 2>../annot_core/annot_core.cegma.errors
            NOTE: Will use specifed local.genewise.gff file instead of running genewise
            FATAL ERROR when running local map 6400: "No such file or directory"

            Ending CEGMA

            #############
            Thanks,
            Alice
            Last edited by aliceb; 09-08-2014, 01:33 AM. Reason: update error message

            Comment


            • #7
              Does the output before this stage imply that you have no core genes? I.e. sometimes when you run CEGMA, the initial BLAST step might only find a small number of core genes. Each successive filtering step of CEGMA typically throws out more candidate core genes and you can end up with none at all. Some of the code might not handle this gracefully.

              Comment


              • #8
                Yes, I did think of that. But I have now been able to get 99% hits on a dataset that crashes against the Anopholes core genes. It seems like there should be some hits there (I am working with a wasp)....

                I have continued to play my two (fasta, nucleotide) datasets and have managed to successfully run one against the core genes and the other against the Anopholes core genes. This is good enough for now, but a bit frustrating as I wanted to compare them....

                If anyone comes across this and has a solution, it would still be useful for me in the future (and perhaps other people hitting this snag)

                Comment


                • #9
                  crashing on 2.5

                  I have Cegma 2.5 freshly installed and I am getting similar errors:


                  Would love to be able to run the software....


                  ********************************************************************************
                  ** MAKING INITIAL GENE PREDICTIONS FOR CORE GENES (GENEWISE + GENEID) **
                  ********************************************************************************

                  RUNNING: local_map -n local -f -h /build/CEGMA_v2.5/data/hmm_profiles -i KOG genome.chunks.fa 2>/out/S376-cegma.cegma.errors
                  FATAL ERROR when running local map 6400: "No such file or directory"

                  Ending CEGMA




                  In my .cegma.errors file it says this:

                  Warning Error
                  Unable to open gene.stat as gene stats file
                  Warning Error
                  Could not read gene statistics in gene.stat
                  Warning Error
                  Could not open BLOSUM62.bla as a filename for read Blast matrix
                  Warning Error
                  Could not open file codon.table as codon table file
                  Warning Error
                  Could not read codon table file in codon.table
                  Fatal Error
                  Could not build objects!
                  Can't run genewise -splice_gtag -quiet -gff -pretty -alb -hmmer /build/CEGMA_v2.5/data/hmm_profiles/KOG0002.hmm /tmp/genomic18349.fa > /tmp/genewise18349

                  Comment


                  • #10
                    memo to self -- RTFFAQ


                    The FAQ talks about this being due to a

                    genewise ocnfig being installed incorrectly.

                    I installed wise on an ubuntu container with apt-get

                    this should fix the problem in my running container:

                    export WISECONFIGDIR=/usr/share/wise

                    and this should fix it in my Dockerfile:

                    ENV WISECONFIGDIR /usr/share/wise




                    Maybe this is the root of some of the other problems.

                    Comment


                    • #11
                      As time marches along, there will only ever be more problems like this because CEGMA has been locked in development using some older versions of tools. As people install newer versions of things like HMMER and genewise (well, maybe that's not a tool that will be updated much either), things are likely to break.

                      If we ever get new funding, we have many plans for a completely new version of CEGMA, but without money we can't spend any more time on it unfortunately.

                      Regards,

                      Keith

                      Comment


                      • #12
                        So the environment variable didn't help with the problem . ( although the command would run if I put it on the command line ).


                        Luckily the docker container approach comes configured. Don't waste time trying to get this installed on your system... just use the docker container -- then it is just a 1 liner

                        Comment


                        • #13
                          The VM works well too, haven't tried the docker container yet.

                          One word on whole genomes - every contig or scaffold set has been fine so far, but running it on whole genomes with long chromosomes has failed repeatedly.

                          Should long chromosomes be split into arbitrary scaffolds ?

                          Comment

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