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  • GeneMark-ES error: parse_ET.pl line 213 Invalid regression data

    I am trying to run GeneMark-ES on a fungal genome. I get this error only when I include the intron coordinates option --ET.

    When the program starts section ET_B training step, and while creating the symbolic link in the ET_C_1 to ET_B, it crashes in the parsing script with the following error:

    Must input more than one data point! at /home/myname/Applications/GeneMarkES/parse_ET.pl line 213.
    Invalid regression data
    error on call: /home/myname/Applications/GeneMarkES/parse_ET.pl --section ET_C --cfg /home/myname/projectX/Maker/GeneMark/run.cfg --v
    I am using GeneMark-ES Suite version 4.21
    I used tophat2 2.0.13 to perform my alignment


    As recommended, I created the introns file for GeneMark from the tophat alignment using the script /home/myname/Applications/GeneMarkES/bet_to_gff.pl --bet junctions.bed --gff tophat_introns.gff --label Tophat2

    I am running GeneMark using the command

    gmes_petap.pl --ES --fungus --ET tophat_introns.gff --et_score 10 --min_contig 150000 --cores 12 --sequence mydraftgenome.fasta


    Has anyone came across something similar? Meanwhile I am repeating the tophat alignment and will try again.

  • #2
    I traced a little into the failing script and apparently the hash with introns gets reduced to just one entry in a noise reduction step, after which the script fails. I am not sure in this case if it is a problem with the tophat output though.

    Comment


    • #3
      same problem

      hello sir
      when i trying to run GeneMark-ES on a fungal genome, i got a same problem with yours, so i wonder if you get the solution for this? and if you could give me some advises here, thank u for your time !

      Comment

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