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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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Can't call method "setLeftLinkedHit" #179

Closed Ghanizadeh1980 closed 1 year ago

Ghanizadeh1980 commented 1 year ago

Hi,

Can somebody help me with the error message below, please? I was running RepeatMasker, and everything was running smoothly for about 2 hours, then suddenly, this message popped up. Here is the command."sudo docker run -it --rm -vpwd:pwd dfam/tetools:latest RepeatMasker /home/dieter/GB/medaka/consensus.fasta -lib /home/dieter/GB/repeatmodeller/GB-families.fa -pa 8 -gff -dir /home/dieter/GB/repeatmasker/"

"Can't call method "setLeftLinkedHit" on an undefined value at /opt/RepeatMasker/ProcessRepeats line 3726."

Regards,

Hossein.

yingnansun commented 1 year ago

I met the same error today,Have you solved it?

Ghanizadeh1980 commented 1 year ago

No, I am still waiting on one of the contributors to respond.

yingnansun commented 1 year ago

I switched to an older version to solve this problem

Ghanizadeh1980 commented 1 year ago

Thanks for that but I hope they fix this issue in the latest version.

rmhubley commented 1 year ago

Yup...this is a bug although I am surprised by how this doesn't pop up in our tests runs. So for the daring it's an easy hotfix. For those less so, please use a previous version or in about a week I should have a patch release available.

Hotfix: In the ProcessRepeats script change line 3726 from:

  # RMH: 8/22/22 Fixed a bug reported by David Gordon and others where on rare occasions an
  #   identifier is omitted in the *.out file.
        $newRight->setLeftLinkedHit( $newHit );

To:

    # RMH: 8/22/22 Fixed a bug reported by David Gordon and others where on rare occasions an
    #      identifier is omitted in the *.out file.
    if ( $newRight ) {
       $newRight->setLeftLinkedHit( $newHit );
    }
Ghanizadeh1980 commented 1 year ago

Thanks, Robert. That worked for me.