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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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Resume RepeatMasker from "processing output" #231

Closed CongLiu37 closed 7 months ago

CongLiu37 commented 9 months ago

Hello,

I am running repeatmasker with a self-made repeat library. Here is the commands: singularity run ~/Softwares/dfam-tetools-latest.sif RepeatMasker -xsmall -lib /flash/repeat.fa -pa 64 -gff -nolow -norna -no_is -qq /flash/genome.fa -dir /flash The running time went beyond my permission and the job was killed at "processing output". Here is how the output looks like: image Here is the output files that had been generated: image Is there any way to resume the RepeatMasker pipeline based on these files?

Sincerely,

Cong

rmhubley commented 7 months ago

Sorry for the delay. If ProcessRepeats has started (noted by the "Processing Output:" log output), you can re-start this last step by running:

./ProcessRepeats -a filename.fa.cat.gz

Where, in this case filename is simply "genome".