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PASA- annotation comparison step

Hi everyone,

I am currently running PASA for transcript annotation and am stuck in the annotation comparison phase, which has been running for more than 48 hours. I do not see any errors in my SLURM .out file. The same script completed successfully for my 1-hour dataset, but now I am running the control and other time points for a time-series experiment. Is it normal for the annotation comparison step to take this long. Also, the size of dataset is not very different from each other. Would specifying --CPU 20 in the PASA script help speed up this step

$PASAHOME/Launch_PASA_pipeline.pl -c 12hrs_annotationCompare.config -A -g /path_to_reference_genome -t 12hrs_transcripts.fasta.clean
rna-seq pasa genomeassembly
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updated by kalavattam • kalavattam • written by rachana • rachana

Crossposted*: https://www.reddit.com/r/bioinformatics/comments/1r3v2j2/pasa_annotation_comparison_step/

PASA’s developer maintains a community support board: https://groups.google.com/g/pasapipeline-users

Upstream of PASA is Trinity (same developer), and the Trinity support board tends to be more active: https://groups.google.com/g/trinityrnaseq-users

Activity across both has slowed in recent years, but these boards may still be the best place to get targeted help.

*(It’s recommended to avoid crossposting.)

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written by kalavattam • kalavattam

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