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COMBINE-lab / salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
https://combine-lab.github.io/salmon
GNU General Public License v3.0
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error: commlib error: got read error #580

Open BeatrizdeToledo opened 4 years ago

BeatrizdeToledo commented 4 years ago

Good evening, I have been trying to do some alignments using salmon but I get this error after a few hours.

error: commlib error: got read error (closing "compute-0-19.local/shepherd_ijs/1")

Your "qlogin" request could not be scheduled, try again later.

Here is one example of the codes I used that didn't work, some others worked fine. for this I built a decoy-aware transcriptome file.

salmon quant --libType A -1 L395_gfp_plus_Track_3446_3455_R1.fastq -2 L395_gfp_plus_Track-3446-3455_R2.fastq -i desalttama_salmon_index31 -p 12 --writeUnmappedNames --writeMappings -o desalttama_salmon_index31_quant_L395

I used This qlogin qlogin -q all.q -l h_rt=48:00:00 -l mem_free=10G -R yes -now n -pe smp 1

How can I solve this issue? Thank you Beatriz

BeatrizdeToledo commented 3 years ago

It is important to note that my run is taking many hours and most of the times do not finish