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victoriapascal / gutsmash

gutSMASH
GNU Affero General Public License v3.0
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Short run #3

Open TKSJ2020 opened 3 years ago

TKSJ2020 commented 3 years ago

Hello,

I am trying to run gutsmash in the standalone version but just one of my samples is taking over couple of days already and because I have still 187 samples to go I was wondering if there would be a faster way to run it that could still give me comprehensive results to compare the samples later.

This was my command: python3 run_gutsmash.py -c 32 --genefinding-tool prodigal-m --cb-knownclusters --enable-genefunctions ../C1.052018.contigs.fasta --output-dir C1.052018_gutsmash_28072021

Thank you in advance for any advice!

Best regards

victoriapascal commented 2 years ago

Hi,

Sorry for the late reply. If instead of a fasta file you provide the annotated genbank file, gutSMASH will take much less time to run. Otherwise, I'm not sure how you could speed up the process.

Best,

Victòria