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victoriapascal / gutsmash

gutSMASH
GNU Affero General Public License v3.0
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RuntimeError: diamond failed to run: version #13

Open ChenTianYi99 opened 1 year ago

ChenTianYi99 commented 1 year ago

Hi.

I am encountering this problem: "RuntimeError: diamond failed to run: version -> Error: Option is not permitted for this workflow: threads". The following is my order: "python3 run_gutsmash.py --output-dir /lustre/home/gutsmash --genefinding-tool prodigal-m --cb-knownclusters --enable-genefunctions --cb-general --cb-knownclusters bin_marked.fa".

So how to fix the problem? Looking forward to your reply. Thanks in advance.

WenxinHe616 commented 12 months ago

Hello : ) I have the same problem as you. Have you solved it?

ChenTianYi99 commented 11 months ago

Hi, @WenxinHe616 You should first download gutsmash from https://github.com/victoriapascal/gutsmash (for example /lustre/home/gutsmash-gutsmash). Then I deleted "--thread" and "--tmpdir" in diamond.py (line 33-34), and then changed "MUSCLE" into "muscle" in muscle.py (line 48) (the files are in /gutsmash-gutsmash/antismash/common/subprocessing). You can try to see if the tool works well.

Best Tianyi Chen

WenxinHe616 commented 11 months ago

Hello : ) Thank you, Tianyi~ This error was resolved after I changed diamond to version 0.8.36. The software runs normally after eliminating other faults.

Best Wenxin