Open 778055611 opened 1 year ago
so I want to know ,whether I need split my input file? Is it too large to run Virsorter2?
You do not need to split with 144 CPU cores. The error might be your input file path (~/result/megahit/total.contigs.fa
) does not exist or it's empty..
You do not need to split with 144 CPU cores. The error might be your input file path (
~/result/megahit/total.contigs.fa
) does not exist or it's empty..
thanks for your reply,maybe it is because that my -j parameter too large. and I want to know how to set --min-length parameter? Am I just to set --min-length=1000? could you please give me some advice. thank you again
I recommend 5kb as the minimal length. See details in here: https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-5qpvoyqebg4o/v3
I recommend 5kb as the minimal length. See details in here: https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-5qpvoyqebg4o/v3
thanks for your reply which heleps me a lot. thank you again.
Dear Virsorter2 team, thank you again for your awesome work ,but when I use a single sample to test using the following code " virsorter run -i ~/testfile/FC03.contigs.fa -w ~/result/Virsorter2/total-result/result --min-length 1500 -j 144 all" ,It works well. But when I merged all of my contigs.fa files to run " virsorter run -i ~/result/megahit/total.contigs.fa -w ~/result/Virsorter2/total-result --min-length 1500 -j 144 all",Imet the following error:"Error in rule circular_linear_split: jobid: 8 output: iter-0/pp-seqname-length.tsv conda-env: /share/lu/VirSorter2-Workpath/db/conda_envs/2270d576 shell:
Exiting because a job execution failed. Look above for error message
*** An error occurred. Detailed errors may not be printed for certain rules. Refer to the log file of the failed command for troubleshooting Issues can be raised at: https://github.com/jiarong/VirSorter2/issues Or send an email to virsorter2 near gmail.com if you do not use GitHub"
could you please give me some advice ?thank you again.