CRITICAL:No config.yaml dectected from previous run

[stevens-1]

Hello Jiarong: I installed and tested Virsorter 2. Since I have a lot of data to process, I used a small portion of the data to test different run parameters for subsequent processing options. The command I used was virsorter run -w test.out -i final_assembly.fasta --min-length 1500 -j 4 all, which runs correctly and produces complete results. When I plan to use --min-score 0.7 for the calculation, I get an error： virsorter run -w test.out -i test.fa --include-groups ‘dsDNAphage,ssDNA’ --min-score 0.7 --label rerun classify [2024-09-18 10:08 INFO] VirSorter 2.2.4 [2024-09-18 10:08 INFO] /mnt/disk1/home/weny24/.conda/envs/vs2/bin/virsorter run -w test.out -i test.fa --include-groups dsDNAphage,ssDNA -- min-score 0.7 --label rerun classify [2024-09-18 10:08 CRITICAL] No config.yaml dectected from previous run I adjusted the current working directory to make sure the filenames are not duplicated, and I observed a config.yaml file in the test.out folder after the first correct run, and I'm not sure what to do about it to get it to run correctly --min-score

[jiarong]

Hi, you need to keep the previous config.yaml (exactly the same) in order to run.

[stevens-1]

Hello Jiarong: Thanks for your reply, yes I did keep the previously generated config.yaml file, I moved the changed file to the current working directory and it still shows the same error. So where should this file be placed in order for it to work properly?

[jiarong]

You do not need to move anything. You just need to use the same output directory for -w from previous run. I assume it should be test.out.

[stevens-1]

I think I understand, I saved the results of the previous run separately, while keeping the original folder name and config.yaml file, and ran it again and prompted: virsorter run -w test.out -i final_assembly.fasta --include-groups "dsDNAphage,ssDNA" --min-score 0.7 --label rerun classify [2024-09-18 18:13 INFO] VirSorter 2.2.4 [2024-09-18 18:13 INFO] /mnt/disk1/home/weny24/.conda/envs/vs2/bin/virsorter run -w test.out -i final_assembly.fasta --include-groups dsDNAphage,ssDNA --min-score 0.7 --label rerun classify [2024-09-18 18:13 CRITICAL] --min-length has changed from 1500 to 0; but --min-length has not effect on classify step; The whole pipeline has to be rerun if --min-length changes

[jiarong]

You forgot the --min-length 1500 used in previous run. Here is the typical scenario of using classify:

# Run1: default score cutoff 0.5
virsorter run -w test.out -i final_assembly.fasta --include-groups "dsDNAphage,ssDNA" --min-score 0.5 --min-length 1500
# Run2: more strict score 0.7; with `--label` the results from Run1 will NOT be overwritten.
virsorter run -w test.out -i final_assembly.fasta --include-groups "dsDNAphage,ssDNA" --min-score 0.7 --min-length 1500 --label rerun classify

[stevens-1]

Thank you very much for your patience in replying, It is now running successfully, thank you again for your help!

[Jokendo-collab]

I am working on different projects and when I run is on multiple projects I get the error:

[2024-11-06 16:17 CRITICAL] No config.yaml dectected from previous run
[2024-11-06 16:17 INFO] VirSorter 2.2.3

How Can I make a config file to work with totally different projects in different folders?