mob-suite
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phac-nml
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
I am having problems running mob_suite installed with: % git clone https://github.com/phac-nml/mob-suite.git % cd mob-suite % python setup.py install I get a error code 255 Please help me fix this....
It appears that mob_recon expects blast results for the mge report generation, but such blast results are not necessarily generated: ``` Traceback (most recent call last): File "/tmp/global2/nyoungblut/code/dev/ll_pipelines/llg/.snakemake/conda/db9f22b4bb1b99b6c9c05ebc0a31965c/bin/mob_recon", line 10,...
Hello, `mob-suite` uses `multiprocessing.cpu_count()` to ge the number of cpus via `mob_init.py`. `multiprocessing.cpu_count()` return the number of cpu in the machine, But this is not the same as the number...
If the output directory does not exist, then mob_recon throws the following error: ``` File "/tmp/global2/nyoungblut/code/dev/snakemake/conda/297281b9ce2235c6b590b2c1c641c5a2/bin/mob_recon", line 10, in sys.exit(main()) File "/tmp/global2/nyoungblut/code/snakemake/conda/297281b9ce2235c6b590b2c1c641c5a2/lib/python3.8/site-packages/mob_suite/mob_recon.py", line 1053, in main os.mkdir(args.outdir, 0o755) FileNotFoundError: [Errno...
Thanks for the great tool! https://github.com/phac-nml/mob-suite/pull/159 addresses unstable ordering when sorting contig-link counts. When assigning contigs to clusters, it feels the priority should be correctness, and then stability. One option...
We noticed an issue whereby the order of a fasta impacted the plasmid assignment. I.e. moving a contig from the start of a fasta to the end moved it from...
I am encountering an issue with the reconstruction of plasmid sequences using mob_recon. While all other files are successfully generated, the actual sequences remain absent. The recurring warning message I...
Hello, Thank you for creating a great tool. I used mob-recon to check a big dataset which included assemblies of different level (short-only, long-only, hybrid) and I noticed that some...
Hi! Can it be possible to run batch of samples in mob_recon, then share command line for this run as i tried many possible ways like run command line in...
Hi, I'm using mob_recon (v3.1.7) on some assemblies and I've noticed that it fails when using a gzip-compressed file and succeeds when using the same file, but decompressed. It looks...
