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MicrobialDarkMatter / nanomotif

Nanomotif - a tool for identifying methylated motifs in metagenomic samples
MIT License
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find-motifs #33

Closed jpinus closed 2 months ago

jpinus commented 2 months ago

I use nanomotif 0.2.1 as an conda environment and followed the instructions outlined in the documentation(https://nanomotif.readthedocs.io/en/latest/required_files.html) meticulously for the input files. However, I encountered a couple of issues with the initial command execution of nanomotif.

The command mentioned in the documentation nanomotif find_motifs ASSEMBLY.fasta PILEUP.bed CONTIG_BIN.tsv -t THREADS --out OUT is not running as expected. It seems there's a discrepancy in the command syntax. According to the error message I received, "find_motifs" should be "find-motifs". Even after correcting the command syntax to "nanomotif find-motifs assembly.fasta OUT.bed contig_bin.tsv -t 60 --out OUT_nanomotif", I encountered another issue. The execution didn't produce the expected output file "bin-motifs.tsv". It appears that this might be due to the omission of "CONTIG_BIN.tsv" in the initial command.

SorenHeidelbach commented 2 months ago

Yes, there was a problem in the renaming of arguments, in version 0.2.1 the corresponding command is "complete-workflow", but we recommend using the latest version: 0.4.1 and use the motif_discovery command

jpinus commented 2 months ago

@SorenHeidelbach I use the conda installation: command: conda install -c bioconda nanomotif

this is installing nanomotif 0.1.20

How can I specify that the newest version, 0.4.1 can be installed?

SorenHeidelbach commented 2 months ago

Yes, the bioconda channel is currently facing some issues regarding checks. We will upload the newest version once it has been fixed.

Currently you can intall the newest version using pip, see here.