Time for looping through several files

raw-lab / MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

BSD 3-Clause "New" or "Revised" License

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Time for looping through several files #22

Open mpdoane2 opened 2 weeks ago

mpdoane2 commented 2 weeks ago

Hi, I'm attempting get CAZy annotation using:

metacerberus.py --prodigal "$file_path" --hmm CAZy --dir_out "$output_dir"

in which the file_path points towards an fna file of contigs. The process has been running for nearly 20 hours, but the time.tsv pipeline is only 9 minutes.

hpc-node019 Pipeline_time 0:09:44.052514 /scratch/user/user/cazy_out/cazy_output/SAGCFN_22_01149_S3

Is there an issue with the next step, saving the graph barcharts?

Thank you Mike

decrevi commented 2 weeks ago

Hello, I am looking into this. It does seem to be an issue either with the plots or creating the gff/genbank files.

which version of MetaCerberus are you using?

Thank you, -Jose

decrevi commented 2 weeks ago

Hello, I have found and fixed the issue. I will push an updated version shortly with this fix, thank you for bringing this to my attention!

-Jose

mpdoane2 commented 2 weeks ago

Hi Jose,

Thank you for looking into this so quickly. For your information, the version I have is 1.3.0 March 2024.

Thank you again. I'll try running this again soon.

Cheers Mike