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anuradhawick / MetaBCC-LR

Reference-free Binning of Metagenomics Long Reads using Coverage and Composition
https://doi.org/10.1093/bioinformatics/btaa441
MIT License
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MetaBCC-LR cannot locate the output folder (FileNotFoundError: [Errno 2] No such file or directory: 'metaBCCLR_default_params_output/misc/filtered_reads.fasta') #3

Closed hdore closed 3 years ago

hdore commented 4 years ago

Hello,

Thank you for this tool, I can't wait to see the result on my Nanopore dataset. It is currently running :) I just wanted to report a "bug": I got the following error a few minutes after launching the job: FileNotFoundError: [Errno 2] No such file or directory: 'metaBCCLR_default_params_output/misc/filtered_reads.fasta'

I figured that it was because the folder "metaBCCLR_default_params_output" that I put in the --output argument already existed before I launched MetBCC-LR. I think this might be because of this part of the MetaBCC-LR script: if not os.path.exists(output): os.makedirs(output) os.makedirs(f"{output}/images") os.makedirs(f"{output}/misc")

Since the last 2 lines are included in the if loop, the folders "images" and "misc" are not created when the output folder already exists, hence the error.

I hope this can help others!

Hugo

anuradhawick commented 4 years ago

Thank you very much for catching this bug. We will fix this soon.

Please let us know the expectation-performance gap. We are working on a second version and would love to have some input.

Best regards Anuradha

hdore commented 4 years ago

Thank you! I also had trouble with the installation because of my gcc version (and probably also the g++ version, but it's not listed as a dependency so I'm not sure).

I just ran into another error while tuning sensitivity but I'll open a different issue for an easier tracking.

Best,

Hugo

anuradhawick commented 4 years ago

Thanks for the suggestions and comments. Much appreciated. We will attend them soon.

Best regards Anuradha