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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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Error when trimming fastq files #4

Closed kclambi1 closed 9 months ago

kclambi1 commented 1 year ago

Trimming fastq step errors out with non-zero exit status and does not trim files. Full traceback:

**STEP 3: Trimming fastq files Traceback (most recent call last): File "/Users/xxxx/miniconda3/envs/metacerberus/bin/metacerberus.py", line 693, in sys.exit(main()) File "/Users/xxxx/miniconda3/envs/metacerberus/bin/metacerberus.py", line 421, in main shutil.copy(value, os.path.join(reportpath, key, f"qc{name}.html")) File "/Users/xxxx/miniconda3/envs/metacerberus/lib/python3.10/shutil.py", line 417, in copy copyfile(src, dst, follow_symlinks=follow_symlinks) File "/Users/xxxx/miniconda3/envs/metacerberus/lib/python3.10/shutil.py", line 233, in copyfile if _samefile(src, dst): File "/Users/xxxx/miniconda3/envs/metacerberus/lib/python3.10/shutil.py", line 210, in _samefile return os.path.samefile(src, dst) File "/Users/xxxx/miniconda3/envs/metacerberus/lib/python3.10/genericpath.py", line 100, in samefile s1 = os.stat(f1)

TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType**

Something is getting passed as null somewhere, or potentially writing the same file being read?

raw-lab commented 1 year ago

What type of fastq are you using (oxford, pacbio, illumina)? If you can attach a few hundred reads here if you would like?

kclambi1 commented 1 year ago

These are nanopore minion reads.

Command: metacerberus.py --fraggenescan /Users/xxxx/Downloads/fastq_pass/ --nanopore --meta --dir_out /Users/xxxx/Downloads/lambda_vir-only_dir/

So since '--nanopore' is being specified, it is odd. The trimming output directories are created, however they are empty.

FAS12900_pass_efb8dd88_0.fastq.zip

raw-lab commented 9 months ago

This is a Mac issues. We recommend installing using: OSX-ARM (M1/M2) protocol on the readme: conda create -y -n metacerberus conda activate metacerberus conda config --env --set subdir osx-64 conda install -y -c conda-forge mamba python=3.10 "pydantic<2" mamba install -y -c bioconda -c conda-forge metacerberus metacerberus.py --setup

This should fix the Mac bug. If you have any other issues let us know? Closing for now. Will re-open if you have the issue.

Thank you for using MetaCerberus.

many thanks, RAW lab