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Puumanamana / CoCoNet

Tool for unsupervised contig binning from viral metagenomes
Apache License 2.0
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error message #1

Open lingyi-owl opened 3 years ago

lingyi-owl commented 3 years ago

Dear CoCoNet developer,

I am really interested in your tool. I tried to run it on my metagenomic dataset. It failed because of some errors. I don't really understand what the error message means. I wonder if you can help me with the issue.

Thanks!

Best, Lingyi

My code is: coconet --fasta path/to/scaffolds.fasta \ --coverage path/to/*.bam \ --output path/to/coconet_output/

The error message is: Traceback (most recent call last): File "/home/lingyi/miniconda3/envs/coconet/bin/coconet", line 10, in sys.exit(main()) File "/home/lingyi/miniconda3/envs/coconet/lib/python3.6/site-packages/coconet/coconet.py", line 41, in main preprocess(cfg) File "/home/lingyi/miniconda3/envs/coconet/lib/python3.6/site-packages/coconet/coconet.py", line 66, in preprocess min_qual=cfg.min_mapping_quality, flag=cfg.flag, fl_range=cfg.fl_range File "/home/lingyi/miniconda3/envs/coconet/lib/python3.6/site-packages/coconet/tools.py", line 47, in wrapper return func(*args, **kwargs) File "/home/lingyi/miniconda3/envs/coconet/lib/python3.6/site-packages/coconet/preprocessing.py", line 216, in bam_list_to_h5 shutil.rmtree(tmp_dir) File "/home/lingyi/miniconda3/envs/coconet/lib/python3.6/shutil.py", line 490, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/home/lingyi/miniconda3/envs/coconet/lib/python3.6/shutil.py", line 488, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/home/lingyi/scripts/tmp42'

Puumanamana commented 3 years ago

Hi Lingyi,

Sorry I didn't see your message earlier. I should have fixed this issue in a previous update, did you try with the latest version of CoCoNet (how did you install CoCoNet)?

Cédric