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coconet run error~ #6
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Hi @Puumanamana, I'm getting the same error with the following command.
This is the output I get.
I tried changing the parameter Appreciate any help to fix this problem. Thanks! |
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Hi !@Puumanamana
run pipeline :
coconet run
--fasta R63.contigs.fa
--bam R63_sort.bam
--output coconet_binning_results
--threads 16
err report:
00:50:09 (Mem: 0.2 GB) INFO: Using 16 threads
00:50:09 (Mem: 0.2 GB) INFO: Features: coverage, composition
00:50:11 (Mem: 0.2 GB) INFO: Processing 681,530 contigs
00:50:17 (Mem: 0.2 GB) INFO: Length filter (L>2048 bp) -> 43,057 contigs remaining
00:56:50 (Mem: 0.2 GB) INFO: Complete contigs filtering (DTR > 10 bp) -> 42993 contigs remaining
00:56:50 (Mem: 0.2 GB) INFO: Processing alignments and converting to h5 format
01:19:26 (Mem: 0.5 GB) INFO: Coverage filtering summary:
- 28,185,071 total reads
- 87.3% reads (mapped)
- 100.0% reads (primary alignments)
- 81.8% reads (mapq>30)
- 100.0% reads (coverage>50%)
- 74.7% reads (flag & 3596 == 0)
01:20:29 (Mem: 0.5 GB) INFO: 43,057 contigs are only present in the composition. Taking the intersection (0 contigs)
01:20:29 (Mem: 0.5 GB) INFO: Prevalence filter (prevalence>=2) -> 0 contigs remaining
01:20:29 (Mem: 0.5 GB) INFO: Making train/test examples
Traceback (most recent call last):
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/coconet/bin/coconet", line 10, in
sys.exit(main())
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/coconet/lib/python3.7/site-packages/coconet/coconet.py", line 61, in main
make_train_test(cfg)
File "/public/home/bioinfo_wang/00_software/miniconda3/envs/coconet/lib/python3.7/site-packages/coconet/coconet.py", line 167, in make_train_te
assembly_idx = dict(test=np.random.choice(n_ctg, n_ctg_for_test))
File "mtrand.pyx", line 909, in numpy.random.mtrand.RandomState.choice
ValueError: a must be greater than 0 unless no samples are taken
Any idea about this problem?
Thanks!
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