search

Puumanamana / CoCoNet

Tool for unsupervised contig binning from viral metagenomes
Apache License 2.0
15 stars 1 forks source link

coconet run error~ #6

Open ChaoXianSen opened 1 year ago

ChaoXianSen commented 1 year ago

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:

Any idea about this problem?

Thanks!

Vini2 commented 2 months ago

Hi @Puumanamana,

I'm getting the same error with the following command.

coconet run --fasta contigs.fasta --bam bam_files/*.bam --output coconet_results --threads 64

This is the output I get.

15:39:32 (Mem:  0.4 GB)    <CoCoNet>    INFO: Using 64 threads
15:39:32 (Mem:  0.4 GB)    <CoCoNet>    INFO: Features: coverage, composition
15:39:34 (Mem:  0.4 GB) <preprocessing> INFO: Processing 571,798 contigs
15:39:38 (Mem:  0.4 GB) <preprocessing> INFO: Length filter (L>2048 bp) -> 31,394 contigs remaining
15:42:22 (Mem:  0.4 GB) <preprocessing> INFO: Complete contigs filtering (DTR > 10 bp) -> 31207 contigs remaining
15:42:22 (Mem:  0.4 GB) <preprocessing> INFO: Processing alignments and converting to h5 format
15:45:10 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 1,000 contigs processed
15:46:22 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 2,000 contigs processed
15:47:07 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 3,000 contigs processed
15:47:43 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 4,000 contigs processed
15:48:13 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 5,000 contigs processed
15:48:39 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 6,000 contigs processed
15:49:03 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 7,000 contigs processed
15:49:25 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 8,000 contigs processed
15:49:44 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 9,000 contigs processed
15:50:03 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 10,000 contigs processed
15:50:19 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 11,000 contigs processed
15:50:35 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 12,000 contigs processed
15:50:50 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 13,000 contigs processed
15:51:03 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 14,000 contigs processed
15:51:17 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 15,000 contigs processed
15:51:28 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 16,000 contigs processed
15:51:40 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 17,000 contigs processed
15:51:51 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 18,000 contigs processed
15:52:02 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 19,000 contigs processed
15:52:13 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 20,000 contigs processed
15:52:26 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 21,000 contigs processed
15:52:36 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 22,000 contigs processed
15:52:45 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 23,000 contigs processed
15:52:54 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 24,000 contigs processed
15:53:03 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 25,000 contigs processed
15:53:11 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 26,000 contigs processed
15:53:19 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 27,000 contigs processed
15:53:27 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 28,000 contigs processed
15:53:35 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 29,000 contigs processed
15:53:43 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 30,000 contigs processed
15:53:50 (Mem:  0.8 GB) <preprocessing> DEBUG: Coverage: 31,000 contigs processed
15:53:55 (Mem:  0.7 GB) <preprocessing> INFO: Coverage filtering summary:
                                              - 32,155,348 total reads
                                              - 94.9% reads (mapped)
                                              - 100.0% reads (primary alignments)
                                              - 89.1% reads (mapq>30)
                                              - 98.2% reads (coverage>50%)
                                              - 89.2% reads (flag & 3596 == 0)
15:54:11 (Mem:  0.7 GB) <preprocessing> INFO: 31,394 contigs are only present in the composition. Taking the intersection (0 contigs)
15:54:11 (Mem:  0.7 GB) <preprocessing> INFO: Prevalence filter (prevalence>=2) -> 0 contigs remaining
15:54:11 (Mem:  0.7 GB)   <learning>    INFO: Making train/test examples
Traceback (most recent call last):
  File "/home/mall0133/miniconda3/envs/coconet/bin/coconet", line 10, in <module>
    sys.exit(main())
  File "/home/mall0133/.local/lib/python3.7/site-packages/coconet/coconet.py", line 61, in main
    make_train_test(cfg)
  File "/home/mall0133/.local/lib/python3.7/site-packages/coconet/coconet.py", line 167, in make_train_test
    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

I tried changing the parameter --min-ctg-len to 1024, 512 and 256 but all still failed giving the same error.

Appreciate any help to fix this problem.

Thanks!