bam2feat error: Return code -11

[AroneyS]

I think I've managed to install it correctly (v1.2.2 via pip), but I am running into an error with bam2feat as below. I think its a different issue to #21 due to having warnings like Cannot read alignment score at position: .

Do you have any advice? Bam files were created using minimap2.

2024-04-11 15:24:44.558] [svc] [�[32minfo�[m] Processing contig: NODE_16712_length_2673_cov_12.221925
[2024-04-11 15:24:44.559] [svc] [�[32minfo�[m] Getting per-read characteristics
[2024-04-11 15:24:44.558] [svc] [�[32minfo�[m] Processing contig: NODE_212_length_27811_cov_24.420450
[2024-04-11 15:24:44.559] [svc] [�[32minfo�[m] Getting per-read characteristics
[2024-04-11 15:24:44.566] [svc] [�[32minfo�[m] Processing contig: NODE_5071_length_4796_cov_26.411306
[2024-04-11 15:24:44.566] [svc] [�[32minfo�[m] Getting per-read characteristics
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 0
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 1
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 2
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 3
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 4
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 5
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 6
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 7
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 8
[2024-04-11 15:24:44.573] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 9
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 10
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 11
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 12
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 13
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 14
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 15
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 16
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 17
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 18
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 19
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 20
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 21
[2024-04-11 15:24:44.574] [svc] [�[33m�[1mwarning�[m] Cannot read alignment score at position: 22
[2024-04-11 15:24:44.574] [svc] [
Traceback (most recent call last):
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/bin/resmico", line 10, in <module>
    sys.exit(main())
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/lib/python3.10/site-packages/resmico/__main__.py", line 52, in main
    args.func(args)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/lib/python3.10/site-packages/resmico/commands/bam2feat.py", line 80, in main
    bam2feat.main(args)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/lib/python3.10/site-packages/resmico/bam2feat.py", line 284, in main
    feat_files = run_bam2feat(bam_fasta, exe, args)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/lib/python3.10/site-packages/resmico/bam2feat.py", line 256, in run_bam2feat
    return [x for x in res]
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/lib/python3.10/site-packages/resmico/bam2feat.py", line 256, in <listcomp>
    return [x for x in res]
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/lib/python3.10/site-packages/resmico/bam2feat.py", line 227, in _run_bam2feat
    bam2feat(bam_sub, ref_tmp, outdir_feat, exe['bam2feat'], args)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/lib/python3.10/site-packages/resmico/bam2feat.py", line 190, in bam2feat
    run_cmd(cmd)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/fee5edea63eb33e4a3eddd1d49648ebd_/lib/python3.10/site-packages/resmico/bam2feat.py", line 99, in run_cmd
    raise ValueError('Return code: {}'.format(rc))
ValueError: Return code: -11

[AroneyS]

I reinstalled Resmico using the pip from source method and I now get a different error:

[2024-05-07 13:45:32.368] [svc] [�[32minfo�[m] Uncompressed fasta file detected. Using BamTools
[2024-05-07 13:45:32.369] [svc] [�[32minfo�[m] Processing contig: NODE_5091_length_4403_cov_21.562787
[2024-05-07 13:45:32.369] [svc] [�[32minfo�[m] Getting per-read characteristics
[2024-05-07 13:45:32.386] [svc] [�[32minfo�[m] Computing entropy and GC percent

Traceback (most recent call last):
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/bin/resmico", line 10, in <module>
    sys.exit(main())
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/__main__.py", line 52, in main
    args.func(args)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/commands/bam2feat.py", line 80, in main
    bam2feat.main(args)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat.py", line 284, in main
    feat_files = run_bam2feat(bam_fasta, exe, args)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat.py", line 256, in run_bam2feat
    return [x for x in res]
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat.py", line 256, in <listcomp>
    return [x for x in res]
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat.py", line 227, in _run_bam2feat
    bam2feat(bam_sub, ref_tmp, outdir_feat, exe['bam2feat'], args)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat.py", line 190, in bam2feat
    run_cmd(cmd)
  File "/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat.py", line 99, in run_cmd
    raise ValueError('Return code: {}'.format(rc))
ValueError: Return code: -6

[AroneyS]

Also get this other error outside of the log:

*** stack smashing detected ***: /mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat terminated
======= Backtrace: =========                    
/lib64/libc.so.6(+0x7731f)[0x7f980250631f]                                                             
/lib64/libc.so.6(__fortify_fail+0x37)[0x7f980258f767]                                             
/lib64/libc.so.6(__fortify_fail+0x0)[0x7f980258f730]                                              
/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat(+0x21bba)[0x55f0a412ebba]
/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat(+0x27a56)[0x55f0a4134a56]
/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat(+0x1e667)[0x55f0a412b667]
/pkg/suse12/software/GCCcore/9.3.0/lib64/libgomp.so.1(GOMP_parallel+0x42)[0x7f980294d3d2]                                                                                                                      
/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat(+0x18eef)[0x55f0a4125eef]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f98024b2ac5]                                                                                                                                                       
/mnt/hpccs01/work/microbiome/ibis/SRA/results/benchmarking/20240129/.snakemake/conda/b89c45308a715f067df5b9f1955ffb05_/lib/python3.9/site-packages/resmico/bam2feat(+0x1dfd9)[0x55f0a412afd9]

[AroneyS]

The contig where it failed (NODE_5091_length_4403_cov_21.562787) has Ns in it. Is that the issue?

[nick-youngblut]

The contig where it failed (NODE_5091_length_4403_cov_21.562787) has Ns in it. Is that the issue?

Yeah, that's almost definitely the issue. Why does the contig contain N's? Is it actually a scaffold?

[AroneyS]

Yep, turns out they were scaffolds. Resmico finishes for me now.
Do you plan on supporting scaffolds in the future?

[nick-youngblut]

Do you plan on supporting scaffolds in the future?

Likely not, given that the feature table generation software was highly optimized for contigs (no N values).