vamb: error: unrecognized arguments: --jgi output/mapping/cobinning/bam_contigs_depths.txt

[francesco-ricci]

Hello,

I get the following error:

usage: vamb outdir tnf_input rpkm_input [options]
vamb: error: unrecognized arguments: --jgi output/mapping/cobinning/bam_contigs_depths.txt

This is possibly related to the format of the file bam_contigs_depths.txt. After inspection, this file seems fine to me:

contigName contigLen totalAvgDepth Blank-3_L7_-to-contigs.sorted.bam Blank-3_L7_-to-contigs.sorted.bam-var FR2A1_L7_-to-contigs.sorted.bam FR2A1_L7_-to-contigs.sorted.bam-var FR2A2_L7_-to-contigs.sorted.bam FR2A2_L7_-to-contigs.sorted.bam-var FR2A3_L7_-to-contigs.sorted.bam FR2A3_L7_-to-contigs.sorted.bam-var FR2B1_L7_-to-contigs.sorted.bam FR2B1_L7_-to-contigs.sorted.bam-var FR2B2_L7_-to-contigs.sorted.bam FR2B2_L7_-to-contigs.sorted.bam-var FR2B3_L7_-to-contigs.sorted.bam FR2B3_L7_-to-contigs.sorted.bam-var FR2C1_L7_-to-contigs.sorted.bam FR2C1_L7_-to-contigs.sorted.bam-varFR2C2_L7_-to-contigs.sorted.bam FR2C2_L7_-to-contigs.sorted.bam-var FR2C3_L7_-to-contigs.sorted.bam FR2C3_L7_-to-contigs.sorted.bam-var SWSC1-1_L7_-to-contigs.sorted.bam SWSC1-1_L7_-to-contigs.sorted.bam-var SWSC2-1_L7_-to-contigs.sorted.bam SWSC2-1_L7_-to-contigs.sorted.bam-var
S1Ck127_1077651_flag_0_multi_2.9778_len_1029 1029 5.86121 0 0 0 0 0 0 0 0 0.632537 0.865957 0.682594 0.745388 0.828214 0.657236 1.12059 1.71893 0.666667 0.689446 1.9306 5.12158 0 0 0 0
S1Ck127_4669795_flag_1_multi_3.0000_len_1001 1001 4.57932 0 0 0.0987074 0.286722 0 0 0 0 0.622797 0.538728 0.336075 0.223391 0.616921 0.236605 1.23032 0.666889 1.49824 2.135 0.176263 0.145364 0 0 0 0
S1Ck127_10417218_flag_1_multi_3.0000_len_1678 1678 4.56937 0 0 0.196335 0.181464 0.78534 0.954528 0.196335 0.157889 0.39267 0.631552 0.196335 0.342569 0.441754 0.637067 0.66623 0.709735 1.49804 3.5049 0.196335 0.157888 0 0 0 0
S1Ck127_12572503_flag_1_multi_4.0000_len_1061 1061 5.53128 0 0 0.472009 0.834107 0.329308 0.550774 1.15258 4.76901 0 0 0.448957 0.502612 1.31723 1.04102 1.31723 1.84321 0.164654 0.137693 0.329308 0.550775 0 0 0 0

Any clue why this might happen?

Thanks
Francesco

[vinisalazar]

Hi @francesco-ricci,

The problem here seems to be that the vamb command line is not accepting the --jgi option. This option was added in Vamb v2. Although the Metaphor environment specifies vamb v3.0.2, it is possible it may have installed an older one. Could you confirm the vamb version installed in the environment?

Or possibly, delete the vamb environment and let Metaphor reinstall it. Hopefully that fixes the problem.

Let me know how it goes.

[francesco-ricci]

Thansk Vini, I have vamb v4.1.3.

[vinisalazar]

Did you do any manual installation of vamb at all? Metaphor by default uses v3.0.2. Deleting and reinstalling it should solve the problem.

I will patch this on the next version of Metaphor, so as to use the latest version of vamb (along with the mkl problem you reported on the other issue). Should be done about a week from now.

[francesco-ricci]

Can't remember I might have tried to update vamb among the various fixes I tried.

I'll follow your advice thanks Vini!

[francesco-ricci]

Hi VIni,

so I uninstalled metaphor and reinstalled it, but vamb was not installed. When I try to install vamb v3.0.2 I get the following error message:

(metaphor) [fricci@m3-login2 output]$ mamba install vamb==3.0.2

Looking for: ['vamb==3.0.2']

bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pkgs/r/linux-64 No change
pkgs/main/linux-64 No change
pkgs/main/noarch No change
pkgs/r/noarch No change

Pinned packages:

• python 3.11.*

warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
Could not solve for environment specs
The following packages are incompatible
└─ vamb 3.0.2 is installable with the potential options
├─ vamb 3.0.2 would require
│ └─ python >=3.6,<3.7.0a0 , which can be installed;
└─ vamb 3.0.2 would require
└─ python >=3.7,<3.8.0a0 , which can be installed.

[francesco-ricci]

Managed to fix this by using pip to install vamb==3.0.9 and then I had to modify the vamb script pasecontigs.py [by changing _vambtools.PushArry(_np.int) to _vambtools.PushArry(nt)]

[francesco-ricci]

Still getting an error from vamb:

Traceback (most recent call last):
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/62c4f57b116324c01c3221a9b5c2a0ef_/bin/vamb", line $
from vamb.main import main
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/62c4f57b116324c01c3221a9b5c2a0ef_/lib/python3.7/si$
from . import cluster
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/62c4f57b116324c01c3221a9b5c2a0ef_/lib/python3.7/si$
import torch as torch
File "/home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/62c4f57b116324c01c3221a9b5c2a0ef/lib/python3.7/si$
from torch.C import * # noqa: F403
ImportError: /home/fricci/rp24/fra/software/miniconda3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/62c4f57b116324c01c3221a9b5c2a0ef/lib/python3$

I'll wait for you patch Vini.

Thanks
Francesco