Open shaman-narayanasamy opened 1 month ago
Dear @shaman-narayanasamy
Apologies for the slow reply - you caught us on holiday. The version of Vamb you're running is quite old. Would it be possible to run the latest version (v 4.1.3) instead? It's quite likely that the bug has been fixed in the latest version.
Hi @jakobnissen ,
Thanks for the response. No worries!
I installed it using conda/mamba without specifying the version: mamba install -c bioconda vamb
. My bad for assuming that the versions were up to date on conda/mamba:
$ mamba search -c bioconda vamb
Loading channels: done
# Name Version Build Channel
<old versions removed for bevity>
vamb 3.0.2 py37h8902056_2 bioconda
vamb 3.0.2 py37hf01694f_0 bioconda
I then tried pip within a conda environment, but it does not work.
I presume this is because of this note in the README:
Note: An active Conda environment can hijack your system's linker, causing an error during installation. Either deactivate conda, or delete the ~/miniconda/compiler_compats directory before installing with pip.
I don't really want to install it in my base environment, nor do I want to delete the compiler_compats
file fearing that it may affect other environments that I currently have build. Is there any alternative installation method?
Your support is highly appreciated.
Dear authors/maintainers,
First off, thank you for developing and maintaining this wonderful tool! Your efforts are much appreciated.
I would like to inquire about an issue I am facing. Specifically, when I run the command:
$ vamb --outdir U1/vamb --fasta /ibex/scratch/projects/c2188/soil_experiment/metagenomics/assembly/U1/megahit_assembly/final.contigs.fa --jgi U1/contig_depth.txt -m 1500
(error at the bottom). However, simply removing the-m 1500
parameter, i.e.:$ vamb --outdir U1/vamb --fasta /ibex/scratch/projects/c2188/soil_experiment/metagenomics/assembly/U1/megahit_assembly/final.contigs.fa --jgi U1/contig_depth.txt
, seems to run (but I did not let it complete).I tried to look for solutions in issues #48, #96, #65, but did not find a clear solution (apologies if I missed something). In addition, I also ensure that the fasta file and the JGI depth file did not contain any discrepencies:
Could you please advice on how I could debug this issue? I would like to filter out the contigs shorter than 1500 bp, instead of running without any filtering.
Looking forward to hearing from you.
Best regards, Shaman
Your version of Python and Vamb.
vamb=3.0.2=py37h8902056_2
The log file (called
log.txt
) from the output directoryLoading TNF Minimum sequence length: 1500 Loading data from FASTA file /ibex/scratch/projects/c2188/soil_experiment/metagenomics/assembly/U1/megahit_assembly/final.contigs.fa
Loading RPKM Loading RPKM from JGI file U1/contig_depth.txt
$ vamb --outdir U1/vamb --fasta /ibex/scratch/projects/c2188/soil_experiment/metagenomics/assembly/U1/megahit_assembly/final.contigs.fa --jgi U1/contig_depth.txt -m 1500 Traceback (most recent call last): File "/ibex/user/naras0c/conda-environments/vamb_env/bin/vamb", line 11, in
sys.exit(main())
File "/ibex/user/naras0c/conda-environments/vamb_env/lib/python3.7/site-packages/vamb/main.py", line 528, in main
logfile=logfile)
File "/ibex/user/naras0c/conda-environments/vamb_env/lib/python3.7/site-packages/vamb/main.py", line 247, in run
len(tnfs), minalignscore, minid, subprocesses, logfile)
File "/ibex/user/naras0c/conda-environments/vamb_env/lib/python3.7/site-packages/vamb/main.py", line 121, in calc_rpkm
raise ValueError("Length of TNFs and length of RPKM does not match. Verify the inputs")
ValueError: Length of TNFs and length of RPKM does not match. Verify the inputs