Closed erfanshekarriz closed 5 months ago
I've resolved this issue by enforcing the scikit-learn version:
mamba create -c bioconda -n vRhyme python=3 networkx pandas numpy numba scikit-learn==1.2.2 pysam samtools mash mummer mmseqs2 prodigal bowtie2 bwa
Please help me update the installation instructions in the READ.md file. I would also strongly recommend noting the versions of all software above to allow longterm stability and reproducibility.
Best,
Erfan
Hello there.
I was pretty stoked to use vRhyme for my viral binning protocol, but unfortunately haven't been successful in running the program without any errors.
I initially wasn't able to supply my own sorted bam files that come from
minimap2 -x sr
(which is X3-4 times faster and also more accurate than bowtie2 - would recommend adding this as a mapping option). It would give me the same error as Issue #26https://github.com/AnantharamanLab/vRhyme/issues/26
and would not produce the coverage table. I then gave up and thought to instead try out using the internal bowtie2 aligner but still ran into a different error.This is the command I ran:
This time I checked the
log_vRhyme_paired_reads.tsv
and the pairings are correct. I also checked and thevRhyme_coverage_values.tsv
file is not empty .Despite that I get the following log and error:
Any idea on how we can resolve this? I was reading some blogs online saying it's related to the version of scikit-learn. If that is the case can you include the version of the software in the conda installation? This way we are guaranteed to fully reproduce your outcomes.
If you need my raw sequence files I'm happy to somehow send them to you. I can also send you the bam files generated from minimap2.
Best,
Erfan