metaSNV issueshttps://git.embl.de/costea/metaSNV/-/issues2017-11-22T09:50:35Zhttps://git.embl.de/costea/metaSNV/-/issues/1collapse_coverages.py stumbles on empty bam files2017-11-22T09:50:35ZThomas Sebastian Schmidtsebastian.schmidt@embl.decollapse_coverages.py stumbles on empty bam filesI noticed a problem with `collapse_coverages.py`. It seems that the script fails with an error if any of the `bam` files (and therefor the corresponding `cov` files) are empty. This is what I got:
```
$folder_metaSNV/src/collapse_covera...I noticed a problem with `collapse_coverages.py`. It seems that the script fails with an error if any of the `bam` files (and therefor the corresponding `cov` files) are empty. This is what I got:
```
$folder_metaSNV/src/collapse_coverages.py $folder_PROJ
Traceback (most recent call last):
File "[...]/collapse_coverages.py", line 38, in <module>
write_matrix(avg_cov, 'Average_cov', path.join(project_dir, '{}.all_cov.tab'.format(project_name)))
File "[...]/collapse_coverages.py", line 34, in write_matrix
out.write('\t'.join([c[bf] for bf in bamfiles]))
File "[...]/collapse_coverages.py", line 34, in <listcomp>
out.write('\t'.join([c[bf] for bf in bamfiles]))
KeyError: '160400887.210.gut.RepGenomesv9.unique.sorted.bam'
```
I followed up and found that the problematic file `160400887.210.gut.RepGenomesv9.unique.sorted.bam` is indeed empty. My quick workaround will be to add a check that all `bam` files in my (long) bamlist do indeed contain reads, but I think that an empty file should not cause this error.
Not being a python person though, I do not feel comfortable messing with your code and submitting a merge request...https://git.embl.de/costea/metaSNV/-/issues/3Update freeze11 db of representative genomes to most recent version.2018-10-08T22:37:05ZThomas Sebastian Schmidtsebastian.schmidt@embl.deUpdate freeze11 db of representative genomes to most recent version.The current `freeze11` db provided for download is problematic, because it contains multiple representative genomes for some specI clusters. This is a result of genome whitelisting in `proGenomes`.
This will affect `metaSNV` SNV recall,...The current `freeze11` db provided for download is problematic, because it contains multiple representative genomes for some specI clusters. This is a result of genome whitelisting in `proGenomes`.
This will affect `metaSNV` SNV recall, since unique genome mappings are required as an input. With multiple (too) closely related genomes in the ref db, the number of (uniquely) mapping reads will be erroneously low. Thea @rossum has generated a cleaned version of `freeze11` representatives in which she picked the longest genome among candidate representatives.
I'd suggest to update the downloadable db to this version (but see issue #2 re tax ID redundancy).https://git.embl.de/costea/metaSNV/-/issues/4conda version2021-04-20T17:14:13ZAlessio Milaneseconda versionDear metaSNV developer,
I'm writing regarding the conda installation. In particular, there are a bunch of inconsistent libraries with mOTUs.
As a result, if you do:
`conda install -c bioconda motus`
it will install mOTUs 2.1.1 (instead...Dear metaSNV developer,
I'm writing regarding the conda installation. In particular, there are a bunch of inconsistent libraries with mOTUs.
As a result, if you do:
`conda install -c bioconda motus`
it will install mOTUs 2.1.1 (instead of 2.6.0) or give a bunch of problem with inconsistent libraries.
Since mOTUs require only `bwa` and `samtools`, I think that this problem would not be related only to mOTUs.
Talking to @all
@rossum @ext.paolil , do you know if metaSNV works with python 3.7? We would add this requirement in the conda yaml:
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/metasnv/meta.yaml
Talking to Renato, the library `zlib` would also be problematic.
Cheers,
alessio