RefineM issues

Wrong scaffold coverage calculation when using coverage file

5

I ran the refinem scaffold_stats & outliers command with a custom coverage file using the --coverage_file option. Some contigs got flagged as having zero coverage across all samples. However, when...

adityabandla

warning in taxon_profile

Hi, I tried to use refineM to remove contamination based on genomic properties and taxonomic assignments. But I found the targeted bins is hardly refined which is 12% contaminated, so...

Xiaolan89

refinem outliers scaffold_stats.tsv . [2019-08-16 11:45:03] INFO: RefineM v0.0.25 [2019-08-16 11:45:03] INFO: refinem outliers scaffold_stats.tsv . [2019-08-16 11:45:03] INFO: Reading scaffold statistics. [2019-08-16 11:45:03] INFO: Calculating statistics for 1 genomes...

raw937

installation issue

2

Hi, I installed refineM by sudo pip command, but when I tried to confirm its installation by type: refinem --version the error message shows: usage: refinem {scaffold_stats,genome_stats,taxon_profile,taxon_filter,outliers,ssu_erroneous,kmeans,dbscan,split,manual,reference,compatible,modify_bin,filter_bins,unique,bin_compare,call_genes,unbinned} ... refinem: error:...

Xiaolan89

setup.py: Add pysam as a dependency.

I'm not sure what the version requirement should be, but this is needed otherwise: ``` ...lib/python2.7/site-packages/refinem/coverage.py", line 30, in import pysam ImportError: No module named pysam ```

wwood

error during refinem taxon_profile

[nohup.txt](https://github.com/dparks1134/RefineM/files/2815666/nohup.txt) Hi, Thanks for this amazing software. Everything goes well but got an error during this procedure. I have checked the history reported issue. None is related to this. May...

chloelulu

outliers run error

5

Hi, I was trying to run the outlier function but found the following error, any suggestions for the solution? Best, [2018-07-26 20:56:53] INFO: RefineM v0.0.23 [2018-07-26 20:56:53] INFO: refinem outliers...

gaohanlisa