RefineM

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Hi, I'm trying to run taxon_profile with diamond v 0.8.17 but it fails on expected output format. I changed the output_fmt dict in biolib/external/diamond.py to 'standard': 'tab' and it seems...

ghost

Zero coverage for all samples

14

I am having an issue with "refinem outliers" where I'm getting an error: "invalid value encountered in double_scalars." This originally happened in v0.0.22 but after looking at the github issues...

cedwardson4

refinem outliers error during plot

1

Hi, When I run the refinem outliers command, all the text files are created, however the plots are not. Here is the log ``` [2018-03-05 11:42:41] INFO: RefineM v0.0.23 [2018-03-05...

michoug

--cov_corr value

1

Hi, I'm using RefineM with my genomes and 24 samples. In the readme, it is suggested that: "If you have more than 6 data point (i.e. BAM files) comprising your...

palomo11

This would be helpful for improve completeness and potentially linking in 16S fragments.

donovan-h-parks

It appears that the percentage of genes assigned to different taxa are currently incorrect in the majority of tables. The Krona plots appear correct and the genes are classified correctly,...

donovan-h-parks

Taxonomic profiling of contigs and identification of scaffolds with divergent taxonomic classifications would benefit from having reference databases with Eukaryotic organisms. The human genome could be added to identify this...

donovan-h-parks