Lukas Klein

Hi, While this would be really cool, it is probably not possible for the same reasons a conda package isn't possible. Probably now to late for that, but I wrote...

Hi, I don't know what will happen with this project in the future, but I will provide you with a fix. If I can't get it working within metaerg, I...

Ok, I found the problem. The `gene2pathways` hash(map) is always empty, the predictKegg/Metacyc functions have a local variable of the same name. Only the master.tsv file uses this hash. The...

Good morning, The MetaCyc pathways don't really have names, at least easily available. Two ideas: 1) The hack: Instead of `kegg_pathway_id` use `kegg_pathway_name` in `output_reports.pl` 2) R with minpath data...

Hi, Hopefully this helps: The depth file is read here: https://github.com/xiaoli-dong/metaerg/blob/50708247159ad9ed6c05cfa3f75cbdd1d127b8c4/bin/metaerg.pl#L666-L702 The file format was described already in [this issue](https://github.com/xiaoli-dong/metaerg/issues/16#issuecomment-583819438). For every contig the `totalAvgDepth` and the sample names as...

This line only performs a SELECT query, therefore the database is only locked against writing with a shared lock. There seems to be an different error message for locked databases...

No, if you look for usages of the `sample2depth` and `mdepth_values` values in the search and calculated values the depth values are just added together for each step.

Hi, For a recent paper and my bachelor thesis we used MetaErg and other annotation tools to annotate anaerobic digestion metagenomes from biogas plants and I have to say that...

MetaErg also adds the FOAM and TIGRFAM KO hits, wasn't sure, but just found it in the source code.

Hi, Thanks for sharing Metasanity, will have a look. Regarding the maps, maybe MetaErg only uses a subset of annotated KOs? Will search for that in the source.