Updating Database: Error with kraken2_add_taxID

[PeterCx]

Hi Nick,

I am still having trouble updating my database with custom MAGs. I run snakemake using the following command and config file: config-update.yaml.txt

snakemake --use-conda --cores 30 --configfile config-update.yaml

I have attached the snakemake log. The issue is around "kraken2_add_taxID". snakemake_log.txt

Firstly it says missing output files (see snipet from log below). But this file is actually present. It simply unzips the file and places in genome directory.

[Sat Jan 28 16:22:48 2023] rule kraken2_add_taxID: input: /workspace/pot/peterc/Equine/Struo2/MAGs/ERR6929713_bin.678.fna.gz output: tmp/db_update_tmp/peterc/Struo2_112566273/db_update/genomes/MAG_1203_Nanosyncoccus.fna log: /workspace/pot/peterc/Equine/Struo2/Output/logs/db_update/kraken2_add_taxID/MAG_1203_Nanosyncoccus.log jobid: 459 benchmark: /workspace/pot/peterc/Equine/Struo2/Output/benchmarks/db_update/kraken2_add_taxID/MAG_1203_Nanosyncoccus.txt reason: Missing output files: tmp/db_update_tmp/peterc/Struo2_112566273/db_update/genomes/MAG_1203_Nanosyncoccus.fna wildcards: sample=MAG_1203_Nanosyncoccus resources: tmpdir=/tmp, time=59, mem_gb_pt=6

Later it is unable to produce the done files as a result and it is doomed from the get go. I have no idea how to solve it so help is appreciated. I have attached all other relevant files which may help diagnose the problem.

names.dmp.txt Sample_Table.txt

Many thanks

Kind regards,

P