DRAM

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Database download interrupted

3

An error occurred during the database download process, is there anyone know how to fix it? /data5/baidefeng/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:126: UserWarning: Database does not exist at path None warnings.warn("Database does not exist at...

baidefeng

### Description of the bug strand and e-value column have the headers backwards ### System information DRAM v2 beta9 and below ### Command used and terminal output ```console ``` ###...

madeline-scyphers

The NF code doesn't have a testing suite should. https://github.com/nf-core and https://nf-co.re/docs/guidelines/pipelines/recommendations/testing has some good resources on testing NF. We might want to add nf-core as as dev dependency. nf-core/nf-core...

madeline-scyphers

methylotrophy_distillate tsv exists, just need to add flag to enable

madeline-scyphers

downloading the databases

3

Hi, I want to run DRAMv2 on our HPC, but I'm having trouble downloading data through globus. Since my institute is not in the list, I signed up with my...

vdejager

It can't find the files to combine (they reside in the pipelene's ```work``` dir). Adding ```runOptions = '--bind '``` to ```singularity { }``` doesn't help (because of ```singularity.autoMounts = true```?)...

stas-malavin

As the devs have stated that they will not further maintain version 1, I am posting here my collection of fixes and tips that enabled me to use v1.5 including...

captaindet

problem with the combine_annotations step

2

Hi! I am trying to run DRAM2 on an HPC cluster using the singularity_slurm profile. The COMBINE_ANNOTATIONS step fails because the file .._sql_formatted_viral_hits.csv created at the previous stage SQL_VIRAL cannot...

ssvassiliev

Question about DRAM-v output

2

Hi, I have run DRAM-v on Virsorter2 processed sequences and got amg_summary.tsv. In that output file, AMGs are listed, so to say, in two groups: some have TRUE in the...

deminatanja

% conda env create -f environment.yaml -n DRAM Channels: - conda-forge - bioconda - defaults Platform: osx-arm64 Collecting package metadata (repodata.json): done Solving environment: failed PackagesNotFoundError: The following packages are...

jarojasva