DRAM
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WrightonLabCSU
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
I run: I run: ``` DRAM-setup.py prepare_databases --output_dir {output.dbdir} --threads {threads} --verbose --skip_uniref ``` and get the error. No such file or directory: refseq_viral.20220909.mmsdb_h ``` 2:04:29.500055: DRAM databases and forms...
Hi there, I've been tried to annotate contigs assembled from high-coverage fastq files for a while using different DRAM versions (1.3.5 and 1.4.0.rc3), trusting the memory requirements specified on DRAM...
Hello, I got the amg summary file, but there are some genes identified as AMG (score < 4) but without gene_id, gene_description, category, header, subheader, and module. Why are these...
Dear Team, We are facing error with the dram database download issue and getting the traceback ``` File "/scratch/gencore/.eb/2.0/software/dram/1.3.5/bin/DRAM-setup.py", line 158, in args.func(**args_dict) File "/scratch/gencore/.eb/2.0/software/dram/1.3.5/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 374, in prepare_databases db_handler.populate_description_db(output_dbs['description_db_loc'],...
Hello I just installed DRAM with conda on a fresh miniconda3 install on two independent HPC's After running the ```DRAM-setup.py prepare_databases --output_dir DRAM_data``` step, I get the following error on...
 A mistake is reported a when I used this software, so if this has run correctly ? thanks~! output: amg_summary.tsv、product.html、vMAG_stats.tsv.
https://github.com/WrightonLabCSU/DRAM/blob/a5f225718c5ff312ec8ccaefbb61daaa12452705/scripts/DRAM.py#L35 Shouldn't the -o 'output' option be required? If I omit it an exception is thrown because the default -o parameter is NoneType ``` (DRAM) cmkobel@login-5 ~/userwork/dram $ DRAM.py annotate...
Hello Thanks for maintaining DRAM In the [wiki under section 3a DRAM distill](https://github.com/WrightonLabCSU/DRAM/wiki/3a.-Running-DRAM#dram-distill) there is a link to an example https://shafferm.github.io/examples/dram/ But that link goes to a 404 page on...
The DRAM database config file is restricted from users - it is written and maintained fully within the DRAM code (e.g., https://github.com/WrightonLabCSU/DRAM/blob/a5f225718c5ff312ec8ccaefbb61daaa12452705/mag_annotator/database_handler.py#L28-L33). Storing / maintaining the config file in the...
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Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes