DRAM

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kofam non-zero exit status

3

Hello, I've installed and set up DRAM via bioconda and print_config seems to show databases are set up correctly. However, when I try and run DRAM I get the following...

theo-llewellyn

Custom database

7

Hi, On the main github page it says DRAM can also use custom user databases. Is it explained somewhere how to do this? I have fasta files containing protein sequences...

slambrechts

Hi, I see that minimum bitScore of a search to retain hits is 60 by default. I am working with custom databases and I notice in the `annotations.tsv` file that...

slambrechts

Strainer filtering by fastas or scaffolds

1

Hello! I ran DRAM on a bunch of isolate genomes, and now the "gene.faa" file contains all the predicted proteins merged. I wanted to split them back by genome using...

geboro

How to add classification for each genome in the html heatmap

3

Hello, I am wondering how to add classification information for each genome like in the NAR paper in the html heatmap output. Thanks, Jianshu

jianshu93

DataFrame is highly fragmented warning

2

Hi All, I was running the MAG annotation process and got the following warning: `0:09:51.057434: Getting reverse best hits from peptidase DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:120: PerformanceWarning: DataFrame is highly fragmented. This is usually...

smdabdoub

subprocess.CalledProcessError: mmseqs

7

Hello, I am receiving a subprocess.CalledProcessError after running the following code: DRAM.py annotate -i '/scratch1/flores5/GF_fastq/02_ASSEMBLE/contigs/*.fa' -o annotation 33 fastas found 2021-07-06 00:54:28.962181: Annotation started 0:00:00.022096: Retrieved database locations and descriptions...

cflores10

Is there a way to "restart" DRAM after it stops after an error ?

9

Hello, I launch DRAM on 300 MAG and DRAM stops after about 200 MAG :-( (see error message below). Is there a way to "restart" DRAM from where he stops...

francis29029

DRAM_setup.py error

1

greetings, having some trouble setting up the databases required for DRAM. Trying this through an SGE submission queue. I've attached my submission (DRAM_setup.sh) and the output log (DRAM_setup.log). Any assistance...

TonyMane

DRAM setup.py errror: TypeError: not all arguments converted during string formatting

1

Hi Mike, I tried to solve the last error and modified the download url, but there appear other errors , please see below (viral-id-sop) [huqy@login1 ~]$ DRAM-setup.py prepare_databases --skip_uniref --output_dir...

Edward-Tristan