DRAM

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DRAM-v : Extraction of flag information for manual annotation?

1

Hi, I have obtained multiple viral sequences identified by several tools. Now I want to annotate AMGs manually based on KEGG database. According to DRAM-v, several flags are designated to...

ChenTianYi99

Set up databases in one directory in server and want to use them in another directory/new session

2

Hi, thanks in advanced. I am trying to run DRAM in a server and the databases had to be set up in a shared directory by another user because of...

nuriaher

Using DRAM to distill annotations from alternative annotation pipelines

3

Hello I was wondering if it is possible to use DRAM's distill annotations on annotations done outside of DRAM. I am working with soil metagenomes which 1) want to use...

ChristopherBurgess-USDA

AttributeError: 'NoneType' object has no attribute 'split'

2

Hello develloper, i am getting the following error with dram.py annotate. I verified all my database and looks ok. Any idea about this: AttributeError: 'NoneType' object has no attribute 'split'...

ayixon

DRAM-v annotations.tsv columns change

1

Hello, I have used DRAM-v annotate several times (same settings), but I noticed that the columns in the annotations.tsv file change sometimes. The position of the columns 'pfam_hits', 'cazy_hits', vogdb_description',...

cdebuck

hmmsearch not parallelized

3

dear DRAM team, I found that the hmmsearch is really slow and ran just in 2 threads but I have 200 genomes to search. Would that be possible to make...

jianshu93

DRAM on viral contigs instead of DRAM-v

2

Hi Michael, First, thank you for developing this nice tool ! I'm writing this message to make sure what i'm doing is correct or not and get some your advice....

miasungeunlee

Suggestion: Decouple DRAM-v from VirSorter Requirement

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>When you ran `DRAM-v.py` did you provide the VIRSorter affi contigs tab file? Or did you not provide anything for the `-v` flag? If you didn't provide that then you...

btemperton

Peptidase database

3

Hello, I install DRAM using conda recently. When I run the annotate command, it shows the error: DRAM.py annotate -i 'test/*.fna' -o annotation --threads 10 2 fastas found 2021-02-16 11:54:54.257147:...

VictorBorin

DRAM.py error message for tRNAscan-SE

2

Hello, I put the following code in: DRAM.py annotate --min_contig_size 1000 --threads 28 -i /fs/ess/PAS1802/Audra/MicEuk_gDNA_optimization/sequencing_run3/augustus/21BE/21BE-1000.fasta -o /fs/ess/PAS1802/Audra/MicEuk_gDNA_optimization/sequencing_run3/DRAM/21BE-annotation I would also say that I previously ran this on another file and...

Audra-Leigh