DRAM

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DRAM_setup not preparing all databases

13

Hi there! Running DRAM using linux bash, not in a conda environment. When I run DRAM_setup normally it only prepares the uniref database file, when I run it with "skip...

etod5987

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

1

Hi, **I used the DRAM in conda environment with some errors. Can you tell me how to fix it, Thanks.** $DRAM-v.py annotate -i /data/liaohp/project1/virus/Virsorter-SOP/all-final--viral-combined-derep.fa -o annotation 2021-08-05 11:15:49.638597: Viral annotation...

hannet91

KeyError: 'K16716' when using DRAM-v.py annotate

3

Hi Michael Thank you for providing a very powerful tool. I got some errors when using DRAM-v.py annotations. **The command was : DRAM-v.py annotate -i BH0-vs2-pass2/for-dramv/final-viral-combined-for-dramv.fa -v BH0-vs2-pass2/for-dramv/viral-affi-contigs-for-dramv.tab -o BH0-dramv-annotate...

shujieH

subprocess.CalledProcessError

5

Hello, We are facing error: "Failed to mmap memory dataSize=80676316565 File=DRAM_data/database_files/pfam.mmsmsa. Error 12." while preparing for database. It is halting with "subprocess.CalledProcessError: Command '['mmseqs', 'msa2profile', 'DRAM_data/database_files/pfam.mmsmsa', 'DRAM_data/database_files/pfam.mmspro', '--match-mode', '1', '--threads',...

ghost

Error message saying fasta location returns no paths

1

Hello, Prior to this, I have been able to use DRAm v 1.0 and 1.2 successfully with no issues. After downloading some genomes in .fa format and trying to run...

dsgregoire

`DRAM` running time

4

Hi, I am racently using DRAMv and follow this protocol `https://www.protocols.io/view/viral-sequence-identification-sop-with-virsorter2-btv8nn9w?step=1`. Could you tell how much time DRAMv will take ? How can I estimate the time?

ZeroDesigner

Is it possible to resume the database preparation step?

5

Hello DRAM developers, I am running database setup without KEGG on a university cluster with 1Tb of memory. The process has been running for over 15 hours, it seems new...

rzhan186

Issue with DRAM-v distill - error with "auxilary score"

1

Hi, I ran the latest dramv on putative vMAGs obtained from both virsorter2 and vibrant, followed by dereplication at 0.99 with CD-HIT to get putative vMAGs. I was hoping to...

aprabhu90

No distillate information found warning

3

Hi, There are too many warnings like the following when I run `DRAM-v.py distill -i annotation/annotations.tsv -o annotation/distilled.` ``` /DRAM/lib/python3.9/site-packages/mag_annotator/summarize_vgfs.py:101: UserWarning: No distillate information found for gene TS03-LD14_NODE_934__full-cat_1_15 warnings.warn("No distillate...

ucassee

only CAZy annotation information in distilled files

4

I appear to be having the same issue as #53 with richly annotated MAGS but only CAZy annotation information in the final distillate. I note the this was solved by...

gruningerrj