DRAM

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Hello, I am trying to run DRAM analysis: `DRAM.py annotate -i 'Prevotella_data/prevotellas_GR25.fa' -o annotation` But I always get stuck in this error: FileNotFoundError: [Errno 2] No such file or directory:...

tabaresr

cp12 identification

1

In my results I have the genes that go with cp12 (calvin cycle inhibitor) but I don't see cp12 in the annotations. However, I do see it in the virsorter...

Drob84761

Can we delete the database files after the processing of the databases is done?

2

Hi @rmFlynn ! After the processing of the databases can I delete these database files listed below? 16GB Pfam-A.full.gz 2GB kofam_profiles.tar.gz 42GB uniref90.fasta.gz 1GB viral.merged.protein.faa.gz 1GB kofam_ko_list.tsv.gz 1GB merops_peptidases_nr.faa 1GB...

saras224

Hi @rmFlynn @ileleiwi @rdenise I ran DRAM for 9 MAGs and it gave me an **error that the object has no attribute query**, can you please go through the log...

saras224

Hi, My lab's been using DRAM for a little bit and it has been incredibly helpful. I was just wondering if there was anyway to reorganize the heatmap based on...

robcli

I performed the following command and came across an issue as below. DRAM-v.py annotate -i vs2-pass2/for-dramv/final-viral-combined-for-dramv.fa -v vs2-pass2/for-dramv/viral-affi-contigs-for-dramv.tab -o dramv-annotate --skip_trnascan --threads 32 . Could you help on this matter?...

Altay88

Error while annotating MAGs

1

Hi @mrobbert While running the DRAM annotation command I encountered this error:  Please help me resolve the error so that I can proceed further. Thanks in...

saras224

155796 killed

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Here is my command, `DRAM-setup.py prepare_databases --output_dir DRAM` And this is de report error, ``` /beegfs/home/syl/anaconda3/envs/vs2/lib/python3.10/site-packages/mag_annotator/database_handler.py:166: UserWarning: Database does not exist at path None warnings.warn( /beegfs/home/syl/anaconda3/envs/vs2/lib/python3.10/site-packages/mag_annotator/database_handler.py:123: UserWarning: Database does not...

TKsh6

Hi! @rmFlynn I have downloaded database files but I do not know how to provide database location to the database_handler.py script. When I run the analysis I get the following...

saras224

VOG annotations Description_Db_Updated: Unknown, or Never

1

After a fresh run of prepare_databases with no errors, when I have DRAM print settings, I get the following: ``` VOG annotations: Description_Db_Updated: Unknown, or Never Citation: J. Thannesberger, H.-J....

smdabdoub