Closed Thexiyang closed 4 years ago
Hello,
Can you send me the results of running DRAM-setup.py print_config
. It looks to me like something is wrong with your amg_database.tsv
file which is listed as the AMG database
. If the location of AMG database
is set then can you look at that file and see if there is a header called KO
in that file.
Indeed. It is the issue of AMG database. The file is not right. I cannot use wget
to download 'https://raw.githubusercontent.com' due to the collection issue, so I changed to link 'https://github.com/shafferm/DRAM/blob/master/data/amg_database.tsv'. However, the produced AMG file is totally different. Strange. Could you also add the flag for AMG database location in DRAM-setup.py prepare_databases
, like others, e.g. --etc_module_database_loc
for ETC_MODULE_DATABASE_LOC
? Thanks!
Sorry for the late reply. I was on vacation last week.
I think that using wget
on the page directly will get the html for that page and not the raw file. Did you use this command to get the file from raw wget https://raw.githubusercontent.com/shafferm/DRAM/master/data/amg_database.tsv
.
--amg_database
has been added and will be included in a new release. Thanks for catching that! Also if you want to update the DRAM tsv files automatically and separate from the databases then you can use the command DRAM-setupy.py update_dram_forms --output_dir {your_DRAM_db_folder}
.
Thanks for the very nice tool! I performed the following command and came across an issue as below.
DRAM-v.py annotate -i viral.fasta -v VIRSorter_affi-contigs.tab -o test-cat1-annotation --min_contig_size 1000 --use_uniref --skip_trnascan --verbose --threads 20
Could you help on this matter? Thanks!