ZarulHanifah

Here you go: ``` Processed search databases KEGG db: None KOfam db: /fs03/ie79/db/DRAM_data/kofam_profiles.hmm KOfam KO list: /fs03/ie79/db/DRAM_data/kofam_ko_list.tsv UniRef db: None Pfam db: /fs03/ie79/db/DRAM_data/pfam.mmspro dbCAN db: /fs03/ie79/db/DRAM_data/dbCAN-HMMdb-V9.txt RefSeq Viral db: /fs03/ie79/db/DRAM_data/refseq_viral.20210917.mmsdb...

Amazing! What is the code to plot that? It is much simpler with genbank files, but from the tutorial, it wasn't clear how to start from `GFF.parse()` to get to...

``` fig, ax = plt.subplots() gff_path = "results/ALL_PROKKA/ATCC_13124/ATCC_13124.gff" gff_records = [] with open(gff_path) as in_handle: for rec in GFF.parse(in_handle): gff_records.append(rec) start, end = 0, 5000 record = BiopythonTranslator().translate_record(gff_records[0][start:end]) record.plot(ax= ax)...

Sorry for coming in, just want to ask, does `augur translate` currently assumes that all CDS in the genbank file are forward strand? I am working on orf virus, and...

I can't install it on my device. Some python software installation failure happened.

Hmm, I will try to find the logs later. But just to let you know, I ended up doing the run on another comp. But I did the basecalling on...

Sorry for the late reply, and thank you for the comments. Well, I am pretty sure I still have plenty of space. A slight difference in my setup is that...

I have the same question. Just jumping into this thread

I havent been able to sort this out. I'm preparing a GDrive link with the relevant files...

Thank you very much for the prompt reply! Now I see; so I am familiar with QIIME, but only for the downstream analysis part (For my previous work, I used...