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Hi!
I just tried a new clean set up of cenote-taker2, and I get this error:
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Aligning provided reads to contigs over cutoff to determine coverage.
time update: making bowtie2 indices 01-25…
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cp: ‘/home/users/s/saini7/scratch/MS3/Cenote-Taker2/dummy_template.sbt’ and ‘/home/users/s/saini7/scratch/MS3/Cenote-Taker2/dummy_template.sbt’ are the same file
tail: cannot open ‘viruses_am_ct_9m25…
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Hello Mike,
I'm using Cenote-Taker2 to identify viral contig and detect certain virus species. I've been working with your test data in order to see if I could get your tool working on the server b…
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Hello, I've tried both importaning known viral contigs for annotation only, and the original metagenome from which they came for virus prediction and annotation, and neither time are there any viral a…
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Hi Mike,
I'm having difficulties reproducing your test contig example. For instance, annotation for end features is missing for the contigs. Could you please provide what the output should look lik…
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Dear CT2 team,
I had a problem with "PLEASE REQUEST AN API_KEY FROM NCBI" when running CT2, it seems that casused by eutils.
does CT2 parse the taxonomic rank information by this way? How could I f…
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Dear CT2 team,
I get the contig taxonomic classification from ```*blastx.out```, for example:
> contig1 Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviri…
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I want to annotate a sequence that I am confident of. It is a densovirus, with ITRs that have internal repeat structure. I do not want cenote-take to reorientate or edit the sequence before annotating…
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Hi Mike,
I just wanted to clarify if I'm expected to see some phage contigs even if I set phage pruning to True. I read your notes (https://github.com/mtisza1/Cenote-Taker2/wiki#notes-on-virus-taxono…
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On running:
`python ~/apps/CenoteTaker2/run_cenote-taker2.py -c $S.scaffolds.fasta --srr_number $S --known_strains blast_knowns --blastn_db /data/BLAST_databases/nt --reads1 $S/$S.trim.1.fq.gz --r…