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mtisza1 / Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
MIT License
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Contigs in the CONTIG_SUMMARY.tsv have neither ".rotate.fasta" nor ".tax_guide.blastx.out" #32

Closed cn6659 closed 1 year ago

cn6659 commented 2 years ago

Hi,

In the CONTIG_SUMMARY.tsv, ERR1301564_a1_ct40759 exists as below.

ERR1301564_k79_72066 ERR1301564_a1_ct40759 Unknown DTR 1611 Prodigal 0 none BLASTN not conducted

But, in the DTR_contigs_with_viral_domain, ERR1301564_a1_ct40759 has only fna file.

**ls ERR1301564_a1_ct4075*** ERR1301564_a1_ct40759.fna

Success Case has .rotate.fasta, .tax_guide.blastx.out as well as .fna.

**ls ERR1301564_a1_ct38931*** ERR1301564_a1_ct38931.AA.fasta ERR1301564_a1_ct38931.rotate.fasta ERR1301564_a1_ct38931.trans.fasta ERR1301564_a1_ct38931.fna ERR1301564_a1_ct38931.tax_guide.blastx.out

Why the contig in the CONTIG_SUMMARY.tsv has no .rotate.fasta, .tax_guide.blastx.out?

mtisza1 commented 2 years ago

Hi,

Thanks for bringing up the issue, and I'm sorry for the delayed reply. I was working to update Cenote-Taker 2 to v2.1.5. is your run title (-r) "ERR1301564_a1_ct4075"? If so, it is too long and it is causing problems with some tools in the script.

Run titles "Must be less than 18 characters, using ONLY letters, numbers and underscores (_)"

In v2.1.5, I've made a checkpoint to ensure all run titles are appropriately formatted. You can update your version with the instructions on the README.

If you continue to have issues, please send a log file of the run that gave you problems.

Best,

Mike