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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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erro:grep: sequin directory/*.fsa: No such file or directory when using latest cenote-Taker2.0.1 #38

Closed xsq2022 closed 1 year ago

xsq2022 commented 1 year ago

Hi Mike, Thank you for Cenote-Taker2! However, I am facing a problem when i run the commond: This is my code: python /media/home/user05/anaconda3/envs/cenote-taker2/bin/run_cenote-taker2.0.1.py --contigs /media/atm1/user05/virome1018/spades_contig/xunyu/XSQ_xunyu.contig.fa --run_title xunyu --template_file /media/home/user05/Cenote-Taker2/dummy_template.sbt --mem 250 --cpu 24 --prune_prophage true

grep: sequin_directory/.fsa: No such file or directory head: cannot open 'sequin_directory/.fsa' for reading: No such file or directory

bioawk: can't open file sequin_directory/.fsa source line number 1 length cat: '.rotate.AA.called_hmmscan.txt': No such file or directory head: cannot open 'no_end_contigs_with_viral_domain/sequin_directory/*.fsa' for reading: No such file or directory

grep: no_end_contigs_with_viral_domain/sequin_directory/.fsa: No such file or directory head: cannot open 'no_end_contigs_with_viral_domain/sequin_directory/.fsa' for reading: No such file or directory

head: cannot open 'no_end_contigs_with_viral_domain/sequin_directory/*.fsa' for reading: No such file or directory

head: cannot open 'no_end_contigs_with_viral_domain/sequin_directory/*.fsa' for reading: No such file or directory

grep: no_end_contigs_with_viral_domain/sequin_directory/.fsa: No such file or directory head: cannot open 'no_end_contigs_with_viral_domain/sequin_directory/.fsa' for reading: No such file or directory

bioawk: can't open file no_end_contigs_with_viral_domain/sequin_directory/*.fsa source line number 1

cat: 'no_end_contigs_with_viral_domain/.AA.hmmscan2.sort.out': No such file or directory head: cannot open 'no_end_contigs_with_viral_domain/.fna' for reading: No such file or directory Summary file made: xunyu.tsv removing ancillary files Looking forward to your reply.

mtisza1 commented 1 year ago

Hi,

Thanks for opening this issue. Before I try to figure out this issue in depth, would it be possible for you to re-install or update Cenote-Taker 2 to version 2.1.5? My guess is that you used the anaconda package, and, unfortunately, I can't provide support for that.

The easiest solution, I believe, would be a re-install following these instructions.

FWIW, my guess is that your input fasta file did not contain any sequences that Cenote-Taker 2 identified hallmark genes in.

Best,

Mike

xsq2022 commented 1 year ago

Thank you very much. I will try it.---- Replied Message ----FromMike @.>Date11/03/2022 05:22 @.> @.**@.>SubjectRe: [mtisza1/Cenote-Taker2] erro:grep: sequin directory/*.fsa: No such file or directory when using latest cenote-Taker2.0.1 (Issue #38) Hi, Thanks for opening this issue. Before I try to figure out this issue in depth, would it be possible for you to re-install or update Cenote-Taker 2 to version 2.1.5? My guess is that you used the anaconda package, and, unfortunately, I can't provide support for that. The easiest solution, I believe, would be a re-install following these instructions. FWIW, my guess is that your input fasta file did not contain any sequences that Cenote-Taker 2 identified hallmark genes in. Best, Mike

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