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tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor
GNU General Public License v3.0
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barrnap doesn't create any output #61

Open neelam19051 opened 2 years ago

neelam19051 commented 2 years ago

Hi, I am using barrnap for 16s rRNA extraction and it show me this result without creating any output. Tseemann sir i am big fan of you. First of all its great tool, will you please tell me how to use barrnap of >400 complete genome .

This is barrnap 0.9 [barrnap] Written by Torsten Seemann [barrnap] Obtained from https://github.com/tseemann/barrnap [barrnap] Detected operating system: linux [barrnap] Adding /home/bvs/neelam/barrnap/bin/../binaries/linux to end of PATH [barrnap] Checking for dependencies: [barrnap] Found nhmmer - /home/bvs/neelam/barrnap/bin/../binaries/linux/nhmmer [barrnap] Found bedtools - /home/bvs/neelam/bedtools2/bin/bedtools [barrnap] Will use 96 threads [barrnap] Setting evalue cutoff to 1e-06 [barrnap] Will tag genes < 0.8 of expected length. [barrnap] Will reject genes < 0.25 of expected length. [barrnap] Using database: /home/bvs/neelam/barrnap/bin/../db/bac.hmm [barrnap] Copying STDIN to a temporary file: /tmp/ZMQNSyGJ92 [barrnap] Scanning /tmp/ZMQNSyGJ92 for bac rRNA genes... please wait [barrnap] Command: nhmmer --cpu 96 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/home/bvs/neelam/barrnap/bin/../db/bac.hmm' '/tmp/ZMQNSyGJ92' [barrnap] Found: 16S_rRNA CP080286.1 L=1531/1585 1978676..1980206 + 16S ribosomal RNA [barrnap] Found: 16S_rRNA CP080286.1 L=1531/1585 248408..249938 - 16S ribosomal RNA [barrnap] Found: 16S_rRNA CP080286.1 L=1531/1585 1020190..1021720 - 16S ribosomal RNA [barrnap] Found: 16S_rRNA CP080286.1 L=1530/1585 6068907..6070436 - 16S ribosomal RNA [barrnap] Found: 23S_rRNA CP080286.1 L=2888/3232 1016830..1019717 - 23S ribosomal RNA [barrnap] Found: 23S_rRNA CP080286.1 L=2888/3232 1980680..1983567 + 23S ribosomal RNA [barrnap] Found: 23S_rRNA CP080286.1 L=2888/3232 245047..247934 - 23S ribosomal RNA [barrnap] Found: 23S_rRNA CP080286.1 L=2888/3232 6065546..6068433 - 23S ribosomal RNA [barrnap] Found: 5S_rRNA CP080286.1 L=110/119 1983714..1983823 + 5S ribosomal RNA [barrnap] Found: 5S_rRNA CP080286.1 L=110/119 244791..244900 - 5S ribosomal RNA [barrnap] Found: 5S_rRNA CP080286.1 L=110/119 1016574..1016683 - 5S ribosomal RNA [barrnap] Found: 5S_rRNA CP080286.1 L=110/119 6065290..6065399 - 5S ribosomal RNA [barrnap] Found 12 ribosomal RNA features. [barrnap] Sorting features and outputting GFF3... [barrnap] Writing hit sequences to: output_rrna.fna [barrnap] Running: bedtools getfasta -s -name+ -fo 'output_rrna.fna' -fi '/tmp/ZMQNSyGJ92' -bed '/tmp/PM4zayBzOc' index file /tmp/ZMQNSyGJ92.fai not found, generating... [barrnap] Done.

Thank you!