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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Fails at blast step? #559

Open raw937 opened 3 years ago

raw937 commented 3 years ago

Hello,

It continues to fail at the blastp step. Any thoughts? cat \/projects\/raw_lab\/Cerberus\/data\/prokka_results_RW1\/\/RW1.IS.tmp.30508.faa | parallel --gnu --plain -j 8 --block 6121 --recstart '>' --pipe blastp -query - -db /users/taouk/.conda/envs/cerberus_env/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/projects\/raw_lab\/Cerberus\/data\/prokka_results_RW1\/\/RW1.IS.tmp.30508.blast 2> /dev/null

many thanks, Rick

kapsakcj commented 3 years ago

If you remove the this bit 2> /dev/null from the end of that long one-liner, and re-run it manually, you should be able to see the error message that is spit out. Should give you a better idea what went wrong