yujiehu0823
commented
3 years ago I have the same issue with Prokka v1.14.6. Anybody who can tell me why?
Running: cat PROKKA_08222021/PROKKA_08222021.IS.tmp.12440.faa | parallel --gnu --plain -j 4 --block 2321 --recstart '>' --pipe blastp -query - -db /home/huyujie/miniconda3/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_08222021/PROKKA_08222021.IS.tmp.12440.blast 2> /dev/null
Could not run command: cat PROKKA_08222021/PROKKA_08222021.IS.tmp.12440.faa | parallel --gnu --plain -j 4 --block 2321 --recstart '>' --pipe blastp -query - -db /home/huyujie/miniconda3/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > PROKKA_08222021/PROKKA_08222021.IS.tmp.12440.blast 2> /dev/null
juliadouglasf
We are trying to install and run prokka in our Linux system but we have plenty of errors. After solving some problems with conda and perl versions we get this error message:
Could not run command: cat prokka_results_file\/prokka_results_file.IS.tmp.10227.faa | parallel --gnu --plain -j 8 --block 78751 --recstart '>' --pipe blastp -query - -db /programas/anaconda/v3-2020.11/envs/ucm03/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka_results_file\/prokka_results_file.IS.tmp.10227.blast 2> /dev/null
We have looked for some information and looks as a problem with the prokka database.
https://www.biostars.org/p/417712/
We have installed prokka 1.14 and blast 2.9 version.
If possible, we would like to know what are we doing wrong, because prokka was one of our basic tools in our laboratory.
Thank you for all the information you can supply,
Alonso.