Closed fedeserral closed 3 years ago
Hi, I am trying to run prokka with docker but it doesn´t work.
When I run this commmand:
docker run -v $PWD:/data staphb/prokka:latest prokka --compliant --locustag HP27 --genus Klebsiella --species pneumoniae --kingdom Bacteria --gcode 11 --proteins Klebsiella_pneumoniae_taxonomy_570.fasta --outdir HP27_anotacion HP27_Klebsiella_pneumoniae_careful_adapter.fasta
I have the following error: could not run command: cat hp27_anotacion\/prokka_03022021.proteins.tmp.1.faa | parallel --gnu --plain -j 4 --block 210342 --recstart '>' --pipe blastp -query - -db hp27_anotacion/proteins -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > hp27_anotacion\/prokka_03022021.proteins.tmp.1.blast 2> /dev/null
can you help me, please?
thank you!
Hi, I am trying to run prokka with docker but it doesn´t work.
When I run this commmand:
docker run -v $PWD:/data staphb/prokka:latest prokka --compliant --locustag HP27 --genus Klebsiella --species pneumoniae --kingdom Bacteria --gcode 11 --proteins Klebsiella_pneumoniae_taxonomy_570.fasta --outdir HP27_anotacion HP27_Klebsiella_pneumoniae_careful_adapter.fasta
I have the following error: could not run command: cat hp27_anotacion\/prokka_03022021.proteins.tmp.1.faa | parallel --gnu --plain -j 4 --block 210342 --recstart '>' --pipe blastp -query - -db hp27_anotacion/proteins -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > hp27_anotacion\/prokka_03022021.proteins.tmp.1.blast 2> /dev/null
can you help me, please?
thank you!