Setup of prokka databases
I'm trying to set up the databases for use with IMP. I write the command $impy init with the output:
[x] Found IMP docker-r3lab.uni.lu/imp/imp 1.4.1
IMP image found
Executing IMP command:
docker run --rm --name home_adam_Desktop_imp_db -v /home/adam/imp-db:/home/imp/databases -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL_GROUP_ID=`id -g $USER`" docker-r3lab.uni.lu/imp/imp:1.4.1 snakemake -s /home/imp/code/rules/ini/init
usermod: no changes
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 ALL
1 prokka_databases
2
rule prokka_databases:
output: cm/Bacteria.i1i, genus/Staphylococcus.phr, hmm/CLUSTERS.hmm.h3f, kingdom/Archaea/sprot.phr, hmm/essentials_genes.hmm
Softlinking /usr/bin/../db to /home/imp/databases
--2018-05-02 15:49:50-- https://webdav-r3lab.uni.lu/public/R3lab/IMP/prokka-1.11.tar.gz
Resolving webdav-r3lab.uni.lu (webdav-r3lab.uni.lu)... failed: Name or service not known.
wget: unable to resolve host address 'webdav-r3lab.uni.lu'
Error in job prokka_databases while creating output files cm/Bacteria.i1i, genus/Staphylococcus.phr, hmm/CLUSTERS.hmm.h3f, kingdom/Archaea/sprot.phr, hmm/essentials_genes.hmm.
RuleException:
CalledProcessError in line 110 of /home/imp/code/rules/ini/databases.rules:
Command '
### prokka by default will look databases where is located the binary.
### we have to softlink to put the binary somewhere and the databases somewhere else.
### the author don't want to add an option to locate the database.
if [[ "/home/imp/databases" = /* ]]
then
PP=/home/imp/databases;
else
PP=$PWD//home/imp/databases;
fi
cd $(dirname $(which prokka))/.. && ln -fs $PP db
echo "Softlinking $(dirname $(which prokka))/../db to $PP"
TMPDIR=$(mktemp -d -t "XXXXXX")
wget https://webdav-r3lab.uni.lu/public/R3lab/IMP/prokka-1.11.tar.gz --no-check-certificate -O $TMPDIR/prokka.tgz
tar -xzf $TMPDIR/prokka.tgz --strip-components=1 -C $TMPDIR
mkdir -p /home/imp/databases
cp -r $TMPDIR/db/* /home/imp/databases/.
rm -rf $TMPDIR
wget https://webdav-r3lab.uni.lu/public/R3lab/IMP/essential.hmm --no-check-certificate -O /home/imp/databases/hmm/essentials_genes.hmm
prokka --setupdb
' returned non-zero exit status 4
File "/usr/lib/python3.4/concurrent/futures/thread.py", line 54, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message
I have had issues downlaoding the other databases too but managed to get around that using the --enter command but the prokka still will not work.
Adam