failed database download
Hello, I tried to run impy init but I get problems with the downloading of the db.
federico@federico-VirtualBox:~/impyInstall$ impy -d ./imp-db/ init[x] Found IMP docker-r3lab.uni.lu/imp/imp 1.4
IMP image found
Executing IMP command:
docker run --rm --name home_federico_impyInstall_imp_db -v /home/federico/impyInstall/imp-db:/home/imp/databases -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL_GROUP_ID=`id -g $USER`" docker-r3lab.uni.lu/imp/imp:1.4 snakemake -s /home/imp/code/rules/ini/init
usermod: no changes
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 ALL
1 checkm_data
1 filtrering_database_index
1 kegg_information
1 prokka_databases
1 sortmerna_databases
1 sortmerna_databases_index
1 trimmomatic_adapters
8
rule sortmerna_databases:
output: sortmerna/rfam-5.8s-database-id98.fasta, sortmerna/silva-arc-16s-id95.fasta, sortmerna/silva-bac-16s-id90.fasta, sortmerna/silva-euk-18s-id95.fasta, sortmerna/rfam-5s-database-id98.fasta, sortmerna/silva-arc-23s-id98.fasta, sortmerna/silva-bac-23s-id98.fasta, sortmerna/silva-euk-28s-id98.fasta
--2017-02-23 11:11:44-- https://webdav-r3lab.uni.lu/public/R3lab/IMP/sortmerna.2.0.tgz
Resolving webdav-r3lab.uni.lu (webdav-r3lab.uni.lu)... failed: Name or service not known.
wget: unable to resolve host address 'webdav-r3lab.uni.lu'
Error in job sortmerna_databases while creating output files sortmerna/rfam-5.8s-database-id98.fasta, sortmerna/silva-arc-16s-id95.fasta, sortmerna/silva-bac-16s-id90.fasta, sortmerna/silva-euk-18s-id95.fasta, sortmerna/rfam-5s-database-id98.fasta, sortmerna/silva-arc-23s-id98.fasta, sortmerna/silva-bac-23s-id98.fasta, sortmerna/silva-euk-28s-id98.fasta.
RuleException:
CalledProcessError in line 27 of /home/imp/code/rules/ini/databases.rules:
Command '
TMPD=$(mktemp -d -t --tmpdir=/home/imp/output/tmp "XXXXXX")
wget https://webdav-r3lab.uni.lu/public/R3lab/IMP/sortmerna.2.0.tgz --no-check-certificate -O $TMPD/sortmerna.tgz
tar -xzf $TMPD/sortmerna.tgz --strip-components=1 -C $TMPD
mkdir -p sortmerna
mv $TMPD/rRNA_databases/*.fasta sortmerna/.
rm -rf $TMPD
' returned non-zero exit status 4
File "/home/imp/code/rules/ini/databases.rules", line 27, in __rule_sortmerna_databases
File "/usr/lib/python3.4/concurrent/futures/thread.py", line 54, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message
(venv) federico@federico-VirtualBox:~/impyInstall$ cd /home/imp/output/tmp
bash: cd: /home/imp/output/tmp: No such file or directory
(venv) federico@federico-VirtualBox:~/impyInstall$
The problem seems not to be the connection as I can download the files with wget
(venv) federico@federico-VirtualBox:~/impyInstall$ wget https://webdav-r3lab.uni.lu/public/R3lab/IMP/sortmerna.2.0.tgz
--2017-02-23 12:11:26-- https://webdav-r3lab.uni.lu/public/R3lab/IMP/sortmerna.2.0.tgz
Resolving webdav-r3lab.uni.lu (webdav-r3lab.uni.lu)... 10.4.0.57
Connecting to webdav-r3lab.uni.lu (webdav-r3lab.uni.lu)|10.4.0.57|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 16137730 (15M) [application/x-gzip]
Saving to: ‘sortmerna.2.0.tgz’
100%[============================================================>] 16.137.730 11,5MB/s in 1,3s
2017-02-23 12:11:28 (11,5 MB/s) - ‘sortmerna.2.0.tgz’ saved [16137730/16137730]``
Can you help or provide alternative way to get all the files? Thank you