impy run failing when trying to update tbl2asn
When running the pipeline with:
impy run -m input/MG.R1.fq -m input/MG.R2.fq -o outputdir --single-omics
The pipeline will reach step 12 and then fail with this error:
12 of 38 steps (32%) done
rule update_tbl2asn:
output: Analysis/tbl2asn.updated
[tbl2asn] This copy of tbl2asn is more than a year old. Please download the current version.
--2017-05-30 14:06:22-- ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
=> '/tmp/tbl2asn.gz'
Resolving ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)... 130.14.250.12, 2607:f220:41e:250::10
Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|130.14.250.12|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /toolbox/ncbi_tools/converters/by_program/tbl2asn ... done.
==> SIZE linux64.tbl2asn.gz ... 5342401
==> PASV ... done. ==> RETR linux64.tbl2asn.gz ... done.
Length: 5342401 (5.1M) (unauthoritative)
017-05-30 14:06:32 (954 KB/s) - '/tmp/tbl2asn.gz' saved [5342401]
mv: cannot move '/tmp/tbl2asn' to '/usr/bin/tbl2asn': Permission denied
Error in job update_tbl2asn while creating output file Analysis/tbl2asn.updated.
RuleException:
CalledProcessError in line 46 of /home/imp/code/rules/Analysis/prokka.rule:
Command '
OUT=$(tbl2asn -hp /tmp 2>&1)
echo $OUT
if [[ "$OUT" =~ "copy of tbl2asn is more than a year old" ]]; then
wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz -O /tmp/tbl2asn.gz
gzip -f -d /tmp/tbl2asn.gz
chmod +x /tmp/tbl2asn
mv /tmp/tbl2asn /usr/bin
fi
' returned non-zero exit status 1
File "/usr/lib/python3.4/concurrent/futures/thread.py", line 54, in run
Will exit after finishing currently running jobs.
Hope you can help me with this issue!