Error with tbl2asn when running with testdata
I have permission issues inside of the docker container and tbl2asn cannot be moved to /usr/bin
. Any ideas how to fix this?
$ impy -a idba --threads 24 --memtotal 200 --memcore 200 run -m testdata/raw_data/metagenomics/mg.r1.fq -m testdata/raw_data/metagenomics/mg.r2.fq -t testdata/raw_data/metatranscriptomics/mt.r1.fq -t testdata/raw_data/metatranscriptomics/mt.r2.fq -o testdata/output | tee testdata/log.txt
(...)
22 of 58 steps (38%)
done
[2046/5879]
rule update_tbl2asn:
output: Analysis/tbl2asn.updated
[tbl2asn] This copy of tbl2asn is more than a year old. Please
download the current version.
--2018-02-09 10:12:02--
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)... 130.14.250.10,
2607:f220:41e:250::7
Connecting to ftp.ncbi.nih.gov (ftp.ncbi.nih.gov)|130.14.250.10|: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 ... 5342980
==> PASV ... done. ==> RETR linux64.tbl2asn.gz ... done.
Length: 5342980 (5.1M) (unauthoritative)
0K .......... .......... .......... .......... .......... 0%
158K 33s
50K .......... .......... .......... .......... .......... 1%
460K 22s
100K .......... .......... .......... .......... .......... 2%
45.2M 14
(...)
5100K .......... .......... .......... .......... .......... 98%
72.7M 0s
5150K .......... .......... .......... .......... .......... 99%
67.5M 0s
5200K .......... ....... 100%
69.7M=1.1s
2018-02-09 10:12:04 (4.69 MB/s) - '/tmp/tbl2asn.gz' saved [5342980]
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.
/home/imp/data/metagenomics/mg.r1.fq => Preprocessing/mg.r1.fq
/home/imp/data/metagenomics/mg.r2.fq => Preprocessing/mg.r2.fq
/home/imp/data/metatranscriptomics/mt.r1.fq => Preprocessing/mt.r1.fq
/home/imp/data/metatranscriptomics/mt.r2.fq => Preprocessing/mt.r2.fq
Exiting because a job execution failed. Look above for error message