Description
Hi,
I am trying to run the dkfz/embl workflow. I tried several ways and none is working. I will start with this one for now:
I tried this:
dockstore tool launch --local-entry Dockstore.cwl --json Dockstore-BTCA-SG.json
The first error was: [pool-2-thread-1] ERROR io.dockstore.common.FileProvisioning - Could not copy run1_63/f0e0d978-3e32-4444-a07a-26049b2594e6.embl-delly_1-0-0-preFilter.20150805.somatic.sv.bedpe.txt to
--------------------------------------------------------------
I changed the files into the local files to make sure it is running which started at least to run. However, then I got SGE error. Here I paste the tail of the run and the head of the error:
PATH=/ansible/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PWD=/mzcPqR
SHLVL=1
HOME=/mzcPqR
PYTHONPATH=/ansible/lib:
GOSU_VERSION=1.10
_=/usr/bin/env
- gosu root sed -i s/placeholder/a5d5e3610d19/g /etc/ansible/hosts
- cat /etc/ansible/hosts
[master]
a5d5e3610d19
[all_groups:children]
master - gosu root chmod -R a+wrx /root
- gosu root ansible-playbook /root/docker-start.yml -c local
PLAY [master] *****************************************************************
GATHERING FACTS ***************************************************************
ok: [a5d5e3610d19]
TASK: [grid-engine | SGE | Install gridengine-client] *************************
failed: [a5d5e3610d19] => {"failed": true, "parsed": false}
invalid output was: Traceback (most recent call last):
File "/root/.ansible/tmp/ansible-tmp-1630411341.08-166582691979749/apt", line 1763, in
main()
File "/root/.ansible/tmp/ansible-tmp-1630411341.08-166582691979749/apt", line 492, in main
cache.update()
File "/usr/lib/python2.7/dist-packages/apt/deprecation.py", line 98, in deprecated_function
return func(*args, **kwds)
File "/usr/lib/python2.7/dist-packages/apt/cache.py", line 441, in update
raise FetchFailedException(e)
I hope I can get answer soon as it is really a bottleneck for my project.
Thanks in advance