Rachelmarty20
commented
1 year ago yazbeck, I am having the same issue. Have you been able to resolve this? Thanks!
Open yazbeck opened 3 years ago
Rachelmarty20
commented
1 year ago yazbeck, I am having the same issue. Have you been able to resolve this? Thanks!
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: GOSUVERSION=1.10 =/usr/bin/env
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