Closed mattbawn closed 4 years ago
HI Matt,
several things are to consider here:
speclist
file from UniProt; this is likely a problem of network access, see #22 .I believe the later errors in Python scripts follw from that
pantagruel -i database/environ_pantagruel_database.sh TASK5 TASK6 TASK7 TASK8 TASK9
the job failed with no error; this is because pantagruel does not recognise the tasks if you call them TASK5
, etc. the correct syntax is using digits associated to tasks:
pantagruel -i database/environ_pantagruel_database.sh 5 6 7 8 9
or using the task names e.g. core genetrees reconciliations
; see manual here
By the way, is this error about interproscan at all ? after installing Interproscan, you seem to have run the task 3; interproscan annotation is task 4. can you update the thread regarding the interproscan error when you have properly tested task 4 please? Note it is not an error really, just a message saying that you can't use that (facultative!) task when you don't have the underlying software.
Also, you got me interested saying you have a singularity container set up for pantagruel. Havve you used the Dockerfile set up by @pveber here: https://github.com/flass/pantagruel/blob/master/etc/Dockerfile ?
or did you set up your own? is it it a proper Singularity recipe? if the latter, could you please circulate the recipe, as it would be very valuable to other users - and myself, as i admit I could not find the time to get started on this, and I would really appreciate having a basis to work upon for releasing some stable installation (finally!)
The Dockerfile has now been fully tested and the image generated from it support properly the running of Pantagruel (except task 04 that needs InterProScan installed on the side). This is all documented in the INSTALL doc. A static docker image will soon be released on dockerhub.
Hi Florent,
To bypass the previous issue. I ran Pantagruel without providing annotation and got as far as
04
.with the error:
InterproScan was not found on this machine: cannot run this (facultative) task of Pantagruel pipeline; exit now
I tried to bypass the
InterproScan
step by running:pantagruel -i database/environ_pantagruel_database.sh TASK5 TASK6 TASK7 TASK8 TASK9
but the job failed with no errors.
We then installed
InterproScan
in the pantagruel singularity containerbut I again got:
Can you please tell me how Pantagruel calls InterproScan?
Thanks,
Matt