Triggered a re-run for everything in galaxyproject/iwc#73 ... we'll need to tune the command a bit so we can run a specific workflow
if you use an older version (not from weg) but the local install version from 2021-10-18 it works
I have installed this one
and you can now run your pangolin with this version instead of latest version from web
but this version does not seem to have Omicron included yet
:(
Uh, really weird cause I got B.1.1.529 annotated with latest from web until Wednesday last week.
Going to dive into changelogs later today.
I guess you saw it, but the tests for pe-wgs-ivar-analysis.ga_0 also started failing at the pangolin step
pangolearn updated to 2021-11-25
constellations updated to v0.0.29
pango-designation updated to v1.2.110
Job stats:
job count min threads max threads
-------------------- ------- ------------- -------------
add_failed_seqs 1 1 1
align_to_reference 1 1 1
all 1 1 1
generate_report 1 1 1
get_constellations 1 1 1
hash_sequence_assign 1 1 1
pangolearn 1 1 1
scorpio 1 1 1
total 8 1 1
Warning: couldn't parse the following string: # nuc:G11287T - ignoring
[Sun Dec 12 17:00:19 2021]
Error in rule get_constellations:
jobid: 7
output: /tmp/tmp3gwbt4h9/get_constellations.txt
shell:
scorpio list --constellations /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.429.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cAY.4.2.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cP.2.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.617.1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.617.2+K417N.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cP.3.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.525.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cA.23.1+E484K.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cBA.2.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.617.3.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.621.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.1.529.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cBA.1_probable.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cA.23.1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cBA.1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cAY.4.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.617.2.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.351.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.427.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.526.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.1.318.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cAV1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cP.1.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cC.37.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.1.7+E484K.json /tmp/tmpqvdc3evd/job_working_directory/000/17/working/datadir/constellations/definitions/cB.1.1.7.json --pangolin > /tmp/tmp3gwbt4h9/get_constellations.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Exiting because a job execution failed. Look above for error message
Yeah, investigating currently, but this multi-component architecture of pangolin doesn't make debugging easy :(
bgruening: could you find out, which version of scorpio the .eu installed pangolin is using? That's the only version info I don't have.
Seems you can run
pangolin --all-versions to find out (I guess we should include that command in the wrapper and print the result so that things are more transparent)
Not sure yet, but this seems like a very good candidate for the problem (scorpio v0.3.15 release notes):
Allows comments in constellation files
The latest from web functionality updates constellations, but not scorpio
Well, yes, upgrading scorpio locally from 0.3.14 to 0.3.15 fixes it.
otoh, cov-lineages/constellations@564121a is the last commit that made it into constellations 0.0.29
otoh, cov-lineages/constellations@564121a is the last commit that made it into constellations 0.0.29
Puh, it's the warning in the output above:
Warning: couldn't parse the following string: # nuc:G11287T - ignoring
This line is in the new
definitions/cBA.1.json and now we only need to find out if it's there on purpose or just a typo.
maybe it works now
However, that strange line will parse as an empty string in scorpio 0.3.15 and I don't believe that's the intention
So I still have hopes that it'll get fixed upstream in constellations, and then things would work again everywhere, not just on .eu
The thing is the warning doesn't happen with 0.3.15 (that's why I imagine nobody noticed what I think is a typo)
I guess scorpio is not pinned in the pangolin package
I'll trigger a new build, that would fix it at least for the container usage
ah, that fix was only applied for version 3.1.17
Can we merge galaxyproject/tools-iuc#4287 ?
So my issue got addressed (they removed the line completely and https://github.com/cov-lineages/constellations/releases/tag/v0.0.30 is out
That means that pangolin latest from web should simply work again.
As for the pangolin 3.1.17 update, I don't know for sure yet. I guess it'll be fine, and dependency-pinning is sth I was looking forward to.
So why not try and see.
So why not try and see.
i can confirm that the fix is live - i did not have to update pangolin to get the database fix. thanks wm75 (Wolfgang Maier) for getting this to the right place upstream!
i should say - working properly for me now on our internal galaxy server as well as usegalaxy.eu
I've just noticed that the ivar-based fast workflow seem to be missing the S insertion at 22204.
It is picked up by wm75 (Wolfgang Maier) 's workflow.
It is picked up by wm75 (Wolfgang Maier) 's workflow.
NC_045512.2 22204 . T TGAGCCAGAA 10152 PASS AF=0.603814;DP=472;DP4=92,104,118,167;HRUN=1;SB=5;INDEL;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGAAGAt|D215EPED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGAA|INFO_REALIGN_3_PRIME)
pvanheusden: FYI ^^ - Ill try to have a look as soon as I can get my head above water.
We're tracking the people that want to be part of the workflow working group (I guess at this point that's just the synonym for the IWC) and that will be available to do some work over the next few months in an internal spreadsheet. So far we've got John, Wolfgang, Simon and me, but if you want to be part of the group and you don't have access / don't know about the spreadsheet let me know and I'll make sure you're added
Excellent @heylf, I've added you to the spreadsheet ... and if I can figure out how to share the meeting calendar I'll drop a link. The next meeting is Monday the 17th, at 4pm CET