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Phil Ewels
@ewels
true
Paolo Di Tommaso
@pditommaso
I think singularity hub is going to be deprecated in favour of Singularity library
Sven F.
@sven1103
ah nice
thanks for sharing Paolo!
Paolo Di Tommaso
@pditommaso
not sure, but I think they are going to provide an on-premises version
BTW have you moved to slack ?
Sven F.
@sven1103
yup
you can join using this link http://nf-core-invite.herokuapp.com
Paolo Di Tommaso
@pditommaso
I think I've joined but I don't remember the login url anymore .. this why I don't like slack :satisfied:
KochTobi
@KochTobi
Sven F.
@sven1103

I think I've joined but I don't remember the login url anymore .. this why I don't like slack :satisfied:

:joy:

KochTobi
@KochTobi
damn without the -
Sven F.
@sven1103
yup
Paolo Di Tommaso
@pditommaso
ahhh :joy:
KochTobi
@KochTobi
always gets me....
Sven F.
@sven1103
nf-core was already taken
-.-
Paolo Di Tommaso
@pditommaso
ohh, that's why I was not able to login there :satisfied:
Screenshot 2018-12-04 at 20.53.26.png
KochTobi
@KochTobi
Manage passwords ...
Sven F.
@sven1103
omg
Paolo Di Tommaso
@pditommaso
this think they have a different password for each channel I will never digest ..
Sven F.
@sven1103
yeah, this is kind of annyoing
Paolo Di Tommaso
@pditommaso
should I launch a nextflow channel on spectrum .. :satisfied:
Sven F.
@sven1103
huh, don't know this one
:D
Phil Ewels
@ewels
That’s the one that’s just been bought by GutHub right?
@pditommaso - this is why I use the slack clients though! Keeps all of the different organisations together easily. Only need to do it once on mobile and once on desktop :)
Paolo Di Tommaso
@pditommaso
That’s the one that’s just been bought by GutHub right?
yep !
this is why I use the slack clients though
nice, to not sure I want another source of distraction ! :satisfied:
Qi ZHAO
@likelet
hi, a simple question. Why the $workDir in config file can not be recognized by NF
N E X T F L O W  ~  version 19.01.0
Launching `RNAseqPipe/main.nf` [thirsty_hamilton] - revision: a2f41a936f
This workflow requires Nextflow version 0.26 or greater -- You are running version 19.01.0
ERROR ~ GTF file not found: $workDir/Genome/gencode.chr22.gtf

 -- Check '.nextflow.log' file for details
image.png
seems paste the wrong place again ...
Pontus Frehult
@pontus

Hi all, I'm trying to help NGI Sweden debug an issue where 19.01.0 incorrectly thinks slurm jobs are gone and give up, but am not sure how much farther I'm gonna get without some tips.

I've gotten down to checkActiveStatus in ./modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy

Feb-27 08:46:35.309 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > map does not contain jobId: 557670

but I also have an strace for this controller run, and have lines like

30833 write(1, "557514 CD\n557315 CD\n557670 R\n557671 R\n", 38 <unfinished ...>

for all the invocations of squeue (any attempt to get queue status that has gotten so far as execv). I also see corresponding read lines.

For some of these I see

Feb-27 08:38:55.328 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > cmd exit: 0
557514 CD
557315 CD
557670 R
557671 R

Feb-27 08:38:55.335 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status >
job: 557514: DONE
job: 557315: DONE
job: 557670: RUNNING
job: 557671: RUNNING

which is fine, but I also see quite a few

Feb-27 08:39:55.354 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > cmd exit: 0

Feb-27 08:39:55.355 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status >
(empty)

leading up to

Feb-27 08:39:55.355 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > map does not contain jobId: 557670

Any tips on getting further with this?

Paolo Di Tommaso
@pditommaso
this should be reported in the NF project https://github.com/nextflow-io/nextflow/issues
Paolo Di Tommaso
@pditommaso
actually I think it's related to this nextflow-io/nextflow#1045
Alexander Peltzer
@apeltzer
Also we’ve moved to slack in nf core :-)
Paolo Di Tommaso
@pditommaso
I guess he confused it for NF channel
Alexander Peltzer
@apeltzer
Yes :-)
Phil Ewels
@ewels
I wonder if we should close this chat group to avoid future confusion... :/
For future readers: Reminder that we have moved to Slack. See nf-co.re to get an invite (top right of any page) or visit https://nf-core-invite.herokuapp.com/ directly.
Alexander Peltzer
@apeltzer
Yes - makes sense, alreay put up the info in the header too
sureshhewa
@sureshhewabi
Can nextflow log file location customized by passing as a params?
Alexander Peltzer
@apeltzer
Reminder that we have moved to Slack. See nf-co.re to get an invite (top right of any page) or visit https://nf-core-invite.herokuapp.com/ directly.
:smile:
Phil Ewels
@ewels
Also this is for nf-core, not to be confused with the gitter channel for nextflow itself: https://gitter.im/nextflow-io/nextflow