These are chat archives for nextflow-io/nextflow

23rd
Nov 2017
Maxime Garcia
@MaxUlysse
Nov 23 2017 08:18
@pditommaso Did you had the time to look at my .command.run file ?
Paolo Di Tommaso
@pditommaso
Nov 23 2017 08:19
yes
Maxime Garcia
@MaxUlysse
Nov 23 2017 08:21
Do you have any idea ?
Paolo Di Tommaso
@pditommaso
Nov 23 2017 08:21
about what? :)
Maxime Garcia
@MaxUlysse
Nov 23 2017 08:27
sorry meeting ;-)
Paolo Di Tommaso
@pditommaso
Nov 23 2017 08:27
:+1:
Maxime Garcia
@MaxUlysse
Nov 23 2017 10:02
Back after two meetings ;-)
So my question is, do you have any idea why I can't read files in s3 buckets from Batch ?
My input file is a tsv file in a s3 bucket and it was read, but not the file in the s3 bucket listed inside
But I'm guessing the input file was read from my computer, so probably not the same right invovlved
Paolo Di Tommaso
@pditommaso
Nov 23 2017 10:29
The main question is permission issue or missing file?
Sorry can't help much this morning
Maxime Garcia
@MaxUlysse
Nov 23 2017 10:42
No problem, the file is here, so I'm guessing permission rights
André M. Ribeiro-dos-Santos
@andremrsantos
Nov 23 2017 12:50
Hi everyone, I need some help. Can I write a process that tries on command and on fail defaults to other?
Paolo Di Tommaso
@pditommaso
Nov 23 2017 12:58
mmmmm
I would say there isn't any built-in mechanism/pattern for that
But likely it can be handled with some tricks
Paolo Di Tommaso
@pditommaso
Nov 23 2017 13:17
@MaxUlysse if still not working open an issue including NF output, .nextflow.log file and task .command.run, .command.log, .command.out and .command.err
Maxime Garcia
@MaxUlysse
Nov 23 2017 13:19
I'm looking into permissions rights, and if still nothing else, I'm opening an issue
Thanks
André M. Ribeiro-dos-Santos
@andremrsantos
Nov 23 2017 13:23
@pditommaso do have any examples?
Paolo Di Tommaso
@pditommaso
Nov 23 2017 13:23
I should learn more about use case, how/why it's failing this task?
it's killed by the batch scheduler or for some reason it may not complete with a zero exit code?
Alexander Peltzer
@apeltzer
Nov 23 2017 14:48
Hey guys
I have an issue with the NGI-RNASeq pipeline and the specification of 'task.attempts' which is not set to 1 in my script apparently when used on the PBS scheduler automatically.
Whenever the script tries to execute the dynamic resources, the process fails because the task.attemps is set to '[:]' which I found out using a simple sysout statement in the config file...
"The first time the process is executed the task.attempt is set to 1, thus it will request a two GB of memory and one hour of maximum execution time."
clusterOptions = { "-l ppn=${process.cpus}:walltime=${process.time}:mem=${process.memory}:cfc" }
Paolo Di Tommaso
@pditommaso
Nov 23 2017 15:32
it's task.attempt not task.attemps
Alexander Peltzer
@apeltzer
Nov 23 2017 15:34
Okay, sorry that was a typo here. But in the script its actually correct: process { cpus = { check_max( 1 * task.attempt, 'cpus' ) } memory = { check_max( 8.GB * task.attempt, 'memory' ) }
Paolo Di Tommaso
@pditommaso
Nov 23 2017 15:35
still some problem at least on formatting
so, you are saying that you get a task.attempt == [:] ?
Alexander Peltzer
@apeltzer
Nov 23 2017 15:37
Yes! I added a simple System.error.println(task.attempt) before this check_max(...) call and it returns [:] on the command line
Paolo Di Tommaso
@pditommaso
Nov 23 2017 15:38
please create a replicate test case and open an issue if that's confirmed
Alexander Peltzer
@apeltzer
Nov 23 2017 15:38
It makes sense, my actual error on the console is that the multiplication can't work on 1* [:] for not matching data types
Ok
Thanks!
Paolo Di Tommaso
@pditommaso
Nov 23 2017 15:41
welcome