These are chat archives for nextflow-io/nextflow

28th
Aug 2018
lucky
@Lucky-lai
Aug 28 2018 06:45
i use splitCsv to split a big file, throw error:java.lang.OutOfMemoryError: GC overhead limit exceeded.
i find splitFasta has the parameter "file:true",in order to not incur in a "OutOfMemoryException",but not find in splitCsv
is there some way to avoid this error?
Shellfishgene
@Shellfishgene
Aug 28 2018 09:16
If I use publishDir with move mode (for the last process), will nf repeat exection when rerun with the -resume option or does it find them as cached?
David Mas-Ponte
@davidmasp
Aug 28 2018 11:04

Hi, I was playing with the private server configuration file to see if I could "install" pipes directly through nextflow from our gitlab server.

This works fine the first time.

$ nextflow run dmas/hello -hub agendas
N E X T F L O W  ~  version 0.30.0
Pulling dmas/hello ...
 downloaded from GIT_REPO_URL
Launching `dmas/hello` [mad_woese] - revision: c9b0ec7286 [master]
[warm up] executor > local
[f9/32e605] Submitted process > sayHello (4)
[47/78e060] Submitted process > sayHello (1)
[19/628431] Submitted process > sayHello (3)
[62/4b15fa] Submitted process > sayHello (2)
Bonjour world!
Hola world!
Hello world!
Ciao world!

but then if you want to re-run it, I get this message.

$ nextflow run dmas/hello -hub agendas
N E X T F L O W  ~  version 0.30.0
Corrupted git repository at path: /home/dmas/.nextflow/assets/dmas/hello
Is this the expected behaviour? Should the pipeline be able to re-run once installed right? Am I doing something wrong then?
I also tried to first pull and then run and the same happens. In this case it didn't even run the first time. I also tried pulling the hello repo from the nextflow-io github site (the public repo) and this works well (executes more than one time).
Paolo Di Tommaso
@pditommaso
Aug 28 2018 11:18
Hola, yes it should work
There something odd in that repo
Change local repo and try to verify it with plain git tool
David Mas-Ponte
@davidmasp
Aug 28 2018 11:33
You mean this?
$ cd ~/.nextflow/assets/dmas/hello/
$ git fsck --full
Checking object directories: 100% (256/256), done.
Checking objects: 100% (46/46), done.
or this?
$ cd ~/.nextflow/assets/dmas/hello/
$ nextflow run main.nf
N E X T F L O W  ~  version 0.30.0
Launching `main.nf` [golden_gutenberg] - revision: b9f107bada
[warm up] executor > local
[57/f97cd8] Submitted process > sayHello (1)
[45/8eefd7] Submitted process > sayHello (2)
[79/ddee0a] Submitted process > sayHello (4)
[70/8d962e] Submitted process > sayHello (3)
Bonjour world!
Ciao world!
Hola world!
Hello world!
Paolo Di Tommaso
@pditommaso
Aug 28 2018 11:39
Either, therefore it looks fine
Run again the one failing as: nextflow -trace nextflow run dmas/hello
Then open an issue including the .nextflow.log file
David Mas-Ponte
@davidmasp
Aug 28 2018 12:24
okay will do, thanks