These are chat archives for nextflow-io/nextflow

18th
Nov 2015
Robert Syme
@robsyme
Nov 18 2015 15:31
This message was deleted

Hi all.
I'm getting an odd error when running nextflow on our cluster:

rsyme@magnus-1:~/scratch/03-dijon> nextflow run .
tput: unknown terminal "xterm-256color"
tput: unknown terminal "xterm-256color"
tput: unknown terminal "xterm-256color"
tput: unknown terminal "xterm-256color"
tput: unknown terminal "xterm-256color"
N E X T F L O W  ~  version 0.16.2
Launching ./main.nf
ERROR ~ Not such file: /home/rsyme/bin/main.nf

 -- Check '.nextflow.log' file for details

Where the log looks like this

I'm not too concerned about the tput lines, but I'm not sure why nextflow is looking for ~/bin/main.nf
Paolo Di Tommaso
@pditommaso
Nov 18 2015 15:36
umm
it happens only with 0.16.2 ?
could also try to run it in this way
bash -x `which nextflow` run  .
and pasting the output log ?
Robert Syme
@robsyme
Nov 18 2015 15:50
It's not short...
Paolo Di Tommaso
@pditommaso
Nov 18 2015 15:52
:)
it looks that tput get confused by screen
are you using screen right?
Robert Syme
@robsyme
Nov 18 2015 16:01
I had to run it inside byobu to save the log to output (for some reason 2>&1 > log.txt didn't redirect the -x output, but the same error occurs when using vanilla ssh.
Paolo Di Tommaso
@pditommaso
Nov 18 2015 16:01
but what if you run nextflow run main.nf ?
Robert Syme
@robsyme
Nov 18 2015 16:03
Same error. (Not such file) :(
I suspect that the environment loaded by the cluster has borked my bash config somehow.
Paolo Di Tommaso
@pditommaso
Nov 18 2015 16:04
!
well but using an absolute path it must work
nextflow run $PWD/main.nf
Robert Syme
@robsyme
Nov 18 2015 16:06
Yup. That fixes it. I'll have a dig around and let you know if I figure it out.
Thanks Paolo.
Paolo Di Tommaso
@pditommaso
Nov 18 2015 16:07
you are welcome !