what is exit status - negative sign

[Kemin Zhou]

Three of my processes exited with exit '-'.  something like the following:

status: COMPLETED; exit: -; error: -; workDir: /data/work/7d/7c4c4872b319e4c1b6c6fbd8aa28d5 started: 1648010396665; exited: -; ]

On the command line output,

[e2/acca6a] process > myprocess (SeraAF00025HBC15)  [ 64%] 41 of 64, cached: 21, failed: 3, retries: 3

When I looked at the .command.log file and the work directory, it seems the process went well and finished successfully.  Does Anyone have any ideas?

Appreciate your help!

--

Kemin Zhou

510 862 2276

[Noah Legall]

Strange, and I am not seeing anything documented about this behaviour. I would consider adding an 'errorStrategy' to your process so your workflow can continue even when it hits this weird error. 
https://www.nextflow.io/docs/latest/process.html#errorstrategy

I would suggest a few extra things tho for trouble shooting. I'm curious to know if you run the process with the data that is creating the issues if it will still throw an error or if it will continue up to a point. That way you can isolate if this is an issue of your data or your computing environment. I wish I can be more help here but this is what I can suggest in the meantime.

[drhp...@gmail.com]

Hi Kemin,

status: COMPLETED; exit: -; error: -; workDir: /data/work/7d/7c4c4872b319e4c1b6c6fbd8aa28d5 started: 1648010396665; exited: -; ]

I assume you got this from the .nextflow.log file?

If I remember correctly, you will get exit: - for native NF processes i.e. those run by the master NF job. Conventional processes that are run on compute nodes should have an exit: 0.

https://www.nextflow.io/docs/latest/process.html#native-execution

Where was myprocess executed? 

Cheers,

Harshil