Error when executing ksrates test in nextflow

[dawickell]

I am trying to get ksrates running on my laptop (Macbook M1 Pro running macOS Monterey) using nextflow. I am able to get nextflow to run successfully but when I try to run the test example I get the following error:

$ nextflow run VIB-PSB/ksrates --config ./config_elaeis.txt
N E X T F L O W  ~  version 22.04.0
Launching `https://github.com/VIB-PSB/ksrates` [determined_bernard] DSL2 - revision: bfbb623720 [master]

K S R A T E S   -   N E X T F L O W   P I P E L I N E   (v1.1.1)
----------------------------------------------------------------

Configuration file:                    ./config_elaeis.txt
Logs folder:                           logs_3cf4463c
Preserve leftover files:               false

Command line:               nextflow run VIB-PSB/ksrates --config ./config_elaeis.txt
Launch directory:           /Users/wickell/ksrates
Work directory:             /Users/wickell/ksrates/work
ksrates directory:          /Users/wickell/.nextflow/assets/VIB-PSB/ksrates

Start time:                 2022-04-28T09:05:59.358787-04:00

No such variable: outCheckConfig

 -- Check script '/Users/wickell/.nextflow/assets/VIB-PSB/ksrates/main.nf' at line: 252 or see '.nextflow.log' file for more details

When I check the .nextflow.log file it doesn't tell me much more than the initial error message I have also tried running the next flow pipeline on our server (running Ubuntu 14.04.5) and get the same error.

Any idea what might be going wrong?

[Cecilia-Sensalari]

Hi dawickell,

Thanks for pointing this out! I managed to recreate the same error when using the latest version of Nextflow (22.04.0.5697). Can you try using an older Nextflow version (21.10.6.5660, the version we used to test the code)? In the meantime I will look into how to make the code work with the latest Nextflow version.

A quick way to use a specific version of Nextflow is by adding the NXF_VER environmental varibale (see Nextflow docs):

 NXF_VER=21.10.6 nextflow run VIB-PSB/ksrates --config ./config_elaeis.txt

Best, Cecilia

[dawickell]

Thanks for the quick response. So using the previous version of Nextflow, I definitely made it farther along but now the test example terminates with the following error:

==========================================================================================
The pipeline terminated during process 'setupAdjustment' with the following error message:

Process `setupAdjustment` terminated with an error exit status (127)

Focal species: elaeis
Extracting ortholog species pairs and trios from Newick tree... 

More details may be found in the error report above, in ./.nextflow.log, and/or in the 
following log file: rate_adjustment/elaeis/logs_aec8bc9f/setup_adjustment.log
==========================================================================================

I'm pretty sure this is the result of my local installation failing (a common problem with python packages since upgrading to my current computer) on my laptop. As inspection of the setup_adjustment.log file reveals:

.command.sh: line 30: ksrates: command not found

I have a similar issue on the server and am going to try to get singularity installed and try going that route instead. That being said, this does seemed to have solved my immediate problem with nextflow!

Thanks again, David

[Cecilia-Sensalari]

I'm glad it helped. Did you install the dependencies and ksrates yourself or did you use docker?

[dawickell]

I attempted to install the dependencies manually on my laptop. That being said, I have been able to get the example working on our server using singularity. Thanks again for all your help!

[Cecilia-Sensalari]

Hi, I'll now close this issue, but feel free to add other posts or open a new issue if needed!