[RESOLVED] Turnkey fails missing session folder

Use Questions
1

I’m just starting with qunex and am trying to start with a turnkey job, but I’m getting errors early on. When I try to run the attached code
test_qunex_turnkey.txt (1.1 KB)
, I get the following error:

Running run_turnkey locally on tnxt-0456.cluster
Command log: /scratch/group/congalab/creativity/creativity/processing/logs/runlogs/Log-run_turnkey_2021-06-09_13.58.0285924369.log
Command output: /scratch/group/congalab/creativity/creativity/processing/logs/comlogs/tmp_run_turnkey_sub-001_2021-06-09_13.58.0285924369.log

===> Executing QuNex RunTurnkey workflow…

------------------------ Initiating QuNex Turnkey Workflow -------------------------------

→ Note: Acceptance Test type not specified. Setting default type to: no

→ Note: Turnkey cleaning not specified. Setting default to: no

ERROR: Sessions folder name is missing.

===> ERROR during run_turnkey. Check final QuNex error log output:

/scratch/group/congalab/creativity/creativity/processing/logs/comlogs/error_run_turnkey_sub-001_2021-06-09_13.58.0285924369.log

I confirmed that the study was setup correctly with ${WORK_DIR}/${STUDY_NAME}/sessions existing, although there are no sessions showing in the folder. When I manually ran create_study followed by import_bids and map_bids2nii each participant in my bids folder was imported as a separate session.

1 Like
2

Hi congalab!

Glad you are trying QuNex out. In the run_turnkey call one of the required parameters is missing and that is --sessionsfoldername="sessions". This is a parameter that we had to introduce because of some backwards compatibility issues. In the future we are planning an upgrade to the run_turnkey functionality which will make it more intuitive and user friendly. Our Quick Start (oriadev / qunex / wiki / Overview / QuickStart — Bitbucket) is a good way to get started with run_turnkey.

Cheers, Jure