QuNex error

[Graham Warner]

Hi,

I'm trying to install and test the qunex container using the provide sample HCP data but when I run qunex_container run_turnkey I get an error message saying

"ERROR: --batchfile flag set but file not found in default locations: /usr/local/qunex/data/HCPA001_batch.txt"

It then directs me to /usr/local/qunex/quickstart/processing/logs/comlog/error_run_turnkey_HCPA001_2021-09-09_14.29.0008858079.log which does not exist.

The batchfile does exist at /usr/local/qunex/data/HCPA001_batch.text and has completely open read permissions so I'm not sure why it says it can't be found. The exact command I'm running is

sudo ./qunex_container run_turnkey   --rawdatainput="${RAW_DATA}"   --batchfile="${INPUT_BATCH_FILE}"   --mappingfile="${INPUT_MAPPING_FILE}"   --workingdir="${WORK_DIR}"   --projectname="${STUDY_NAME}"   --path="${WORK_DIR}/${STUDY_NAME}"   --sessions="${SESSIONS}"   --sessionids="${SESSIONS}"   --sessionsfoldername="sessions"   --turnkeytype="${RUNTURNKEY_TYPE}"   --container="${QUNEX_CONTAINER}"   --turnkeysteps="${RUNTURNKEY_STEPS}"

from /usr/local/qunex. Any thoughts on what might be going on?

Thank you,
Graham

[Jure Demsar]

Hi Graham,

Could you please post this issue on the official QuNex forum (https://forum.qunex.yale.edu/). We (the QuNex development team) would prefer to have all QuNex related issues and resolutions documented on our forum. This way other users with similar issues can find solutions to their problems in a more efficient manner.

Thanks, Jure

[Coalson, Timothy Scott (S&T-Student)]

Are you checking your OS'es /usr folder rather than the /usr in the container?  I would expect all paths mentioned by qunex to refer to paths in the container, not OS paths.

Tim

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From: Graham Warner <gcwa...@gmail.com>
Sent: Thursday, September 9, 2021 1:42 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Subject: [hcp-users] QuNex error

 

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