Description:
I have been running QuNex without problem using version 0.90.10. However, I recently downloaded the latest version of the Singularity container (version 0.94.9) and I am getting an error when running the run_turnkeycommand using qunex_container. Please, note that the container seems to work fine when I enter the container and work within it. QuNex also works fine if I revert back to version 0.90.10. I am providing an example call below.
Call:
Container tag qunex_suite-0.94.9.sif accessed via:
export STUDY_NAME=“HBN_BBRF_rerun”
export RAW_DATA=“${WORK_DIR}/${STUDY_NAME}/sessions/inbox/MR”
export INPUT_BATCH_FILE=“${WORK_DIR}/${STUDY_NAME}/sessions/specs/HBN_BBRF_batch1.txt”
export INPUT_MAPPING_FILE=“${WORK_DIR}/${STUDY_NAME}/sessions/specs/HBN_BBRF_mapping1.txt”
export SESSIONS=“NDARAA306NT2,NDARAC462DZH”
export RUNTURNKEY_TYPE=“local”
export RUNTURNKEY_STEPS=“create_session_info”
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=“${QUNEX_CONTAINER}”
–overwrite=“yes”
–turnkeysteps=“${RUNTURNKEY_STEPS}”
–parsessions=“1”
–scheduler=“SLURM,time=23:59:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=day”
Log:
Generated by QuNex 0.94.9 on 2022-09-14_08.55.10.286627
e[36m===> Executing QuNex run_turnkey workflow… e[0m
e[32m------------------------ Initiating QuNex Turnkey Workflow ------------------------------- e[0m
/opt/qunex/bash/qx_utilities/run_turnkey.sh: command substitution: line 534: unexpected EOF while looking for matching `"’
/opt/qunex/bash/qx_utilities/run_turnkey.sh: command substitution: line 535: syntax error: unexpected end of file
e[35m → Note: Acceptance Test type not specified. Setting default type to: no e[0m
e[35m → Note: Turnkey cleaning not specified. Setting default to: no e[0m
e[31mERROR: --paramfile flag missing. Parameter file not specified. e[0m