[2026-04-28T09:36:24+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-04-28T09:36:24+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-dc-11.spider.surfsara.nl.
[2026-04-28T09:36:24+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' ion.summary.summary kind-CWLJob/instance-b53ndr0j v1
/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/pydantic/_internal/_generate_schema.py:2249: UnsupportedFieldAttributeWarning: The 'default' attribute with value None was provided to the `Field()` function, which has no effect in the context it was used. 'default' is field-specific metadata, and can only be attached to a model field using `Annotated` metadata or by assignment. This may have happened because an `Annotated` type alias using the `type` statement was used, or if the `Field()` function was attached to a single member of a union type.
  warnings.warn(
[2026-04-28T09:36:25+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' ion.summary.summary kind-CWLJob/instance-b53ndr0j v1) from description 'CWLJob' ion.summary.summary kind-CWLJob/instance-b53ndr0j v1
[2026-04-28T09:36:25+0200] [MainThread] [W] [cwltool] You have specified '--preserve-entire-environment' while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility.
[2026-04-28T09:36:25+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/linc_calibrator_master/workflows
[2026-04-28T09:36:25+0200] [MainThread] [I] [cwltool] [job ion.summary.summary] /project/ldv/Share/cache/tmp/tmp78c8c3y_$ singularity \
    --quiet \
    run \
    --contain \
    --ipc \
    --cleanenv \
    --no-eval \
    --userns \
    --home \
    /project/ldv/Share/cache/tmp/tmp78c8c3y_:/nJgCan \
    --mount=type=bind,source=/tmp/tmpsyskv38e,target=/tmp \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpumku70yf/flagged_fraction_antenna.json,target=/var/lib/cwl/stg1f389679-0a8c-4fe5-a277-9a1ba63839e7/flagged_fraction_antenna.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmp13qniyb6/flagged_fraction_antenna.json,target=/var/lib/cwl/stg91bde40f-dde1-4f55-9a29-b4a2af7d9462/flagged_fraction_antenna.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpz48sxx_d/Ateam_separation.json,target=/var/lib/cwl/stgfbda478f-1809-4daa-b59c-e6685117bcf3/Ateam_separation.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpc94mloa0/cal_solutions.h5,target=/var/lib/cwl/stge23685c3-4ca6-49be-a507-250070d8fd82/cal_solutions.h5,readonly \
    --pwd \
    /nJgCan \
    --net \
    --network \
    none \
    /project/ldv/Share/run-test/workflows/linc_calibrator_master/workflows/astronrd_linc_latest.sif \
    make_summary.py \
    --Ateam_separation_file \
    /var/lib/cwl/stgfbda478f-1809-4daa-b59c-e6685117bcf3/Ateam_separation.json \
    --bad_antennas \
    '' \
    --demix \
    False \
    --demix_sources \
    VirA_Gaussian,CygA_Gaussian,CasA_Gaussian,TauA_Gaussian \
    --filtered_antennas \
    '*&' \
    --ionex \
    True \
    --min_unflagged \
    0.5 \
    --pipeline \
    LINC \
    --refant \
    '' \
    --run_type \
    calibrator \
    --solutions \
    /var/lib/cwl/stge23685c3-4ca6-49be-a507-250070d8fd82/cal_solutions.h5 \
    --versions \
    '$LINC_DATA_ROOT/.versions' \
    /var/lib/cwl/stg1f389679-0a8c-4fe5-a277-9a1ba63839e7/flagged_fraction_antenna.json \
    /var/lib/cwl/stg91bde40f-dde1-4f55-9a29-b4a2af7d9462/flagged_fraction_antenna.json > /project/ldv/Share/cache/tmp/tmp78c8c3y_/summary.log 2> /project/ldv/Share/cache/tmp/tmp78c8c3y_/summary_err.log
[2026-04-28T09:36:26+0200] [MainThread] [I] [cwltool] [job ion.summary.summary] completed success
[2026-04-28T09:36:26+0200] [MainThread] [I] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: CWL step complete: ion.summary.summary
[2026-04-28T09:36:26+0200] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'CWLJob' ion.summary.summary kind-CWLJob/instance-b53ndr0j v3 used 2.58x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched.
[2026-04-28T09:36:26+0200] [MainThread] [I] [toil.worker] Completed body for 'CWLJob' ion.summary.summary kind-CWLJob/instance-b53ndr0j v3
[2026-04-28T09:36:26+0200] [MainThread] [I] [toil.worker] Not chaining from job 'CWLJob' ion.summary.summary kind-CWLJob/instance-b53ndr0j v3
[2026-04-28T09:36:26+0200] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/toilwf-5da28d98afe45070918352b46dbf45dc/ce57. Set --cleanWorkDir to retain this log
[2026-04-28T09:36:26+0200] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 2.115953 seconds