[2026-04-08T19:19:31+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-04-08T19:19:31+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-10.spider.surfsara.nl.
[2026-04-08T19:19:31+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' ion.summary.summary kind-CWLJob/instance-q6p9ig02 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(
[2026-04-08T19:19:32+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' ion.summary.summary kind-CWLJob/instance-q6p9ig02 v1) from description 'CWLJob' ion.summary.summary kind-CWLJob/instance-q6p9ig02 v1
[2026-04-08T19:19:33+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.
[2026-04-08T19:19:33+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/linc_calibrator_master/workflows
[2026-04-08T19:19:33+0200] [MainThread] [I] [cwltool] [job ion.summary.summary] /project/ldv/Share/cache/tmp/tmptfs7c7hx$ singularity \
    --quiet \
    run \
    --contain \
    --ipc \
    --cleanenv \
    --no-eval \
    --userns \
    --home \
    /project/ldv/Share/cache/tmp/tmptfs7c7hx:/HBAqLk \
    --mount=type=bind,source=/tmp/tmpicgvobfz,target=/tmp \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmp7ef6v52q/flagged_fraction_antenna.json,target=/var/lib/cwl/stg0f31938b-e08b-4f8e-9c95-a85e1f489f9e/flagged_fraction_antenna.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpu3ugvky7/flagged_fraction_antenna.json,target=/var/lib/cwl/stg13ba8af9-1b35-4cc2-b558-8b20538cc5e9/flagged_fraction_antenna.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpw7yckb3h/Ateam_separation.json,target=/var/lib/cwl/stge57cc53c-cd3c-4933-9337-4991ba05a3be/Ateam_separation.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmp7nw4ut27/cal_solutions.h5,target=/var/lib/cwl/stgf75a01d0-ae09-45b0-953f-d3b86b512c6f/cal_solutions.h5,readonly \
    --pwd \
    /HBAqLk \
    --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/stge57cc53c-cd3c-4933-9337-4991ba05a3be/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/stgf75a01d0-ae09-45b0-953f-d3b86b512c6f/cal_solutions.h5 \
    --versions \
    '$LINC_DATA_ROOT/.versions' \
    /var/lib/cwl/stg0f31938b-e08b-4f8e-9c95-a85e1f489f9e/flagged_fraction_antenna.json \
    /var/lib/cwl/stg13ba8af9-1b35-4cc2-b558-8b20538cc5e9/flagged_fraction_antenna.json > /project/ldv/Share/cache/tmp/tmptfs7c7hx/summary.log 2> /project/ldv/Share/cache/tmp/tmptfs7c7hx/summary_err.log
[2026-04-08T19:19:35+0200] [MainThread] [I] [cwltool] [job ion.summary.summary] completed success
[2026-04-08T19:19:35+0200] [MainThread] [I] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: CWL step complete: ion.summary.summary
[2026-04-08T19:19:35+0200] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'CWLJob' ion.summary.summary kind-CWLJob/instance-q6p9ig02 v3 used 1.25x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched.
[2026-04-08T19:19:35+0200] [MainThread] [I] [toil.worker] Completed body for 'CWLJob' ion.summary.summary kind-CWLJob/instance-q6p9ig02 v3
[2026-04-08T19:19:35+0200] [MainThread] [I] [toil.worker] Not chaining from job 'CWLJob' ion.summary.summary kind-CWLJob/instance-q6p9ig02 v3
[2026-04-08T19:19:35+0200] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/toilwf-8990f7a381915caf8b9617e939f477af/9a71. Set --cleanWorkDir to retain this log
[2026-04-08T19:19:35+0200] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 3.506562 seconds