[2026-04-17T03:15:21+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-04-17T03:15:21+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-09.spider.surfsara.nl.
[2026-04-17T03:15:21+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' ion.summary.summary kind-CWLJob/instance-o79w6gnh 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(
[2026-04-17T03:15:23+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' ion.summary.summary kind-CWLJob/instance-o79w6gnh v1) from description 'CWLJob' ion.summary.summary kind-CWLJob/instance-o79w6gnh v1
[2026-04-17T03:15:23+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.
[2026-04-17T03:15:23+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/linc_calibrator_master/workflows
[2026-04-17T03:15:23+0200] [MainThread] [I] [cwltool] [job ion.summary.summary] /project/ldv/Share/cache/tmp/tmpq23y6ozx$ singularity \
    --quiet \
    run \
    --contain \
    --ipc \
    --cleanenv \
    --no-eval \
    --userns \
    --home \
    /project/ldv/Share/cache/tmp/tmpq23y6ozx:/ygpkOE \
    --mount=type=bind,source=/tmp/tmpu6k74unm,target=/tmp \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpcxoxkjpj/flagged_fraction_antenna.json,target=/var/lib/cwl/stgb763590a-a580-4463-95db-5a7ec6f22af1/flagged_fraction_antenna.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpyhuay2ae/flagged_fraction_antenna.json,target=/var/lib/cwl/stg70b5371f-5094-42ad-95a4-7180528d8461/flagged_fraction_antenna.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmptprq35mn/Ateam_separation.json,target=/var/lib/cwl/stgcd514ff0-77d1-4b63-a46c-babe6c7548be/Ateam_separation.json,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpi_cyvo0l/cal_solutions.h5,target=/var/lib/cwl/stg0b654dd0-bf98-4cc3-863f-f7f0db61af89/cal_solutions.h5,readonly \
    --pwd \
    /ygpkOE \
    --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/stgcd514ff0-77d1-4b63-a46c-babe6c7548be/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/stg0b654dd0-bf98-4cc3-863f-f7f0db61af89/cal_solutions.h5 \
    --versions \
    '$LINC_DATA_ROOT/.versions' \
    /var/lib/cwl/stgb763590a-a580-4463-95db-5a7ec6f22af1/flagged_fraction_antenna.json \
    /var/lib/cwl/stg70b5371f-5094-42ad-95a4-7180528d8461/flagged_fraction_antenna.json > /project/ldv/Share/cache/tmp/tmpq23y6ozx/summary.log 2> /project/ldv/Share/cache/tmp/tmpq23y6ozx/summary_err.log
[2026-04-17T03:15:26+0200] [MainThread] [I] [cwltool] [job ion.summary.summary] completed success
[2026-04-17T03:15:26+0200] [MainThread] [I] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: CWL step complete: ion.summary.summary
[2026-04-17T03:15:26+0200] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'CWLJob' ion.summary.summary kind-CWLJob/instance-o79w6gnh v3 used 1.01x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched.
[2026-04-17T03:15:26+0200] [MainThread] [I] [toil.worker] Completed body for 'CWLJob' ion.summary.summary kind-CWLJob/instance-o79w6gnh v3
[2026-04-17T03:15:26+0200] [MainThread] [I] [toil.worker] Not chaining from job 'CWLJob' ion.summary.summary kind-CWLJob/instance-o79w6gnh v3
[2026-04-17T03:15:26+0200] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/toilwf-e87a9e4fb5a95a959dd0cd5899b331ec/876b. Set --cleanWorkDir to retain this log
[2026-04-17T03:15:26+0200] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 4.623912 seconds