[2026-04-19T14:59:58+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-04-19T14:59:58+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-dc-08.spider.surfsara.nl.
[2026-04-19T14:59:58+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' apply_pa.applyPA.applycal kind-CWLJob/g/instance-udrtz8_m 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(
[2026-04-19T14:59:59+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' apply_pa.applyPA.applycal kind-CWLJob/g/instance-udrtz8_m v1) from description 'CWLJob' apply_pa.applyPA.applycal kind-CWLJob/g/instance-udrtz8_m v1
[2026-04-19T14:59:59+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.
[2026-04-19T14:59:59+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/linc_calibrator_master/workflows
[2026-04-19T14:59:59+0200] [MainThread] [I] [cwltool] [job apply_pa.applyPA.applycal] /project/ldv/Share/cache/tmp/tmptdz5z6jd$ singularity \
    --quiet \
    run \
    --contain \
    --ipc \
    --cleanenv \
    --no-eval \
    --userns \
    --home \
    /project/ldv/Share/cache/tmp/tmptdz5z6jd:/MyYvAr \
    --mount=type=bind,source=/tmp/tmpf57bjry6,target=/tmp \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmp702jlaqg/cal_solutions.h5,target=/var/lib/cwl/stgd55960f8-8118-4ead-b05b-f1f38d64c34e/cal_solutions.h5,readonly \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmp_q384f3p/out_L102600000253_SB047_uv.dppp.MS,target=/MyYvAr/out_L102600000253_SB047_uv.dppp.MS \
    --pwd \
    /MyYvAr \
    --net \
    --network \
    none \
    /project/ldv/Share/run-test/workflows/linc_calibrator_master/workflows/astronrd_linc_latest.sif \
    DP3 \
    'steps=[applycal, count]' \
    msout=. \
    applycal.correction=polalign \
    msout.storagemanager.databitrate=0 \
    numthreads=8 \
    msin=/MyYvAr/out_L102600000253_SB047_uv.dppp.MS \
    msin.datacolumn=DATA \
    msout.datacolumn=CORRECTED_DATA \
    applycal.parmdb=/var/lib/cwl/stgd55960f8-8118-4ead-b05b-f1f38d64c34e/cal_solutions.h5 \
    applycal.solset=calibrator \
    msout.storagemanager=Dysco > /project/ldv/Share/cache/tmp/tmptdz5z6jd/applycal_polalign.log 2> /project/ldv/Share/cache/tmp/tmptdz5z6jd/applycal_polalign_err.log
[2026-04-19T15:00:02+0200] [MainThread] [I] [cwltool] [job apply_pa.applyPA.applycal] completed success
[2026-04-19T15:00:02+0200] [MainThread] [I] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: CWL step complete: apply_pa.applyPA.applycal
[2026-04-19T15:00:02+0200] [MainThread] [I] [toil.worker] Completed body for 'CWLJob' apply_pa.applyPA.applycal kind-CWLJob/g/instance-udrtz8_m v2
[2026-04-19T15:00:02+0200] [MainThread] [I] [toil.worker] Not chaining from job 'CWLJob' apply_pa.applyPA.applycal kind-CWLJob/g/instance-udrtz8_m v2
[2026-04-19T15:00:02+0200] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/toilwf-49709715c16753ada1387e6bc11c657c/5b1b. Set --cleanWorkDir to retain this log
[2026-04-19T15:00:02+0200] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 4.516158 seconds