[2026-05-08T07:38:43+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-05-08T07:38:43+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-dc-11.spider.surfsara.nl.
[2026-05-08T07:38:43+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' finalize.11.applytarget kind-CWLJob/instance-03cg57m9 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(
[2026-05-08T07:38:45+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' finalize.11.applytarget kind-CWLJob/instance-03cg57m9 v1) from description 'CWLJob' finalize.11.applytarget kind-CWLJob/instance-03cg57m9 v1
[2026-05-08T07:38:45+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.
[2026-05-08T07:38:45+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/linc_target_stable_april2026/workflows
[2026-05-08T07:39:01+0200] [MainThread] [I] [cwltool] [job finalize.11.applytarget] /project/ldv/Share/cache/tmp/tmp613elizg$ singularity \
    --quiet \
    run \
    --contain \
    --ipc \
    --cleanenv \
    --no-eval \
    --userns \
    --home \
    /project/ldv/Share/cache/tmp/tmp613elizg:/TPZQnR \
    --mount=type=bind,source=/tmp/tmpwsclt3jp,target=/tmp \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmpwknan5rj/cal_solutions.h5,target=/var/lib/cwl/stg8f6e10ca-8204-4dd9-8fd3-ee3bc33caabd/cal_solutions.h5,readonly \
    --pwd \
    /TPZQnR \
    --net \
    --network \
    none \
    /project/ldv/Share/run-test/workflows/linc_target_stable_april2026/workflows/astronrd_linc_latest.sif \
    DP3 \
    steps=[filter,applycal,count] \
    msin.baseline= \
    applycal.correction=TGSSphase_final \
    count.save=True \
    msout.storagemanager.databitrate=10 \
    filter.baseline= \
    filter.remove=True \
    count.jsonfilename=out.json \
    numthreads=2 \
    msin=/TPZQnR/L102600000331_165MHz_uv.dp3concat \
    msin.datacolumn=DATA \
    msout.datacolumn=DATA \
    msout=L102600000331_165MHz_uv_pre-cal.ms \
    applycal.parmdb=/var/lib/cwl/stg8f6e10ca-8204-4dd9-8fd3-ee3bc33caabd/cal_solutions.h5 \
    count.savetojson=True \
    applycal.solset=target \
    msout.storagemanager=Dysco > /project/ldv/Share/cache/tmp/tmp613elizg/applycal_TGSSphase_final.log 2> /project/ldv/Share/cache/tmp/tmp613elizg/applycal_TGSSphase_final_err.log
[2026-05-08T07:43:40+0200] [MainThread] [I] [cwltool] [job finalize.11.applytarget] completed success
[2026-05-08T07:43:40+0200] [MainThread] [I] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: CWL step complete: finalize.11.applytarget
[2026-05-08T07:43:40+0200] [MainThread] [I] [toil.worker] Completed body for 'CWLJob' finalize.11.applytarget kind-CWLJob/instance-03cg57m9 v2
[2026-05-08T07:43:40+0200] [MainThread] [I] [toil.worker] Not chaining from job 'CWLJob' finalize.11.applytarget kind-CWLJob/instance-03cg57m9 v2
[2026-05-08T07:43:40+0200] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/toilwf-244dfef43ab350c982ebc54628daa80f/7cc1. Set --cleanWorkDir to retain this log
[2026-05-08T07:43:40+0200] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 297.525235 seconds