[2026-05-03T13:53:28+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-05-03T13:53:28+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-05.spider.surfsara.nl.
[2026-05-03T13:53:28+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' gsmcal.aoflag.aoflagger kind-CWLJob/instance-68bnva2y 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(
[2026-05-03T13:53:29+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' gsmcal.aoflag.aoflagger kind-CWLJob/instance-68bnva2y v1) from description 'CWLJob' gsmcal.aoflag.aoflagger kind-CWLJob/instance-68bnva2y v1
[2026-05-03T13:53:29+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.
[2026-05-03T13:53:29+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/linc_target_stable_april2026/workflows
[2026-05-03T13:53:29+0200] [MainThread] [I] [cwltool] [job gsmcal.aoflag.aoflagger] /project/ldv/Share/cache/tmp/tmpjgz4q1ac$ singularity \
    --quiet \
    run \
    --contain \
    --ipc \
    --cleanenv \
    --no-eval \
    --userns \
    --home \
    /project/ldv/Share/cache/tmp/tmpjgz4q1ac:/CVRDSu \
    --mount=type=bind,source=/tmp/tmp0rw0pcxg,target=/tmp \
    --mount=type=bind,source=/project/ldv/Share/cache/tmp/tmphi1w6ene/L102600000322_122MHz_uv.dp3concat,target=/CVRDSu/L102600000322_122MHz_uv.dp3concat \
    --pwd \
    /CVRDSu \
    --net \
    --network \
    none \
    /project/ldv/Share/run-test/workflows/linc_target_stable_april2026/workflows/astronrd_linc_latest.sif \
    /bin/sh \
    -c \
    aoflagger -chunk-size 2000 -concatenate-frequency -strategy $LINC_DATA_ROOT/rfistrategies/lofar-hba-wideband.lua -v /CVRDSu/L102600000322_122MHz_uv.dp3concat > /project/ldv/Share/cache/tmp/tmpjgz4q1ac/aoflag.log 2> /project/ldv/Share/cache/tmp/tmpjgz4q1ac/aoflag_err.log
[2026-05-03T13:54:20+0200] [MainThread] [I] [cwltool] [job gsmcal.aoflag.aoflagger] completed success
[2026-05-03T13:54:20+0200] [MainThread] [I] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: CWL step complete: gsmcal.aoflag.aoflagger
[2026-05-03T13:54:20+0200] [MainThread] [W] [toil.fileStores.abstractFileStore] LOG-TO-LEADER: Job 'CWLJob' gsmcal.aoflag.aoflagger kind-CWLJob/instance-68bnva2y v3 used 2.63x more CPU than the requested 1 cores. Consider increasing the job's required CPU cores or limiting the number of processes/threads launched.
[2026-05-03T13:54:20+0200] [MainThread] [I] [toil.worker] Completed body for 'CWLJob' gsmcal.aoflag.aoflagger kind-CWLJob/instance-68bnva2y v3
[2026-05-03T13:54:20+0200] [MainThread] [I] [toil.worker] Not chaining from job 'CWLJob' gsmcal.aoflag.aoflagger kind-CWLJob/instance-68bnva2y v3
[2026-05-03T13:54:20+0200] [MainThread] [I] [toil.worker] Worker log can be found at /tmp/toilwf-52775c46fce8546ea7cf49ee152c6e3b/21a7. Set --cleanWorkDir to retain this log
[2026-05-03T13:54:20+0200] [MainThread] [I] [toil.worker] Finished running the chain of jobs on this node, we ran for a total of 51.902370 seconds