/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(
Already cached git.astron.nl:5000/ldv/bf_double_tgz:latest with Singularity.
INFO:cwl_utils.image_puller:Already cached git.astron.nl:5000/ldv/bf_double_tgz:latest with Singularity.
Already cached git.astron.nl:5000/ldv/bf_double_tgz:v0.5.7 with Singularity.
INFO:cwl_utils.image_puller:Already cached git.astron.nl:5000/ldv/bf_double_tgz:v0.5.7 with Singularity.
Already cached git.astron.nl:5000/ldv/bf_double_tgz:v0.5.7 with Singularity.
INFO:cwl_utils.image_puller:Already cached git.astron.nl:5000/ldv/bf_double_tgz:v0.5.7 with Singularity.
[2026-05-13T19:35:36+0200] [MainThread] [I] [toil.lib.history] Recording workflow creation of dde8315c-bca0-43cf-9125-a503a58389a5 in file:/project/ldv/Share/cache/tmp/tmpjmt0ie6r
[2026-05-13T19:35:36+0200] [MainThread] [I] [toil.cwl.cwltoil] Importing input files...
[2026-05-13T19:35:36+0200] [MainThread] [I] [toil.cwl.cwltoil] Importing tool-associated files...
[2026-05-13T19:35:36+0200] [MainThread] [I] [toil.cwl.cwltoil] Starting workflow
[2026-05-13T19:35:36+0200] [MainThread] [I] [toil.lib.history] Workflow dde8315c-bca0-43cf-9125-a503a58389a5 is a run of /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow/download_and_run_psrfits_requantisation.cwl
[2026-05-13T19:35:36+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-dc-06.spider.surfsara.nl.
[2026-05-13T19:35:36+0200] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging.
[2026-05-13T19:35:38+0200] [MainThread] [I] [toil.leader] 0 jobs are running, 0 jobs are issued and waiting to run
[2026-05-13T19:35:40+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_psrfits_requantisation.cwl.0.fetchdata kind-CWLJob/instance-id9qnktr v1 with job batch system ID: 3 and disk: 1.0 Gi, memory: 256.0 Mi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T19:37:19+0200] [Thread-12] [I] [toil.statsAndLogging] Got message from job at time 05-13-2026 19:37:19: CWL step complete: download_and_run_psrfits_requantisation.cwl.0.fetchdata
[2026-05-13T19:37:19+0200] [Thread-12] [I] [toil.statsAndLogging] download_and_run_psrfits_requantisation.cwl.0.fetchdata.stdout follows:
=========>
Downloading /project/ldv/Share/run-test/datamanager/268603/L427020_SAP000_B000_S2_P018_bf_51e26d56.tar to L427020_SAP000_B000_S2_P018_bf_51e26d56.tar
<=========
[2026-05-13T19:37:23+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v1 with job batch system ID: 6 and disk: 1.0 Gi, memory: 256.0 Mi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T19:37:41+0200] [Thread-9] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob /project/ldv/Share/cache/tmp/tmpjmt0ie6r kind-CWLJob/instance-78lktvu7.
[2026-05-13T19:37:41+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v1
Exit reason: None
[2026-05-13T19:37:41+0200] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v2
[2026-05-13T19:37:41+0200] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-78lktvu7" follows:
=========>
[2026-05-13T19:37:23+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-05-13T19:37:23+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-dc-06.spider.surfsara.nl.
[2026-05-13T19:37:23+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 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(
[2026-05-13T19:37:24+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v1) from description 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v1
[2026-05-13T19:37:25+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.
[2026-05-13T19:37:25+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow
[2026-05-13T19:37:40+0200] [MainThread] [I] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] /project/ldv/Share/cache/tmp/tmpci6l3dcv$ singularity \
--quiet \
run \
--contain \
--ipc \
--cleanenv \
--no-eval \
--userns \
--home \
/project/ldv/Share/cache/tmp/tmpci6l3dcv:/AQbsdJ \
--mount=type=bind,source=/tmp/tmp7sthqls1,target=/tmp \
--pwd \
/AQbsdJ \
--net \
--network \
none \
/project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \
psrfits_requantisation \
L427020_SAP000_B000_S2_P018_bf.tar \
--output-sasid=102600000356
[2026-05-13T19:37:41+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] exited with status: 2
[2026-05-13T19:37:41+0200] [MainThread] [E] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] Job error:
("Error collecting output for parameter 'bf_archive': ../../../../workflows/psrfits_requantisation/steps/requantize.cwl:31:5: Did not find output file with glob pattern: ['102600000356_*.tar'].", {})
[2026-05-13T19:37:41+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] completed permanentFail
[2026-05-13T19:37:41+0200] [MainThread] [E] [toil.cwl.cwltoil] Failed command standard error:
source: /.inject-apptainer-env.sh:284:11: invalid var name
Usage: psrfits_requantisation [options] [output tarball]
psrfits_requantisation: error: no such option: --output-sasid
[2026-05-13T19:37:41+0200] [MainThread] [C] [toil.worker] Worker crashed with traceback:
Traceback (most recent call last):
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/worker.py", line 595, in workerScript
job._runner(
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/job.py", line 3254, in _runner
returnValues = self._run(jobGraph=None, fileStore=fileStore)
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/job.py", line 3137, in _run
return self.run(fileStore)
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2847, in run
raise cwl_utils.errors.WorkflowException(status)
cwl_utils.errors.WorkflowException: permanentFail
[2026-05-13T19:37:41+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-dc-06.spider.surfsara.nl
<=========
[2026-05-13T19:37:41+0200] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v2 with ID kind-CWLJob/instance-78lktvu7 to 3
[2026-05-13T19:37:41+0200] [MainThread] [W] [toil.job] We have increased the default memory of the failed job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v2 to 2147483648 bytes
[2026-05-13T19:37:41+0200] [MainThread] [W] [toil.job] We have increased the disk of the failed job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v2 to the default of 2147483648 bytes
[2026-05-13T19:37:41+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v3 with job batch system ID: 7 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T19:37:41+0200] [Thread-12] [I] [toil.statsAndLogging] psrfits_requantisation.cwl.requantise.requantize.cwl.stderr follows:
=========>
source: /.inject-apptainer-env.sh:284:11: invalid var name
Usage: psrfits_requantisation [options] [output tarball]
psrfits_requantisation: error: no such option: --output-sasid
<=========
[2026-05-13T19:37:59+0200] [Thread-12] [I] [toil.statsAndLogging] psrfits_requantisation.cwl.requantise.requantize.cwl.stderr follows:
=========>
source: /.inject-apptainer-env.sh:39:11: invalid var name
Usage: psrfits_requantisation [options] [output tarball]
psrfits_requantisation: error: no such option: --output-sasid
<=========
[2026-05-13T19:37:59+0200] [Thread-9] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob /project/ldv/Share/cache/tmp/tmpjmt0ie6r kind-CWLJob/instance-78lktvu7.
[2026-05-13T19:37:59+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v3
Exit reason: None
[2026-05-13T19:37:59+0200] [MainThread] [W] [toil.leader] The job seems to have left a log file, indicating failure: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v5
[2026-05-13T19:37:59+0200] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-78lktvu7" follows:
=========>
[2026-05-13T19:37:41+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2026-05-13T19:37:41+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-dc-06.spider.surfsara.nl.
[2026-05-13T19:37:41+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v4
/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(
[2026-05-13T19:37:42+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v4) from description 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v4
[2026-05-13T19:37:43+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.
[2026-05-13T19:37:43+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow
[2026-05-13T19:37:58+0200] [MainThread] [I] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] /project/ldv/Share/cache/tmp/tmp7_7fll85$ singularity \
--quiet \
run \
--contain \
--ipc \
--cleanenv \
--no-eval \
--userns \
--home \
/project/ldv/Share/cache/tmp/tmp7_7fll85:/AOlwYI \
--mount=type=bind,source=/tmp/tmpisbhighi,target=/tmp \
--pwd \
/AOlwYI \
--net \
--network \
none \
/project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow/git.astron.nl:5000_ldv_bf_double_tgz:latest.sif \
psrfits_requantisation \
L427020_SAP000_B000_S2_P018_bf.tar \
--output-sasid=102600000356
[2026-05-13T19:37:58+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] exited with status: 2
[2026-05-13T19:37:58+0200] [MainThread] [E] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] Job error:
("Error collecting output for parameter 'bf_archive': ../../../../workflows/psrfits_requantisation/steps/requantize.cwl:31:5: Did not find output file with glob pattern: ['102600000356_*.tar'].", {})
[2026-05-13T19:37:58+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] completed permanentFail
[2026-05-13T19:37:58+0200] [MainThread] [E] [toil.cwl.cwltoil] Failed command standard error:
source: /.inject-apptainer-env.sh:39:11: invalid var name
Usage: psrfits_requantisation [options] [output tarball]
psrfits_requantisation: error: no such option: --output-sasid
[2026-05-13T19:37:58+0200] [MainThread] [C] [toil.worker] Worker crashed with traceback:
Traceback (most recent call last):
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/worker.py", line 595, in workerScript
job._runner(
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/job.py", line 3254, in _runner
returnValues = self._run(jobGraph=None, fileStore=fileStore)
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/job.py", line 3137, in _run
return self.run(fileStore)
File "/project/ldv/Software/executor-venv-toil9/lib/python3.9/site-packages/toil/cwl/cwltoil.py", line 2847, in run
raise cwl_utils.errors.WorkflowException(status)
cwl_utils.errors.WorkflowException: permanentFail
[2026-05-13T19:37:58+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-dc-06.spider.surfsara.nl
<=========
[2026-05-13T19:37:59+0200] [MainThread] [W] [toil.job] Due to failure we are reducing the remaining try count of job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v5 with ID kind-CWLJob/instance-78lktvu7 to 2
[2026-05-13T19:37:59+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-78lktvu7 v6 with job batch system ID: 8 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
srun: Job step aborted: Waiting up to 122 seconds for job step to finish.
[2026-05-13T19:38:03.980] error: *** JOB 35700295 ON wn-dc-06 CANCELLED AT 2026-05-13T19:38:03 DUE to SIGNAL Terminated ***