/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.
[2026-05-13T21:02:32+0200] [MainThread] [I] [toil.lib.history] Recording workflow creation of b426feed-0961-4cc3-8fdc-51b35f8fab51 in file:/project/ldv/Share/cache/tmp/tmpwv3i5a3y
[2026-05-13T21:02:33+0200] [MainThread] [I] [toil.cwl.cwltoil] Importing input files...
[2026-05-13T21:02:33+0200] [MainThread] [I] [toil.cwl.cwltoil] Importing tool-associated files...
[2026-05-13T21:02:33+0200] [MainThread] [I] [toil.cwl.cwltoil] Starting workflow
[2026-05-13T21:02:33+0200] [MainThread] [I] [toil.lib.history] Workflow b426feed-0961-4cc3-8fdc-51b35f8fab51 is a run of /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow/download_and_run_psrfits_requantisation.cwl
[2026-05-13T21:02:34+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-13.spider.surfsara.nl.
[2026-05-13T21:02:34+0200] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging.
[2026-05-13T21:02:36+0200] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run
[2026-05-13T21:02:38+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_psrfits_requantisation.cwl.0.fetchdata kind-CWLJob/instance-_k96zybg v1 with job batch system ID: 3 and disk: 1.0 Gi, memory: 256.0 Mi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T21:04:17+0200] [Thread-12] [I] [toil.statsAndLogging] Got message from job at time 05-13-2026 21:04:17: CWL step complete: download_and_run_psrfits_requantisation.cwl.0.fetchdata
[2026-05-13T21:04:17+0200] [Thread-12] [I] [toil.statsAndLogging] download_and_run_psrfits_requantisation.cwl.0.fetchdata.stdout follows:
=========>
	Downloading /project/ldv/Share/run-test/datamanager/268678/L427020_SAP000_B000_S2_P008_bf_86242a80.tar to L427020_SAP000_B000_S2_P008_bf_86242a80.tar
<=========
[2026-05-13T21:04:21+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-k_8nmpfj v1 with job batch system ID: 6 and disk: 1.0 Gi, memory: 256.0 Mi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T21:05:03+0200] [Thread-9] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob /project/ldv/Share/cache/tmp/tmpwv3i5a3y kind-CWLJob/instance-k_8nmpfj.
[2026-05-13T21:05:03+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-k_8nmpfj v1
Exit reason: None
[2026-05-13T21:05:03+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-k_8nmpfj v2
[2026-05-13T21:05:03+0200] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-k_8nmpfj" follows:
=========>
	[2026-05-13T21:04:21+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
	[2026-05-13T21:04:21+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-13.spider.surfsara.nl.
	[2026-05-13T21:04:21+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-k_8nmpfj 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(
	[2026-05-13T21:04:22+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-k_8nmpfj v1) from description 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-k_8nmpfj v1
	[2026-05-13T21:04:42+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.
	[2026-05-13T21:04:42+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow
	[2026-05-13T21:05:01+0200] [MainThread] [I] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] /project/ldv/Share/cache/tmp/tmpn49xdqdc$ singularity \
	    --quiet \
	    run \
	    --contain \
	    --ipc \
	    --cleanenv \
	    --no-eval \
	    --userns \
	    --home \
	    /project/ldv/Share/cache/tmp/tmpn49xdqdc:/kRjvwH \
	    --mount=type=bind,source=/tmp/tmpa2k6s_87,target=/tmp \
	    --pwd \
	    /kRjvwH \
	    --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_P008_bf.tar \
	    --output-sasid=102600000357
	[2026-05-13T21:05:02+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] exited with status: 2
	[2026-05-13T21:05:02+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: ['102600000357_*.tar'].", {})
	[2026-05-13T21:05:02+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] completed permanentFail
	[2026-05-13T21:05:02+0200] [MainThread] [E] [toil.cwl.cwltoil] Failed command standard error:
	source: /.inject-apptainer-env.sh:444:11: invalid var name
	Usage: psrfits_requantisation [options] <input LTA tarball> [output tarball]
	
	psrfits_requantisation: error: no such option: --output-sasid
	
	[2026-05-13T21:05:03+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
	
	[2026-05-13T21:05:03+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-la-13.spider.surfsara.nl
<=========
[2026-05-13T21:05:03+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-k_8nmpfj v2 with ID kind-CWLJob/instance-k_8nmpfj to 3
[2026-05-13T21:05:03+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-k_8nmpfj v2 to 2147483648 bytes
[2026-05-13T21:05:03+0200] [MainThread] [W] [toil.job] We have increased the disk of the failed job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-k_8nmpfj v2 to the default of 2147483648 bytes
[2026-05-13T21:05:03+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-k_8nmpfj v3 with job batch system ID: 7 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False
[2026-05-13T21:05:03+0200] [Thread-12] [I] [toil.statsAndLogging] psrfits_requantisation.cwl.requantise.requantize.cwl.stderr follows:
=========>
	source: /.inject-apptainer-env.sh:444:11: invalid var name
	Usage: psrfits_requantisation [options] <input LTA tarball> [output tarball]
	
	psrfits_requantisation: error: no such option: --output-sasid
<=========
[2026-05-13T21:05:20.468] error: *** STEP 35702092.0 ON wn-la-13 CANCELLED AT 2026-05-13T21:05:20 DUE to SIGNAL Terminated ***
[2026-05-13T21:05:20.469] error: *** JOB 35702092 ON wn-la-13 CANCELLED AT 2026-05-13T21:05:20 DUE to SIGNAL Terminated ***