/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. [2026-05-13T19:33:06+0200] [MainThread] [I] [toil.lib.history] Recording workflow creation of 75d1063d-8841-4464-ae65-645187f1fd3b in file:/project/ldv/Share/cache/tmp/tmp2rqa3tmv [2026-05-13T19:33:06+0200] [MainThread] [I] [toil.cwl.cwltoil] Importing input files... [2026-05-13T19:33:06+0200] [MainThread] [I] [toil.cwl.cwltoil] Importing tool-associated files... [2026-05-13T19:33:06+0200] [MainThread] [I] [toil.cwl.cwltoil] Starting workflow [2026-05-13T19:33:06+0200] [MainThread] [I] [toil.lib.history] Workflow 75d1063d-8841-4464-ae65-645187f1fd3b is a run of /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow/download_and_run_psrfits_requantisation.cwl [2026-05-13T19:33:06+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-12.spider.surfsara.nl. [2026-05-13T19:33:06+0200] [MainThread] [I] [toil.realtimeLogger] Starting real-time logging. [2026-05-13T19:33:08+0200] [MainThread] [I] [toil.leader] 1 jobs are running, 0 jobs are issued and waiting to run [2026-05-13T19:33:10+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' download_and_run_psrfits_requantisation.cwl.0.fetchdata kind-CWLJob/instance-p4fcdfxy v1 with job batch system ID: 3 and disk: 1.0 Gi, memory: 256.0 Mi, cores: 1, accelerators: [], preemptible: False [2026-05-13T19:34:35+0200] [Thread-12] [I] [toil.statsAndLogging] Got message from job at time 05-13-2026 19:34:35: CWL step complete: download_and_run_psrfits_requantisation.cwl.0.fetchdata [2026-05-13T19:34:35+0200] [Thread-12] [I] [toil.statsAndLogging] download_and_run_psrfits_requantisation.cwl.0.fetchdata.stdout follows: =========> Downloading /project/ldv/Share/run-test/datamanager/268591/L427020_SAP000_B000_S2_P006_bf_7c0ef7b0.tar to L427020_SAP000_B000_S2_P006_bf_7c0ef7b0.tar <========= [2026-05-13T19:34:39+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v1 with job batch system ID: 6 and disk: 1.0 Gi, memory: 256.0 Mi, cores: 1, accelerators: [], preemptible: False [2026-05-13T19:35:27+0200] [Thread-12] [I] [toil.statsAndLogging] psrfits_requantisation.cwl.requantise.requantize.cwl.stderr follows: =========> source: /.inject-apptainer-env.sh:79:11: invalid var name Usage: psrfits_requantisation [options] [output tarball] psrfits_requantisation: error: no such option: --output-sasid <========= [2026-05-13T19:35:27+0200] [Thread-9] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob /project/ldv/Share/cache/tmp/tmp2rqa3tmv kind-CWLJob/instance-ohtfm_pr. [2026-05-13T19:35:27+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v1 Exit reason: None [2026-05-13T19:35:27+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-ohtfm_pr v2 [2026-05-13T19:35:27+0200] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-ohtfm_pr" follows: =========> [2026-05-13T19:34:39+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2026-05-13T19:34:39+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-12.spider.surfsara.nl. [2026-05-13T19:34:39+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr 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( [2026-05-13T19:34:40+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v1) from description 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v1 [2026-05-13T19:34:50+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. [2026-05-13T19:34:50+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow [2026-05-13T19:35:25+0200] [MainThread] [I] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] /project/ldv/Share/cache/tmp/tmphcc9mmus$ singularity \ --quiet \ run \ --contain \ --ipc \ --cleanenv \ --no-eval \ --userns \ --home \ /project/ldv/Share/cache/tmp/tmphcc9mmus:/SeghRG \ --mount=type=bind,source=/tmp/tmp92o3br8w,target=/tmp \ --pwd \ /SeghRG \ --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_P006_bf.tar \ --output-sasid=102600000356 [2026-05-13T19:35:26+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] exited with status: 2 [2026-05-13T19:35:26+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'].", {}) [2026-05-13T19:35:26+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] completed permanentFail [2026-05-13T19:35:26+0200] [MainThread] [E] [toil.cwl.cwltoil] Failed command standard error: source: /.inject-apptainer-env.sh:79:11: invalid var name Usage: psrfits_requantisation [options] [output tarball] psrfits_requantisation: error: no such option: --output-sasid [2026-05-13T19:35:26+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 [2026-05-13T19:35:26+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-la-12.spider.surfsara.nl <========= [2026-05-13T19:35:27+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-ohtfm_pr v2 with ID kind-CWLJob/instance-ohtfm_pr to 3 [2026-05-13T19:35:27+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-ohtfm_pr v2 to 2147483648 bytes [2026-05-13T19:35:27+0200] [MainThread] [W] [toil.job] We have increased the disk of the failed job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v2 to the default of 2147483648 bytes [2026-05-13T19:35:27+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v3 with job batch system ID: 7 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False [2026-05-13T19:36:21+0200] [Thread-12] [I] [toil.statsAndLogging] psrfits_requantisation.cwl.requantise.requantize.cwl.stderr follows: =========> source: /.inject-apptainer-env.sh:24:11: invalid var name Usage: psrfits_requantisation [options] [output tarball] psrfits_requantisation: error: no such option: --output-sasid <========= [2026-05-13T19:36:22+0200] [Thread-9] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob /project/ldv/Share/cache/tmp/tmp2rqa3tmv kind-CWLJob/instance-ohtfm_pr. [2026-05-13T19:36:22+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v3 Exit reason: None [2026-05-13T19:36:22+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-ohtfm_pr v5 [2026-05-13T19:36:22+0200] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-ohtfm_pr" follows: =========> [2026-05-13T19:35:27+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2026-05-13T19:35:27+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-12.spider.surfsara.nl. [2026-05-13T19:35:27+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr 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( [2026-05-13T19:35:29+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v4) from description 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v4 [2026-05-13T19:35:30+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. [2026-05-13T19:35:30+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow [2026-05-13T19:36:21+0200] [MainThread] [I] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] /project/ldv/Share/cache/tmp/tmp8jwboy9k$ singularity \ --quiet \ run \ --contain \ --ipc \ --cleanenv \ --no-eval \ --userns \ --home \ /project/ldv/Share/cache/tmp/tmp8jwboy9k:/NDkUCn \ --mount=type=bind,source=/tmp/tmpwnxg16ec,target=/tmp \ --pwd \ /NDkUCn \ --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_P006_bf.tar \ --output-sasid=102600000356 [2026-05-13T19:36:21+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] exited with status: 2 [2026-05-13T19:36:21+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'].", {}) [2026-05-13T19:36:21+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] completed permanentFail [2026-05-13T19:36:21+0200] [MainThread] [E] [toil.cwl.cwltoil] Failed command standard error: source: /.inject-apptainer-env.sh:24:11: invalid var name Usage: psrfits_requantisation [options] [output tarball] psrfits_requantisation: error: no such option: --output-sasid [2026-05-13T19:36:21+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 [2026-05-13T19:36:21+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-la-12.spider.surfsara.nl <========= [2026-05-13T19:36:22+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-ohtfm_pr v5 with ID kind-CWLJob/instance-ohtfm_pr to 2 [2026-05-13T19:36:22+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v6 with job batch system ID: 8 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False [2026-05-13T19:37:12+0200] [Thread-9] [E] [toil.batchSystems.singleMachine] Got exit code 1 (indicating failure) from job _toil_worker CWLJob /project/ldv/Share/cache/tmp/tmp2rqa3tmv kind-CWLJob/instance-ohtfm_pr. [2026-05-13T19:37:12+0200] [MainThread] [W] [toil.leader] Job failed with exit value 1: 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v6 Exit reason: None [2026-05-13T19:37:12+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-ohtfm_pr v8 [2026-05-13T19:37:12+0200] [MainThread] [W] [toil.leader] Log from job "kind-CWLJob/instance-ohtfm_pr" follows: =========> [2026-05-13T19:36:22+0200] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG--- [2026-05-13T19:36:22+0200] [MainThread] [I] [toil] Running Toil version 9.1.2-355b72ba0e425619c0367562caf2a337078dba65 on host wn-la-12.spider.surfsara.nl. [2026-05-13T19:36:22+0200] [MainThread] [I] [toil.worker] Working on job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v7 /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( [2026-05-13T19:36:23+0200] [MainThread] [I] [toil.worker] Loaded body Job('CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v7) from description 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v7 [2026-05-13T19:36:24+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. [2026-05-13T19:36:24+0200] [MainThread] [I] [cwltool] Using local copy of Singularity image found in /project/ldv/Share/run-test/workflows/psrfits_requantisation/workflow [2026-05-13T19:37:11+0200] [MainThread] [I] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] /project/ldv/Share/cache/tmp/tmpal6j_m68$ singularity \ --quiet \ run \ --contain \ --ipc \ --cleanenv \ --no-eval \ --userns \ --home \ /project/ldv/Share/cache/tmp/tmpal6j_m68:/rMiVtq \ --mount=type=bind,source=/tmp/tmp289ar937,target=/tmp \ --pwd \ /rMiVtq \ --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_P006_bf.tar \ --output-sasid=102600000356 [2026-05-13T19:37:11+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] exited with status: 2 [2026-05-13T19:37:11+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'].", {}) [2026-05-13T19:37:11+0200] [MainThread] [W] [cwltool] [job psrfits_requantisation.cwl.requantise.requantize.cwl] completed permanentFail [2026-05-13T19:37:11+0200] [MainThread] [E] [toil.cwl.cwltoil] Failed command standard error: source: /.inject-apptainer-env.sh:539:11: invalid var name Usage: psrfits_requantisation [options] [output tarball] psrfits_requantisation: error: no such option: --output-sasid [2026-05-13T19:37:11+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 [2026-05-13T19:37:11+0200] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host wn-la-12.spider.surfsara.nl <========= [2026-05-13T19:37:12+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-ohtfm_pr v8 with ID kind-CWLJob/instance-ohtfm_pr to 1 [2026-05-13T19:37:12+0200] [MainThread] [I] [toil.leader] Issued job 'CWLJob' psrfits_requantisation.cwl.requantise.requantize.cwl kind-CWLJob/instance-ohtfm_pr v9 with job batch system ID: 9 and disk: 2.0 Gi, memory: 2.0 Gi, cores: 1, accelerators: [], preemptible: False [2026-05-13T19:37:12+0200] [Thread-12] [I] [toil.statsAndLogging] psrfits_requantisation.cwl.requantise.requantize.cwl.stderr follows: =========> source: /.inject-apptainer-env.sh:539:11: invalid var name Usage: psrfits_requantisation [options] [output tarball] psrfits_requantisation: error: no such option: --output-sasid <========= srun: Job step aborted: Waiting up to 122 seconds for job step to finish. [2026-05-13T19:37:44.169] error: *** JOB 35700268 ON wn-la-12 CANCELLED AT 2026-05-13T19:37:44 DUE to SIGNAL Terminated ***