Redun¶
Here, we’ll see how to track redun workflow runs with LaminDB.
Note
This use case is based on github.com/ricomnl/bioinformatics-pipeline-tutorial.
# pip install lamindb redun git+http://github.com/laminlabs/redun-lamin-fasta
!lamin init --storage ./test-redun-lamin
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→ initialized lamindb: testuser1/test-redun-lamin
Amend the workflow¶
import lamindb as ln
import json
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→ connected lamindb: testuser1/test-redun-lamin
Let’s amend a redun workflow.py
to register input & output artifacts in LaminDB:
To track the workflow run in LaminDB, add (see on GitHub):
ln.track(params=params)
To register the output file via LaminDB, add (see on GitHub):
ln.Artifact(output_path, description="results").save()
Run redun¶
Let’s see what the input files are:
!ls ./fasta
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KLF4.fasta MYC.fasta PO5F1.fasta SOX2.fasta
And call the workflow:
!redun run workflow.py main --input-dir ./fasta --tag run=test-run 1> run_logs.txt 2>run_logs.txt
Inspect the logs:
!cat run_logs.txt
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→ connected lamindb: testuser1/test-redun-lamin
→ created Transform('voo6oVkh5yT30000'), started new Run('zOIKsc7W...') at 2025-07-14 06:39:55 UTC
→ params: input_dir=./fasta, amino_acid=C, enzyme_regex=[KR], missed_cleavages=0, min_length=4, max_length=75, executor=Executor.default
• recommendation: to identify the script across renames, pass the uid: ln.track("voo6oVkh5yT3", params={...})
! folder i[redun] Run Job c57c0173: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/gBPet3CnLnNv1Gv40000.fasta, hash=53d5ac53), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, mFile(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=76aa4c31)
task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ANqOZxj9OBPwLmiH0000.fasta, hash=13ba1e26), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 41136ab3: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ClDisYKX6gsThIqi0000.fasta, hash=ca68ec0f), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 663f4d38: bioinformatics_pipeline_tutorial.lib.digest_protein_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2TPYJWEEx9xL4pmk0000.fasta, hash=051a8b4d), enzyme_regex='[KR]', missed_cleavages=0, min_length=4, max_length=75) on default
[redun] Run Job 258ea312: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/gBPet3CnLnNv1Gv40000.fasta, hash=53d5ac53), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.peptides.txt, hash=4cd8b8e0), amino_acid='C') on default
[redun] Run Job 77dc5189: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ANqOZxj9OBPwLmiH0000.fasta, hash=13ba1e26), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ANqOZxj9OBPwLmiH0000.peptides.txt, hash=2ae0c08a), amino_acid='C') on default
[redun] Run Job cb5376dd: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/ClDisYKX6gsThIqi0000.fasta, hash=ca68ec0f), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ClDisYKX6gsThIqi0000.peptides.txt, hash=60c26c47), amino_acid='C') on default
[redun] Run Job d60fbcf0: bioinformatics_pipeline_tutorial.lib.count_amino_acids_task(input_fasta=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/.lamindb/2TPYJWEEx9xL4pmk0000.fasta, hash=051a8b4d), input_peptides=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2TPYJWEEx9xL4pmk0000.peptides.txt, hash=4460e3cd), amino_acid='C') on default
[redun] Run Job 8beb6e6d: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.count.tsv, hash=1ebc7bd0)) on default
[redun] Run Job 91730592: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ANqOZxj9OBPwLmiH0000.count.tsv, hash=8a53cf32)) on default
[redun] Run Job 6c0406df: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/ClDisYKX6gsThIqi0000.count.tsv, hash=bb179599)) on default
[redun] Run Job 0475dc37: bioinformatics_pipeline_tutorial.lib.plot_count_task(input_count=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/2TPYJWEEx9xL4pmk0000.count.tsv, hash=de5f1492)) on default
[redun] Run Job 49063be5: bioinformatics_pipeline_tutorial.lib.get_report_task(input_counts=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.count.tsv, hash=1ebc7bd0), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-l...) on default
[redun] Run Job d30d05fb: bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.plot.png, hash=fcbdcdb2), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-la..., input_report=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/protein_report.tsv, hash=98eea799)) on default
INFO redun:scheduler.py:log()- Run Job d30d05fb: bioinformatics_pipeline_tutorial.lib.archive_results_task(inputs_plots=[File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/gBPet3CnLnNv1Gv40000.plot.png, hash=fcbdcdb2), File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-la..., input_report=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/protein_report.tsv, hash=98eea799)) on default
[redun] Run Job 27b5d3d9: redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=76aa4c31)) on default
INFO redun:scheduler.py:log()- Run Job 27b5d3d9: redun_lamin_fasta.finish(results_archive=File(path=/home/runner/work/redun-lamin/redun-lamin/docs/test-redun-lamin/data/results.tgz, hash=76aa4c31)) on default
[redun]
INFO redun:scheduler.py:log()-
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1272, in log_job_statuses
self.log()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: ''
Arguments: ()
[redun] | JOB STATUS 2025/07/14 06:40:10
INFO redun:scheduler.py:log()- | JOB STATUS 2025/07/14 06:40:10
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| JOB STATUS 2025/07/14 06:40:10'
Arguments: ()
[redun] | TASK PENDING RUNNING FAILED CACHED DONE TOTAL
INFO redun:scheduler.py:log()- | TASK PENDING RUNNING FAILED CACHED DONE TOTAL
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| TASK PENDING RUNNING FAILED CACHED DONE TOTAL'
Arguments: ()
[redun] |
INFO redun:scheduler.py:log()- |
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| '
Arguments: ()
[redun] | ALL 0 0 0 0 16 16
INFO redun:scheduler.py:log()- | ALL 0 0 0 0 16 16
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| ALL 0 0 0 0 16 16'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.archive_results_task 0 0 0 0 1 1
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.archive_results_task 0 0 0 0 1 1
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.archive_results_task 0 0 0 0 1 1'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.count_amino_acids_task 0 0 0 0 4 4
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.count_amino_acids_task 0 0 0 0 4 4
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.count_amino_acids_task 0 0 0 0 4 4'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.digest_protein_task 0 0 0 0 4 4
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.digest_protein_task 0 0 0 0 4 4
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.digest_protein_task 0 0 0 0 4 4'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.get_report_task 0 0 0 0 1 1
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.get_report_task 0 0 0 0 1 1
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.get_report_task 0 0 0 0 1 1'
Arguments: ()
[redun] | bioinformatics_pipeline_tutorial.lib.plot_count_task 0 0 0 0 4 4
INFO redun:scheduler.py:log()- | bioinformatics_pipeline_tutorial.lib.plot_count_task 0 0 0 0 4 4
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| bioinformatics_pipeline_tutorial.lib.plot_count_task 0 0 0 0 4 4'
Arguments: ()
[redun] | redun_lamin_fasta.finish 0 0 0 0 1 1
INFO redun:scheduler.py:log()- | redun_lamin_fasta.finish 0 0 0 0 1 1
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| redun_lamin_fasta.finish 0 0 0 0 1 1'
Arguments: ()
[redun] | redun_lamin_fasta.main 0 0 0 0 1 1
INFO redun:scheduler.py:log()- | redun_lamin_fasta.main 0 0 0 0 1 1
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: '| redun_lamin_fasta.main 0 0 0 0 1 1'
Arguments: ()
[redun]
INFO redun:scheduler.py:log()-
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1274, in log_job_statuses
self.log(report_line)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: ''
Arguments: ()
[redun]
INFO redun:scheduler.py:log()-
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1049, in _run
self._process_events(result)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1253, in _process_events
self.log_job_statuses()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1275, in log_job_statuses
self.log()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: ''
Arguments: ()
[redun] Execution duration: 15.45 seconds
INFO redun:scheduler.py:log()- Execution duration: 15.45 seconds
--- Logging error ---
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/logging/__init__.py", line 1163, in emit
stream.write(msg + self.terminator)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/lamindb/core/_context.py", line 120, in write
self.file.write(data)
ValueError: I/O operation on closed file.
Call stack:
File "/opt/hostedtoolcache/Python/3.12.11/x64/bin/redun", line 10, in <module>
client.execute()
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 921, in execute
return args.func(args, extra_args, argv)
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/cli.py", line 1620, in run_command
result = scheduler.run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1135, in run
result: Promise[Result] = self._run(
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 1053, in _run
self.log(f"Execution duration: {duration:.2f} seconds")
File "/opt/hostedtoolcache/Python/3.12.11/x64/lib/python3.12/site-packages/redun/scheduler.py", line 999, in log
self.logger.log(level, (" " * indent) + line)
Message: 'Execution duration: 15.45 seconds'
Arguments: ()
View data lineage:
artifact = ln.Artifact.get(key="data/results.tgz")
artifact.view_lineage()
Show code cell output
Hide code cell output
Track the redun execution id¶
If we want to be able to query LaminDB for redun execution ID, this here is a way to get it:
# export the run information from redun
!redun log --exec --exec-tag run=test-run --format json --no-pager > redun_exec.json
# load the redun execution id from the JSON and store it in the LaminDB run record
with open("redun_exec.json") as file:
redun_exec = json.loads(file.readline())
artifact.run.reference = redun_exec["id"]
artifact.run.reference_type = "redun_id"
artifact.run.save()
Run(uid='zOIKsc7WptNvmIPd', started_at=2025-07-14 06:39:55 UTC, finished_at=2025-07-14 06:40:10 UTC, reference='7794a371-a39b-40b0-9ee1-06c45a50e45d', reference_type='redun_id', branch_id=1, space_id=1, transform_id=1, report_id=7, environment_id=1, created_by_id=1, created_at=2025-07-14 06:39:55 UTC)
Track the redun run report¶
Attach a run report:
report = ln.Artifact(
"run_logs.txt",
description=f"Redun run report of {redun_exec['id']}",
run=False,
visibility=0,
).save()
artifact.run.report = report
artifact.run.save()
Run(uid='zOIKsc7WptNvmIPd', started_at=2025-07-14 06:39:55 UTC, finished_at=2025-07-14 06:40:10 UTC, reference='7794a371-a39b-40b0-9ee1-06c45a50e45d', reference_type='redun_id', branch_id=1, space_id=1, transform_id=1, report_id=8, environment_id=1, created_by_id=1, created_at=2025-07-14 06:39:55 UTC)
View transforms and runs in LaminHub¶

View the database content¶
ln.view()
Show code cell output
Hide code cell output
Artifact
uid | key | description | suffix | kind | otype | size | hash | n_files | n_observations | _hash_type | _key_is_virtual | _overwrite_versions | space_id | storage_id | schema_id | version | is_latest | run_id | created_at | created_by_id | _aux | branch_id | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
id | |||||||||||||||||||||||
8 | 2ckt8FMNqL84ornJ0000 | None | Redun run report of 7794a371-a39b-40b0-9ee1-06... | .txt | None | None | 33569 | AubZJGtTc4bhmSUmoj_1kA | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-07-14 06:40:15.613000+00:00 | 1 | {'af': {'0': True}} | 1 |
6 | 1LcJM28b41qtSOPj0000 | data/results.tgz | None | .tgz | None | None | 68913 | pMSTlgRpuF3rNTD6Yid6_A | None | None | md5 | False | False | 1 | 1 | None | None | True | 1.0 | 2025-07-14 06:40:10.367000+00:00 | 1 | None | 1 |
5 | 2TPYJWEEx9xL4pmk0000 | fasta/PO5F1.fasta | None | .fasta | None | None | 477 | -7iJgveFO9ia0wE1bqVu6g | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-07-14 06:39:58.241000+00:00 | 1 | {'af': {'0': True}} | 1 |
4 | ClDisYKX6gsThIqi0000 | fasta/MYC.fasta | None | .fasta | None | None | 536 | WGbEtzPw-3bQEGcngO_pHQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-07-14 06:39:58.240000+00:00 | 1 | {'af': {'0': True}} | 1 |
3 | ANqOZxj9OBPwLmiH0000 | fasta/SOX2.fasta | None | .fasta | None | None | 414 | C5q_yaFXGk4SAEpfdqBwnQ | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-07-14 06:39:58.239000+00:00 | 1 | {'af': {'0': True}} | 1 |
2 | gBPet3CnLnNv1Gv40000 | fasta/KLF4.fasta | None | .fasta | None | None | 609 | LyuoYkWs4SgYcH7P7JLJtA | None | None | md5 | True | False | 1 | 1 | None | None | True | NaN | 2025-07-14 06:39:58.238000+00:00 | 1 | {'af': {'0': True}} | 1 |
Feature
uid | name | dtype | is_type | unit | description | array_rank | array_size | array_shape | proxy_dtype | synonyms | _expect_many | _curation | space_id | type_id | run_id | created_at | created_by_id | _aux | branch_id | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
id | ||||||||||||||||||||
1 | PM8NrrmDTPsP | input_dir | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-07-14 06:39:55.454000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
2 | XA1AraBxSLYg | amino_acid | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-07-14 06:39:55.454000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
3 | yVLmzCgYgVg8 | enzyme_regex | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-07-14 06:39:55.454000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
4 | nzp52r3kZ7H4 | missed_cleavages | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-07-14 06:39:55.454000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
5 | WywWAMS203eT | min_length | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-07-14 06:39:55.454000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
6 | WW7l2IClru86 | max_length | int | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-07-14 06:39:55.454000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
7 | 3b2SdqhLQprf | executor | str | None | None | None | 0 | 0 | None | None | None | None | None | 1 | None | None | 2025-07-14 06:39:55.454000+00:00 | 1 | {'af': {'0': None, '1': True, '2': False}} | 1 |
FeatureValue
value | hash | space_id | feature_id | run_id | created_at | created_by_id | _aux | branch_id | |
---|---|---|---|---|---|---|---|---|---|
id | |||||||||
1 | ./fasta | G8diGhDfCu78R1WbXfsHOw | 1 | 1 | None | 2025-07-14 06:39:55.526000+00:00 | 1 | None | 1 |
2 | C | DWH4NwytHUEvgLhNFD4SVw | 1 | 2 | None | 2025-07-14 06:39:55.531000+00:00 | 1 | None | 1 |
3 | [KR] | zPuapwAPylpfWRQFOTw9Cg | 1 | 3 | None | 2025-07-14 06:39:55.536000+00:00 | 1 | None | 1 |
4 | 0 | z80ghJXVZe9m59_5-Ydk2g | 1 | 4 | None | 2025-07-14 06:39:55.540000+00:00 | 1 | None | 1 |
5 | 4 | qH_2eaLz5x2RgaZ7dUISLA | 1 | 5 | None | 2025-07-14 06:39:55.545000+00:00 | 1 | None | 1 |
6 | 75 | 0Jv0FUSjNlpGyQd-u141ww | 1 | 6 | None | 2025-07-14 06:39:55.549000+00:00 | 1 | None | 1 |
7 | Executor.default | BaNJiQQLvaFrvOtdglHU7w | 1 | 7 | None | 2025-07-14 06:39:55.554000+00:00 | 1 | None | 1 |
Run
uid | name | started_at | finished_at | reference | reference_type | _is_consecutive | _status_code | space_id | transform_id | report_id | _logfile_id | environment_id | initiated_by_run_id | created_at | created_by_id | _aux | branch_id | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
id | ||||||||||||||||||
1 | zOIKsc7WptNvmIPd | None | 2025-07-14 06:39:55.477549+00:00 | 2025-07-14 06:40:10.412039+00:00 | 7794a371-a39b-40b0-9ee1-06c45a50e45d | redun_id | True | 0 | 1 | 1 | 8 | None | 1 | None | 2025-07-14 06:39:55.478000+00:00 | 1 | None | 1 |
Storage
uid | root | description | type | region | instance_uid | space_id | run_id | created_at | created_by_id | _aux | branch_id | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
id | ||||||||||||
1 | p0dJWtdparDR | /home/runner/work/redun-lamin/redun-lamin/docs... | None | local | None | iQlBPgD8uaqR | 1 | None | 2025-07-14 06:39:36.614000+00:00 | 1 | None | 1 |
Transform
uid | key | description | type | source_code | hash | reference | reference_type | space_id | _template_id | version | is_latest | created_at | created_by_id | _aux | branch_id | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
id | ||||||||||||||||
1 | voo6oVkh5yT30000 | workflow.py | workflow.py | script | """workflow.py."""\n\n# This code is a copy fr... | mHyxrE622q2fluxICu4XDw | None | None | 1 | None | None | True | 2025-07-14 06:39:55.472000+00:00 | 1 | None | 1 |
Delete the test instance:
Show code cell content
Hide code cell content
!rm -rf test-redun-lamin
!lamin delete --force test-redun-lamin
• deleting instance testuser1/test-redun-lamin