Hi everyone,
I would like to run a Netxflow script in galaxy (yes I know it’s strange).
So I made a test but I have a problem that I don’t undertstand, I am able to
launch my Nextflow tool in galaxy but not to complete the analysis.
The log out of galaxy :
> juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Work-dir:
/Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work
[Mac OS X]
juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Script base path does
not exist or is not a directory:
/Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin
juil.-07 19:28:53.988 [main] DEBUG nextflow.Session - Session start invoked
juil.-07 19:28:54.296 [main] DEBUG nextflow.script.ScriptRunner - >
Launching execution
juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - <<
taskConfig executor: null
juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - >>
processorType: 'local'
juil.-07 19:28:54.372 [main] DEBUG nextflow.executor.Executor - [warm up]
executor > local
juil.-07 19:28:54.375 [main] DEBUG n.processor.LocalPollingMonitor -
Creating local task monitor for executor 'local' > cpus=4; memory=16 GB;
capacity=4; pollInterval=100ms; dumpInterval=5m
juil.-07 19:28:54.446 [main] DEBUG nextflow.processor.TaskProcessor -
Creating operator > Testo -- maxForks: 4
juil.-07 19:28:54.477 [main] DEBUG nextflow.script.ScriptRunner - > Await
termination
juil.-07 19:28:54.477 [main] DEBUG nextflow.Session - Session await
juil.-07 19:28:54.579 [Task submitter] DEBUG
nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
juil.-07 19:28:54.584 [Task submitter] INFO nextflow.Session - [37/23b693]
Submitted process > Testo
juil.-07 19:28:54.647 [Task monitor] DEBUG n.processor.TaskPollingMonitor -
Task completed > TaskHandler[id: 1; name: Testo; status: COMPLETED; exit: 0;
error: -; workDir:
/Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work/37/23b693d7b8dbbf227f19b3dd9780a7]
juil.-07 19:28:54.674 [main] DEBUG nextflow.Session - Session await > all
process finished
juil.-07 19:28:54.675 [main] DEBUG nextflow.Session - Session await > all
barriers passed
juil.-07 19:28:54.682 [main] DEBUG nextflow.trace.StatsObserver - Workflow
completed > WorkflowStats[succeedCount=1; failedCount=0; ignoredCount=0;
cachedCount=0; succeedDuration=6ms; failedDuration=0ms; cachedDuration=0ms]
juil.-07 19:28:54.855 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
juil.-07 19:28:54.869 [main] DEBUG nextflow.script.ScriptRunner - >
Execution complete -- Goodbye
And the log in galaxy:
> juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Work-dir:
/Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/27/working/work
[Mac OS X]
juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Script base path does
not exist or is not a directory:
/Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin
juil.-08 11:38:10.001 [main] DEBUG nextflow.Session - Session start invoked
juil.-08 11:38:10.373 [main] DEBUG nextflow.script.ScriptRunner - >
Launching execution
juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - <<
taskConfig executor: null
juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - >>
processorType: 'local'
juil.-08 11:38:10.455 [main] DEBUG nextflow.executor.Executor - [warm up]
executor > local
juil.-08 11:38:10.458 [main] DEBUG n.processor.LocalPollingMonitor -
Creating local task monitor for executor 'local' > cpus=4; memory=16 GB;
capacity=4; pollInterval=100ms; dumpInterval=5m
juil.-08 11:38:10.534 [main] DEBUG nextflow.processor.TaskProcessor -
Creating operator > Testo -- maxForks: 4
juil.-08 11:38:10.591 [main] DEBUG nextflow.script.ScriptRunner - > Await
termination
Can someone help me with this ?
Best,
Luc
------------
Luc Cornet, PhD
Bio-informatician
Mycology and Aerobiology
Sciensano
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