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