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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: %(web_page_url)s To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ |
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