Commit bbd8d57b authored by Esther Vendrell Miras's avatar Esther Vendrell Miras

all

parent eea89b82
Pipeline #10640 canceled with stage
Aug-26 15:01:13.335 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf -profile docker,test
Aug-26 15:01:13.456 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.07.1
Aug-26 15:01:13.502 [main] DEBUG nextflow.cli.Launcher - Operation aborted
nextflow.exception.AbortOperationException: Not a valid project name: main.nf
at nextflow.scm.AssetManager.resolveName(AssetManager.groovy:254)
at nextflow.scm.AssetManager.build(AssetManager.groovy:129)
at nextflow.scm.AssetManager.<init>(AssetManager.groovy:107)
at nextflow.cli.CmdRun.getScriptFile(CmdRun.groovy:332)
at nextflow.cli.CmdRun.run(CmdRun.groovy:246)
at nextflow.cli.Launcher.run(Launcher.groovy:466)
at nextflow.cli.Launcher.main(Launcher.groovy:648)
Aug-26 14:17:05.904 [main] DEBUG nextflow.cli.Launcher - $> nextflow run workflow-block/main.nf -profile docker,test
Aug-26 14:17:05.982 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.07.1
Aug-26 14:17:05.996 [main] INFO nextflow.cli.CmdRun - Launching `workflow-block/main.nf` [high_jang] - revision: b13d7e48f1
Aug-26 14:17:06.031 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/esther/simple-website-with-docker/workflow-block/nextflow.config
Aug-26 14:17:06.034 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/esther/simple-website-with-docker/workflow-block/nextflow.config
Aug-26 14:17:06.078 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker,test`
Aug-26 14:17:06.486 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [test, docker]
Aug-26 14:17:06.533 [main] DEBUG nextflow.Session - Session uuid: f02056d3-466b-4e93-9b02-4db57ab3db76
Aug-26 14:17:06.533 [main] DEBUG nextflow.Session - Run name: high_jang
Aug-26 14:17:06.534 [main] DEBUG nextflow.Session - Executor pool size: 8
Aug-26 14:17:06.563 [main] DEBUG nextflow.cli.CmdRun -
Version: 20.07.1 build 5412
Created: 24-07-2020 15:18 UTC (17:18 CEST)
System: Linux 4.15.0-20-generic
Runtime: Groovy 2.5.11 on OpenJDK 64-Bit Server VM 11.0.4+11-post-Ubuntu-1ubuntu218.04.3
Encoding: UTF-8 (UTF-8)
Process: 27630@mi-pc [127.0.1.1]
CPUs: 8 - Mem: 15.5 GB (5 GB) - Swap: 7.5 GB (7.5 GB)
Aug-26 14:17:06.588 [main] DEBUG nextflow.Session - Work-dir: /home/esther/simple-website-with-docker/work [ext2/ext3]
Aug-26 14:17:06.588 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/esther/simple-website-with-docker/workflow-block/bin
Aug-26 14:17:06.620 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Aug-26 14:17:06.622 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-26 14:17:06.798 [main] DEBUG nextflow.Session - Session start invoked
Aug-26 14:17:06.803 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/esther/simple-website-with-docker/sample_out/stats/trace.txt
Aug-26 14:17:06.843 [main] WARN nextflow.NextflowMeta$Preview - DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
Aug-26 14:17:06.994 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-26 14:17:07.009 [main] DEBUG nextflow.Session - Session aborted -- Cause: Can't find a matching module file for include: ./validation_block
Aug-26 14:17:07.018 [main] ERROR nextflow.cli.Launcher - Can't find a matching module file for include: ./validation_block
java.nio.file.NoSuchFileException: Can't find a matching module file for include: ./validation_block
at nextflow.script.IncludeDef.realModulePath(IncludeDef.groovy:177)
at nextflow.script.IncludeDef.load0(IncludeDef.groovy:112)
at nextflow.script.IncludeDef$load0$1.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:127)
at Script_2d9dc33e.runScript(Script_2d9dc33e:4)
at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
at nextflow.script.BaseScript.run(BaseScript.groovy:200)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:219)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:219)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:127)
at nextflow.cli.CmdRun.run(CmdRun.groovy:274)
at nextflow.cli.Launcher.run(Launcher.groovy:466)
at nextflow.cli.Launcher.main(Launcher.groovy:648)
2020-08-26 14:17:06 - high_jang - b13d7e48f1f11fce424c0bb875f26f3b f02056d3-466b-4e93-9b02-4db57ab3db76 nextflow run workflow-block/main.nf -profile docker,test
This will describe the scripts contained in the image
<html></html>
\ No newline at end of file
this text will describe the test data
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{
"_id": "TCGA:my_gene_predictor_P",
"challenge_id": [
"ACC",
"BRCA"
],
"community_id": "TCGA",
"datalink": {
"attrs": [
"archive"
],
"status": "ok",
"validation_date": "2020-08-26T15:06:09"
},
"participant_id": "my_gene_predictor",
"type": "participant"
}
\ No newline at end of file
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Aug-26 14:19:19.533 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf -profile docker,test
Aug-26 14:19:19.617 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.07.1
Aug-26 14:19:19.631 [main] INFO nextflow.cli.CmdRun - Launching `main.nf` [loving_magritte] - revision: b13d7e48f1
Aug-26 14:19:19.678 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/esther/simple-website-with-docker/workflow-block/nextflow.config
Aug-26 14:19:19.680 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/esther/simple-website-with-docker/workflow-block/nextflow.config
Aug-26 14:19:19.711 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `docker,test`
Aug-26 14:19:20.151 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [test, docker]
Aug-26 14:19:20.201 [main] DEBUG nextflow.Session - Session uuid: 180f960e-82fe-4a46-bb83-1ab6928ae094
Aug-26 14:19:20.201 [main] DEBUG nextflow.Session - Run name: loving_magritte
Aug-26 14:19:20.202 [main] DEBUG nextflow.Session - Executor pool size: 8
Aug-26 14:19:20.231 [main] DEBUG nextflow.cli.CmdRun -
Version: 20.07.1 build 5412
Created: 24-07-2020 15:18 UTC (17:18 CEST)
System: Linux 4.15.0-20-generic
Runtime: Groovy 2.5.11 on OpenJDK 64-Bit Server VM 11.0.4+11-post-Ubuntu-1ubuntu218.04.3
Encoding: UTF-8 (UTF-8)
Process: 27767@mi-pc [127.0.1.1]
CPUs: 8 - Mem: 15.5 GB (5 GB) - Swap: 7.5 GB (7.5 GB)
Aug-26 14:19:20.255 [main] DEBUG nextflow.Session - Work-dir: /home/esther/simple-website-with-docker/workflow-block/work [ext2/ext3]
Aug-26 14:19:20.256 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/esther/simple-website-with-docker/workflow-block/bin
Aug-26 14:19:20.303 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Aug-26 14:19:20.306 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-26 14:19:20.481 [main] DEBUG nextflow.Session - Session start invoked
Aug-26 14:19:20.485 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/esther/simple-website-with-docker/workflow-block/sample_out/stats/trace.txt
Aug-26 14:19:20.515 [main] WARN nextflow.NextflowMeta$Preview - DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
Aug-26 14:19:20.668 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-26 14:19:20.683 [main] DEBUG nextflow.Session - Session aborted -- Cause: Can't find a matching module file for include: ./validation_block
Aug-26 14:19:20.692 [main] ERROR nextflow.cli.Launcher - Can't find a matching module file for include: ./validation_block
java.nio.file.NoSuchFileException: Can't find a matching module file for include: ./validation_block
at nextflow.script.IncludeDef.realModulePath(IncludeDef.groovy:177)
at nextflow.script.IncludeDef.load0(IncludeDef.groovy:112)
at nextflow.script.IncludeDef$load0$1.call(Unknown Source)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:115)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:127)
at Script_2d9dc33e.runScript(Script_2d9dc33e:4)
at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:170)
at nextflow.script.BaseScript.run(BaseScript.groovy:200)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:219)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:219)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:127)
at nextflow.cli.CmdRun.run(CmdRun.groovy:274)
at nextflow.cli.Launcher.run(Launcher.groovy:466)
at nextflow.cli.Launcher.main(Launcher.groovy:648)
......@@ -4,3 +4,4 @@
2020-08-26 14:45:37 3.5s astonishing_mclean ERR b13d7e48f1f11fce424c0bb875f26f3b a0b2b4a1-d6a9-4693-b1c3-4984ed0e3062 nextflow run main.nf -profile docker,test
2020-08-26 14:53:47 3.9s trusting_kare ERR b13d7e48f1f11fce424c0bb875f26f3b 9abe67a8-031c-49fd-80ad-a28921e583eb nextflow run main.nf -profile docker,test
2020-08-26 15:03:24 4s desperate_colden OK b13d7e48f1f11fce424c0bb875f26f3b 49b156f5-47ad-48ec-8e5d-62c9316d7c03 nextflow run main.nf -profile docker,test
2020-08-26 15:06:07 4s adoring_agnesi OK b13d7e48f1f11fce424c0bb875f26f3b 5147e39a-bdd6-4144-b581-2430870ac283 nextflow run main.nf -profile docker,test
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