Jul-16 13:18:38.753 [main] DEBUG nextflow.cli.Launcher - $> /users/tobias.neumann/.local/bin/nextflow run obenauflab/virus-detection-nf --inputDir test -profile slurm -resume Jul-16 13:18:38.822 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.30.2 Jul-16 13:18:39.218 [main] DEBUG nextflow.scm.AssetManager - Git config: /groups/zuber/zubarchive/USERS/tobias/.nextflow/assets/obenauflab/virus-detection-nf/.git/config; branch: master; remote: origin; url: https://github.com/ObenaufLab/virus-detection-nf.git Jul-16 13:18:39.279 [main] DEBUG nextflow.scm.AssetManager - Git config: /groups/zuber/zubarchive/USERS/tobias/.nextflow/assets/obenauflab/virus-detection-nf/.git/config; branch: master; remote: origin; url: https://github.com/ObenaufLab/virus-detection-nf.git Jul-16 13:18:39.547 [main] DEBUG nextflow.scm.AssetManager - Git config: /groups/zuber/zubarchive/USERS/tobias/.nextflow/assets/obenauflab/virus-detection-nf/.git/config; branch: master; remote: origin; url: https://github.com/ObenaufLab/virus-detection-nf.git Jul-16 13:18:39.547 [main] INFO nextflow.cli.CmdRun - Launching `obenauflab/virus-detection-nf` [maniac_kare] - revision: 359ecfbd87 [master] Jul-16 13:18:40.335 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /groups/zuber/zubarchive/USERS/tobias/.nextflow/assets/obenauflab/virus-detection-nf/nextflow.config Jul-16 13:18:40.336 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /groups/zuber/zubarchive/USERS/tobias/.nextflow/assets/obenauflab/virus-detection-nf/nextflow.config Jul-16 13:18:40.343 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `slurm` Jul-16 13:18:40.414 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, sge, slurm] Jul-16 13:18:40.420 [main] WARN nextflow.config.ConfigBuilder - It seems you never run this project before -- Option `-resume` is ignored Jul-16 13:18:40.438 [main] DEBUG nextflow.Session - Session uuid: e8f8b284-53fb-43e4-afce-6c971a8c6593 Jul-16 13:18:40.438 [main] DEBUG nextflow.Session - Run name: maniac_kare Jul-16 13:18:40.439 [main] DEBUG nextflow.Session - Executor pool size: 56 Jul-16 13:18:40.461 [main] DEBUG nextflow.cli.CmdRun - Version: 0.30.2 build 4867 Modified: 16-06-2018 17:49 UTC (19:49 CEST) System: Linux 3.10.0-693.17.1.el7.x86_64 Runtime: Groovy 2.4.15 on Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13 Encoding: UTF-8 (UTF-8) Process: 35923@login-02 [172.16.61.3] CPUs: 56 - Mem: 125.9 GB (1.5 GB) - Swap: 0 (0) Jul-16 13:18:40.483 [main] DEBUG nextflow.Session - Work-dir: /scratch-ii2/users/tobias.neumann [fhgfs] Jul-16 13:18:40.597 [main] DEBUG nextflow.Session - Session start invoked Jul-16 13:18:40.599 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start Jul-16 13:18:40.600 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing Jul-16 13:18:40.729 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Jul-16 13:18:40.731 [main] INFO nextflow.Nextflow - Jul-16 13:18:40.731 [main] INFO nextflow.Nextflow - parameters Jul-16 13:18:40.731 [main] INFO nextflow.Nextflow - ====================== Jul-16 13:18:40.731 [main] INFO nextflow.Nextflow - input directory : test Jul-16 13:18:40.731 [main] INFO nextflow.Nextflow - Centrifuge index : /groups/obenauf/Software/indices/virus/Centrifuge/centrifuge/p+h+v Jul-16 13:18:40.732 [main] INFO nextflow.Nextflow - Salmon index : /groups/obenauf/Software/indices/hg38/salmon/gencode.v28.salmon Jul-16 13:18:40.732 [main] INFO nextflow.Nextflow - bwa index : /groups/obenauf/Software/indices/virus/Centrifuge/bwa/p+h+v_unique.fa Jul-16 13:18:40.732 [main] INFO nextflow.Nextflow - ====================== Jul-16 13:18:40.732 [main] INFO nextflow.Nextflow - Jul-16 13:18:40.741 [main] DEBUG nextflow.Channel - files for syntax: glob; folder: test/; pattern: *.bam; options: null Jul-16 13:18:40.860 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:bamToFastq` matches process bamToFastq Jul-16 13:18:40.865 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Jul-16 13:18:40.865 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Jul-16 13:18:40.872 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Jul-16 13:18:40.873 [main] INFO nextflow.executor.Executor - [warm up] executor > slurm Jul-16 13:18:40.877 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 100; pollInterval: 5s; dumpInterval: 5m Jul-16 13:18:40.879 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: TaskPollingMonitor Jul-16 13:18:40.880 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Jul-16 13:18:40.881 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: slurm Jul-16 13:18:40.882 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Jul-16 13:18:40.904 [main] DEBUG nextflow.Session - >>> barrier register (process: bamToFastq) Jul-16 13:18:40.906 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bamToFastq -- maxForks: 20 Jul-16 13:18:40.925 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:centrifuge` matches process centrifuge Jul-16 13:18:40.927 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Jul-16 13:18:40.927 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Jul-16 13:18:40.927 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Jul-16 13:18:40.928 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Jul-16 13:18:40.928 [main] DEBUG nextflow.Session - >>> barrier register (process: centrifuge) Jul-16 13:18:40.928 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > centrifuge -- maxForks: 20 Jul-16 13:18:40.933 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:salmon` matches process salmon Jul-16 13:18:40.934 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Jul-16 13:18:40.934 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Jul-16 13:18:40.934 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Jul-16 13:18:40.934 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Jul-16 13:18:40.935 [main] DEBUG nextflow.Session - >>> barrier register (process: salmon) Jul-16 13:18:40.935 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > salmon -- maxForks: 20 Jul-16 13:18:40.938 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:bwa` matches process bwa Jul-16 13:18:40.939 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Jul-16 13:18:40.939 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Jul-16 13:18:40.939 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Jul-16 13:18:40.939 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Jul-16 13:18:40.939 [main] DEBUG nextflow.Session - >>> barrier register (process: bwa) Jul-16 13:18:40.940 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > bwa -- maxForks: 20 Jul-16 13:18:40.942 [main] DEBUG nextflow.util.CacheHelper - Config settings `withName:manta` matches process manta Jul-16 13:18:40.943 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: slurm Jul-16 13:18:40.943 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'slurm' Jul-16 13:18:40.943 [main] DEBUG nextflow.executor.Executor - Initializing executor: slurm Jul-16 13:18:40.943 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Jul-16 13:18:40.944 [main] DEBUG nextflow.Session - >>> barrier register (process: manta) Jul-16 13:18:40.944 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > manta -- maxForks: 20 Jul-16 13:18:40.945 [main] DEBUG nextflow.script.ScriptRunner - > Await termination Jul-16 13:18:40.945 [main] DEBUG nextflow.Session - Session await Jul-16 13:18:41.005 [Actor Thread 7] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=docker://obenauflab/virusintegration:latest; path=/groups/zuber/zubarchive/USERS/tobias/.singularity/obenauflab-virusintegration-latest.img Jul-16 13:18:41.102 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process bamToFastq (CCKTHANXX_4#66882_ACAGAT) > jobId: 503016; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 Jul-16 13:18:41.106 [Task submitter] INFO nextflow.Session - [62/e73d0d] Submitted process > bamToFastq (CCKTHANXX_4#66882_ACAGAT) Jul-16 13:18:41.142 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA) > jobId: 503017; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 Jul-16 13:18:41.143 [Task submitter] INFO nextflow.Session - [7c/92f55e] Submitted process > bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA) Jul-16 13:18:41.170 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process bamToFastq (BSF_0449_HTJ32BBXX_4) > jobId: 503018; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a Jul-16 13:18:41.170 [Task submitter] INFO nextflow.Session - [34/2f9603] Submitted process > bamToFastq (BSF_0449_HTJ32BBXX_4) Jul-16 13:23:45.912 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 13:28:45.941 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 13:33:45.963 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 13:38:45.982 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 13:43:45.997 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 13:48:46.013 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 13:53:46.025 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 13:58:46.038 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:03:46.050 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:08:46.060 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:13:46.075 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:18:46.083 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:23:46.091 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:28:46.101 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:33:46.114 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:38:46.131 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:43:46.145 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:48:46.156 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:53:46.171 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 14:58:46.184 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:03:46.196 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:08:46.205 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:13:46.219 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:18:46.234 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:23:46.250 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:28:46.260 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:33:46.274 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:38:46.286 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ] Jul-16 15:43:46.301 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 3 -- pending tasks are shown below ~> TaskHandler[jobId: 503016; id: 2; name: bamToFastq (CCKTHANXX_4#66882_ACAGAT); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/62/e73d0d5692d83dc29adbe71e06c5d3 started: -; exited: -; ] ~> TaskHandler[jobId: 503017; id: 1; name: bamToFastq (CAFW2ANXX_6#RNAseq-MCC-25-1-GCCACA); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/7c/92f55e90cb0a0d693dc20f65a5be21 started: -; exited: -; ] ~> TaskHandler[jobId: 503018; id: 3; name: bamToFastq (BSF_0449_HTJ32BBXX_4); status: SUBMITTED; exit: -; error: -; workDir: /scratch-ii2/users/tobias.neumann/34/2f960358fe8d0cf96b0e3ac989f08a started: -; exited: -; ]