Picked up _JAVA_OPTIONS: -Xms256M -Xmx728M -XX:ParallelGCThreads=1
00:00:00.000	Bds 0.99999e (build 2016-08-26 06:34), by Pablo Cingolani
00:00:00.084	Parsing
00:00:03.497	Initializing
00:00:03.511	Process ID: chipseq.bds.20171207_115442_494
00:00:03.511	Running
00:00:10.960	Waiting for all 'parrallel' to finish.
00:00:10.960	Waiting for parallel 'chipseq.bds.20171207_115442_494_parallel_30' to finish. RunState: OK
00:00:11.201	Executioner factory: Creating new executioner type 'LOCAL'
00:00:11.209	ExecutionerLocal 'Local[33]': Started running
00:00:11.209	ExecutionerLocal 'Local[33]': Queuing task: chipseq.bds.20171207_115442_494_parallel_30/task.postalign_bam.pool_fastq_rep1.line_779.id_10
00:00:11.210	Waiting for all tasks to finish.
00:00:11.210	Wait: Waiting for task to finish: chipseq.bds.20171207_115442_494_parallel_30/task.postalign_bam.pool_fastq_rep1.line_779.id_10, state: SCHEDULED
00:00:11.210	ExecutionerLocal 'Local[33]': Task selected 'chipseq.bds.20171207_115442_494_parallel_30/task.postalign_bam.pool_fastq_rep1.line_779.id_10' on host 'localhost'
00:00:11.316	ExecutionerLocal 'Local[33]': Queuing task: chipseq.bds.20171207_115442_494_parallel_31/task.postalign_bam.pool_fastq_rep2.line_779.id_11
00:00:11.317	Waiting for all tasks to finish.
00:00:11.317	Wait: Waiting for task to finish: chipseq.bds.20171207_115442_494_parallel_31/task.postalign_bam.pool_fastq_rep2.line_779.id_11, state: SCHEDULED
00:00:11.715	ExecutionerLocal 'Local[33]': Task selected 'chipseq.bds.20171207_115442_494_parallel_31/task.postalign_bam.pool_fastq_rep2.line_779.id_11' on host 'localhost'
2017/12/07 11:54:50 fork/exec /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115442_494_parallel_30/task.postalign_bam.pool_fastq_rep1.line_779.id_10.sh: permission denied
Task failed:
	Program & line     : '/home/nico/TF_chipseq_pipeline/modules/postalign_bam.bds', line 779
	Task Name          : 'pool_fastq rep1'
	Task ID            : 'chipseq.bds.20171207_115442_494_parallel_30/task.postalign_bam.pool_fastq_rep1.line_779.id_10'
	Task PID           : '27547'
	Task hint          : 'zcat /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L002_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S'
	Task resources     : 'cpus: -1	mem: -1.0 B	wall-timeout: 8640000'
	State              : 'ERROR'
	Dependency state   : 'ERROR'
	Retries available  : '1'
	Input files        : '[/media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L001_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L002_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L003_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L004_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L005_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L006_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L007_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/1-Ac1_S9_L001_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/1-Ac1_S9_L002_R1_001.fastq.gz]'
	Output files       : '[/media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/1-Ac1_S9_L001_R1_001_pooled.fastq.gz]'
	Script file        : '/media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115442_494_parallel_30/task.postalign_bam.pool_fastq_rep1.line_779.id_10.sh'
	Exit status        : '1'
	Program            : 
		
		# SYS command. line 781
		
		 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/home/nico/TF_chipseq_pipeline/.:/home/nico/TF_chipseq_pipeline/modules:/home/nico/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
		
		# SYS command. line 783
		
		 zcat /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L002_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L003_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L004_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L005_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L006_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-Ac1_S9_L007_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/1-Ac1_S9_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/1-Ac1_S9_L002_R1_001.fastq.gz | gzip -nc > /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/1-Ac1_S9_L001_R1_001_pooled.fastq.gz
		
		# SYS command. line 785
		
		 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

00:00:11.963	Wait: Task 'chipseq.bds.20171207_115442_494_parallel_30/task.postalign_bam.pool_fastq_rep1.line_779.id_10' finished.
Fatal error: /home/nico/TF_chipseq_pipeline/chipseq.bds, line 470, pos 4. Task/s failed.

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
00:00:11.995	Parallel 'chipseq.bds.20171207_115442_494_parallel_30' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: pool_fastq rep1.
00:00:11.995	Waiting for parallel 'chipseq.bds.20171207_115442_494_parallel_31' to finish. RunState: OK
2017/12/07 11:54:50 fork/exec /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115442_494_parallel_31/task.postalign_bam.pool_fastq_rep2.line_779.id_11.sh: permission denied
00:00:12.242	ExecutionerLocal 'Local[33]': Queuing task: chipseq.bds.20171207_115442_494_parallel_32/task.postalign_bam.pool_fastq_ctl1.line_779.id_12
00:00:12.242	Waiting for all tasks to finish.
00:00:12.242	Wait: Waiting for task to finish: chipseq.bds.20171207_115442_494_parallel_32/task.postalign_bam.pool_fastq_ctl1.line_779.id_12, state: SCHEDULED
Task failed:
	Program & line     : '/home/nico/TF_chipseq_pipeline/modules/postalign_bam.bds', line 779
	Task Name          : 'pool_fastq rep2'
	Task ID            : 'chipseq.bds.20171207_115442_494_parallel_31/task.postalign_bam.pool_fastq_rep2.line_779.id_11'
	Task PID           : '27553'
	Task hint          : 'zcat /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L002_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1'
	Task resources     : 'cpus: -1	mem: -1.0 B	wall-timeout: 8640000'
	State              : 'ERROR'
	Dependency state   : 'ERROR'
	Retries available  : '1'
	Input files        : '[/media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L001_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L002_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L003_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L004_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L005_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L006_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L007_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/2-Ac1_S17_L001_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/2-Ac1_S17_L002_R1_001.fastq.gz]'
	Output files       : '[/media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep2/2-Ac1_S17_L001_R1_001_pooled.fastq.gz]'
	Script file        : '/media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115442_494_parallel_31/task.postalign_bam.pool_fastq_rep2.line_779.id_11.sh'
	Exit status        : '1'
	Program            : 
		
		# SYS command. line 781
		
		 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/home/nico/TF_chipseq_pipeline/.:/home/nico/TF_chipseq_pipeline/modules:/home/nico/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
		
		# SYS command. line 783
		
		 zcat /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L002_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L003_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L004_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L005_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L006_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/2-Ac1_S17_L007_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/2-Ac1_S17_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/2-Ac1_S17_L002_R1_001.fastq.gz | gzip -nc > /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep2/2-Ac1_S17_L001_R1_001_pooled.fastq.gz
		
		# SYS command. line 785
		
		 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

00:00:12.318	Wait: Task 'chipseq.bds.20171207_115442_494_parallel_31/task.postalign_bam.pool_fastq_rep2.line_779.id_11' finished.
Fatal error: /home/nico/TF_chipseq_pipeline/chipseq.bds, line 470, pos 4. Task/s failed.

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
00:00:12.332	Parallel 'chipseq.bds.20171207_115442_494_parallel_31' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: pool_fastq rep2.
00:00:12.332	Waiting for parallel 'chipseq.bds.20171207_115442_494_parallel_32' to finish. RunState: OK
00:00:12.721	ExecutionerLocal 'Local[33]': Task selected 'chipseq.bds.20171207_115442_494_parallel_32/task.postalign_bam.pool_fastq_ctl1.line_779.id_12' on host 'localhost'
2017/12/07 11:54:51 fork/exec /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115442_494_parallel_32/task.postalign_bam.pool_fastq_ctl1.line_779.id_12.sh: permission denied
Task failed:
	Program & line     : '/home/nico/TF_chipseq_pipeline/modules/postalign_bam.bds', line 779
	Task Name          : 'pool_fastq ctl1'
	Task ID            : 'chipseq.bds.20171207_115442_494_parallel_32/task.postalign_bam.pool_fastq_ctl1.line_779.id_12'
	Task PID           : '27595'
	Task hint          : 'zcat /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L002_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S'
	Task resources     : 'cpus: -1	mem: -1.0 B	wall-timeout: 8640000'
	State              : 'ERROR'
	Dependency state   : 'ERROR'
	Retries available  : '1'
	Input files        : '[/media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L001_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L002_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L003_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L004_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L005_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L006_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L007_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/1-In1_S5_L001_R1_001.fastq.gz, /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/1-In1_S5_L002_R1_001.fastq.gz]'
	Output files       : '[/media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/ctl1/1-In1_S5_L001_R1_001_pooled.fastq.gz]'
	Script file        : '/media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115442_494_parallel_32/task.postalign_bam.pool_fastq_ctl1.line_779.id_12.sh'
	Exit status        : '1'
	Program            : 
		
		# SYS command. line 781
		
		 if [[ -f $(which conda) && $(conda env list | grep aquas_chipseq | wc -l) != "0" ]]; then source activate aquas_chipseq; sleep 5; fi;  export PATH=/home/nico/TF_chipseq_pipeline/.:/home/nico/TF_chipseq_pipeline/modules:/home/nico/TF_chipseq_pipeline/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)
		
		# SYS command. line 783
		
		 zcat /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L002_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L003_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L004_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L005_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L006_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BCARCAANXX/1-In1_S5_L007_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/1-In1_S5_L001_R1_001.fastq.gz /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/BHJJG3BCXY/1-In1_S5_L002_R1_001.fastq.gz | gzip -nc > /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/ctl1/1-In1_S5_L001_R1_001_pooled.fastq.gz
		
		# SYS command. line 785
		
		 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

00:00:13.243	Wait: Task 'chipseq.bds.20171207_115442_494_parallel_32/task.postalign_bam.pool_fastq_ctl1.line_779.id_12' finished.
Fatal error: /home/nico/TF_chipseq_pipeline/chipseq.bds, line 470, pos 4. Task/s failed.

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
00:00:13.256	Parallel 'chipseq.bds.20171207_115442_494_parallel_32' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: pool_fastq ctl1.
Fatal error: /home/nico/TF_chipseq_pipeline/chipseq.bds, line 379, pos 2. Task/s failed.
chipseq.bds, line 90 :	main()
chipseq.bds, line 93 :	void main() { // chipseq pipeline starts here
chipseq.bds, line 99 :		align() // align and postalign
chipseq.bds, line 330 :	void align() {
chipseq.bds, line 379 :		wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
00:00:13.304	Writing report file 'chipseq.bds.20171207_115442_494.report.html'
00:00:13.329	Program 'chipseq.bds.20171207_115442_494' finished, exit value: 1, tasks executed: 3, tasks failed: 3, tasks failed names: pool_fastq ctl1 , pool_fastq rep2 , pool_fastq rep1.
00:00:13.329	Finished. Exit code: 1
00:00:13.330	ExecutionerLocal 'Local[33]': Killed