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
00:00:00.082	Parsing
00:00:03.507	Initializing
00:00:03.516	Process ID: chipseq.bds.20171207_115700_844
00:00:03.516	Running
00:00:06.862	Executioner factory: Creating new executioner type 'LOCAL'
00:00:06.871	ExecutionerLocal 'Local[30]': Started running
00:00:06.871	ExecutionerLocal 'Local[30]': Queuing task: chipseq.bds.20171207_115700_844/task.postalign_bam.dedup_bam_1_rep1.line_155.id_10
00:00:06.872	Waiting for all tasks to finish.
00:00:06.872	Wait: Waiting for task to finish: chipseq.bds.20171207_115700_844/task.postalign_bam.dedup_bam_1_rep1.line_155.id_10, state: SCHEDULED
00:00:06.873	ExecutionerLocal 'Local[30]': Task selected 'chipseq.bds.20171207_115700_844/task.postalign_bam.dedup_bam_1_rep1.line_155.id_10' on host 'localhost'
2017/12/07 11:57:04 fork/exec /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115700_844/task.postalign_bam.dedup_bam_1_rep1.line_155.id_10.sh: permission denied
Task failed:
	Program & line     : '/home/nico/TF_chipseq_pipeline/modules/postalign_bam.bds', line 155
	Task Name          : 'dedup_bam_1 rep1'
	Task ID            : 'chipseq.bds.20171207_115700_844/task.postalign_bam.dedup_bam_1_rep1.line_155.id_10'
	Task PID           : '1200'
	Task hint          : 'if [[ 0 > 0 ]]; then; sambamba sort -t 3 /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/KrChIP_1-Ac1.bam -n -o /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/KrChIP_1-Ac1.qnmsrt.bam;; samtools view -h /media/nico/data/home2/pro'
	Task resources     : 'cpus: 3	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/KrChIP_1-Ac1.bam]'
	Output files       : '[/media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/KrChIP_1-Ac1.filt.bam]'
	Script file        : '/media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/chipseq.bds.20171207_115700_844/task.postalign_bam.dedup_bam_1_rep1.line_155.id_10.sh'
	Exit status        : '1'
	Program            : 
		
		# SYS command. line 157
		
		 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 165
		
		 if [[ 0 > 0 ]]; then \
						sambamba sort -t 3 /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/KrChIP_1-Ac1.bam -n -o /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/KrChIP_1-Ac1.qnmsrt.bam; \
						samtools view -h /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/KrChIP_1-Ac1.qnmsrt.bam | $(which assign_multimappers.py) -k 0 | \
						samtools view -F 1804 -Su /dev/stdin | \
						sambamba sort -t 3 /dev/stdin -o /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/KrChIP_1-Ac1.filt.bam; \
						rm -f /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/KrChIP_1-Ac1.qnmsrt.bam; \
					    else \
					    	samtools view -F 1804 -q 30 -u /media/nico/data/home2/projects/macrophages/Kr_ChIPseq_Data/KrChIP_1-Ac1.bam | \
					    	sambamba sort -t 3 /dev/stdin -o /media/nico/data/home2/projects/macrophages/chip_ana2/8-ENCODE-pipeline/contr_Ac/align/rep1/KrChIP_1-Ac1.filt.bam; \
					    fi
		
		# SYS command. line 176
		
		 TASKTIME=$[$(date +%s)-${STARTTIME}]; echo "Task has finished (${TASKTIME} seconds)."; sleep 0

00:00:07.626	Wait: Task 'chipseq.bds.20171207_115700_844/task.postalign_bam.dedup_bam_1_rep1.line_155.id_10' finished.
Fatal error: /home/nico/TF_chipseq_pipeline/modules/postalign_bam.bds, line 181, pos 3. 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 366 :		for ( int ctl=0; ctl <= 1; ctl++) { // iterate through inputs (ctl==0 : exp. replicate, ctl==1 : control)
chipseq.bds, line 369 :			for ( int rep=1; rep <= get_num_rep( ctl ); rep++) {
chipseq.bds, line 375 :				if ( no_par ) align( ctl, rep, nth_rep{group} ) // parallel jobs for align() for each replicate and each control
chipseq.bds, line 439 :	void align( int ctl, int rep, int nth_rep ) {
chipseq.bds, line 441 :		if ( is_se( ctl, rep ) ) {
chipseq.bds, line 442 :			align_SE( ctl, rep, nth_rep )
chipseq.bds, line 449 :	void align_SE( int ctl, int rep, int nth_rep ) {
chipseq.bds, line 506 :		if ( is_input_bam( ctl, rep ) || is_input_fastq( ctl, rep ) ) {
chipseq.bds, line 515 :			if ( no_dup_removal ) {
chipseq.bds, line 521 :			else {
chipseq.bds, line 522 :				( filt_bam_, dup_qc_, flagstat_nodup_qc_, pbc_qc_ ) \
chipseq.bds, line 523 :					= dedup_bam( bam_, aln_o_dir, qc_o_dir, group, nth_rep )			
postalign_bam.bds, line 127 :	string[] dedup_bam( string bam, string o_dir, string log_o_dir, string group, int nth_dedup ) {
postalign_bam.bds, line 143 :		if ( out<-in ) {
postalign_bam.bds, line 181 :			wait // wait for filt_bam

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
00:00:07.707	Writing report file 'chipseq.bds.20171207_115700_844.report.html'
00:00:07.731	Program 'chipseq.bds.20171207_115700_844' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: dedup_bam_1 rep1.
00:00:07.731	Finished. Exit code: 1
00:00:07.732	ExecutionerLocal 'Local[30]': Killed