$PATH:
/illumina/thirdparty/gdb/el6/gdb-7.8/bin:/illumina/thirdparty/gdb/gdb-7.8/bin:/illumina/sync/software/unofficial/Isas/packages/mono-4.2.3/bin:/illumina/sync/software/unofficial/Isas/packages/jdk1.6.0_32/bin:/illumina/sync/software/unofficial/Isas/packages/TEE-CLC-10.0.0:/illumina/sync/software/unofficial/Isas/packages/bin:/illumina/sync/software/unofficial/Isas/packages/python-2.7/envs/20151030/bin:/cm/shared/apps/sge/2011.11p1/bin/linux-x64:/cm/shared/apps/sge/2011.11p1/bin/linux-x64:/cm/shared/apps/gcc/4.8.4/bin:/usr/lib64/qt-3.3/bin:/scratch/5233537.1.whole:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/cm/shared/apps/sge/current/bin/linux-x64:/home/svc_sage/bin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:/home/svc_sage/bin
$LD_LIBRARY_PATH:
/illumina/sync/software/unofficial/Isas/packages/mono-4.2.3/lib64:/illumina/sync/software/unofficial/Isas/packages/mono-4.2.3/lib:/illumina/sync/software/unofficial/Isas/packages/lib64:/illumina/sync/software/unofficial/Isas/packages/lib:/illumina/sync/software/unofficial/Isas/packages/boost-1.49.0/lib:/illumina/sync/software/unofficial/Isas/packages/boost-1.54.0/lib:/cm/shared/apps/sge/2011.11p1/lib/linux-x64:/cm/shared/apps/sge/2011.11p1/lib/linux-x64:/cm/shared/apps/gcc/4.8.4/lib:/cm/shared/apps/gcc/4.8.4/lib64:/cm/shared/apps/sge/current/lib/linux-x64
Using mono:
Mono JIT compiler version 4.2.3 (Stable 4.2.3.4/832de4b Mon Apr 18 11:03:10 PDT 2016)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
	TLS:           __thread
	SIGSEGV:       altstack
	Notifications: epoll
	Architecture:  amd64
	Disabled:      none
	Misc:          softdebug 
	LLVM:          supported, not enabled.
	GC:            sgen

Isas GenerateFASTQWorker 1.32.0
  -a
  /illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/Analysis
  -r
  /illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/RunFolder

2017-07-05T17:31:13,Workflow version 1.32.0: Starting Logging for /illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/Analysis
2017-07-05T17:31:13,Run by user: svc_sage
2017-07-05T17:31:13,System node170 with 56 cores and 251.8 GB of RAM
2017-07-05T17:31:13,Free gigabytes of disk space at /illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/Analysis: 97507.32
2017-07-05T17:31:13,Workflow: GenerateFASTQWorker Version=1.32.0
2017-07-05T17:31:14,Getting set of tile numbers from TileSet in RunInfo.xml.
2017-07-05T17:31:14,Running checkpoint 01: Generate FASTQ
2017-07-05T17:31:14,Running checkpoint 01.01: Generate FASTQ.Fastq Generation
2017-07-05T17:31:14,Launch process: /illumina/sync/software/unofficial/Isas/GenerateFASTQWorker/1.32.0/bcl2fastq2/bin/bcl2fastq  --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R "/illumina/scratch/Voyager/170630_A00104_0125_BH2V37DMXX" --sample-sheet "/illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/RunFolder/SampleSheet.csv" -o "/illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/Analysis/Temp_01.01-GenerateFASTQ.FastqGeneration"
2017-07-05T18:12:17,Max job memory (GB): 13.7
2017-07-05T18:12:17,Longest job runtime (Hours): 0.68
2017-07-05T18:12:17,>>>bcl2fastq2 call complete!
2017-07-05T18:12:17,>>>Total fastq generation time: 00:41:03.0
2017-07-05T18:12:17,Launch process: /illumina/sync/software/unofficial/Isas/GenerateFASTQWorker/1.32.0/bcl2fastq2/bin/bcl2fastq --version
2017-07-05T18:12:17,Max job memory (GB): 0.8
2017-07-05T18:12:17,Longest job runtime (Hours): 0.00
2017-07-05T18:12:17,Elapsed time (step/time(sec)/name)	01.01	00:41:03.6	Generate FASTQ.Fastq Generation
2017-07-05T18:12:17,Saving checkpoint results to /illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/Analysis/Checkpoints/01.01-GenerateFASTQ.FastqGeneration.json
2017-07-05T18:12:17,Elapsed time (step/time(sec)/name)	01	00:41:03.6	Generate FASTQ
2017-07-05T18:12:17,Saving Completed Job Information to /illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/Analysis
2017-07-05T18:12:17,Saving checkpoint results to /illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/Analysis/Checkpoints/01-GenerateFASTQ.json
2017-07-05T18:12:17,Total execution time: 00:41:03.6
2017-07-05T18:12:18,Free gigabytes of disk space at /illumina/scratch/Voyager/BUILDS/raptor_builds/IsasNS4/demux/65367/Analysis: 97329.81
2017-07-05T18:12:18,Total execution time: 00:41:04.6