You provided these parameters:
 SLURM workload manager:	no
 Summary Stats to produce:	yes
 Start the pipeline from:	filtering
 A custom mapped BAM:		NA
 Custom filtered FASTQ:		no
 Barcode read:			/data/share/htp/zUMIs_paper/GigaDB/data/demult_HEK_r1.fq.gz
 cDNA read:			/data/share/htp/zUMIs_paper/GigaDB/data/demult_HEK_r2.fq.gz
 Study/sample name:		HEK
 Output directory:		/data/share/htp/zUMIs_paper/GigaDB/run_dir/
 Cell/sample barcode range:	1-6
 UMI barcode range:		7-16
 Retain cell with >=N reads:	100
 Genome directory:		/data/share/htp/zUMIs_paper/GigaDB/reference/STAR5idx_noGTF
 GTF annotation file:		/data/share/htp/zUMIs_paper/GigaDB/reference/Homo_sapiens.GRCh38.84_chrsNamesUCSC.gtf
 Number of processors:		16
 Read length:			50
 Strandedness:			0
 Cell barcode Phred:		17
 UMI barcode Phred:		17
 # bases below phred in CellBC:	1
 # bases below phred in UMI:	1
 Hamming Distance (UMI):	0
 Hamming Distance (CellBC):	0
 Plate Barcode Read:    	NA
 Plate Barcode range:   	NA
 Barcodes:			/data/share/htp/zUMIs_paper/GigaDB/reference/SCRBseq_96_setC_justBCs.txt
 zUMIs directory:		/data/share/htp/zUMIs_paper/GigaDB/zUMIs-master
 STAR executable		STAR
 samtools executable		samtools
 pigz executable		pigz
 Rscript executable		Rscript
 Additional STAR parameters:	
 STRT-seq data:			no
 InDrops data:			no
 Library read for InDrops:	NA
 Barcode read2(STRT-seq):	NA
 Barcode read2 range(STRT-seq):	0-0
 Bases(G) to trim(STRT-seq):	3
 Subsampling reads:		0 


 zUMIs version 0.0.6b