2017-05-22 12:25:04,399 rMATS version: 3.2.5
2017-05-22 12:25:04,400 Start the program with [RNASeq-MATS.py -s1 /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-hind2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-hind2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-hind2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-hind2-paired.fastq -s2 /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-hind2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-hind2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-hind2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-hind2-paired.fastq -gtf gtf/Mus_musculus.Ensembl.NCBIM37.65.gtf -bi /cbcl/forouzme/Projects/PolyA/rMATS/mm9-star/ -t paired -len 72 -novelSS 1 -o colleen-hind-ctrl-KO-mm9-frstrand -libType fr-firststrand ]

2017-05-22 12:25:04,481 ################### folder names and associated input files #############
2017-05-22 12:25:04,481 SAMPLE_1\REP_1	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-hind2-paired.fastq
2017-05-22 12:25:04,481 SAMPLE_1\REP_2	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-hind2-paired.fastq
2017-05-22 12:25:04,481 SAMPLE_1\REP_3	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-hind2-paired.fastq
2017-05-22 12:25:04,481 SAMPLE_1\REP_4	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-hind2-paired.fastq
2017-05-22 12:25:04,481 SAMPLE_2\REP_1	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-hind2-paired.fastq
2017-05-22 12:25:04,481 SAMPLE_2\REP_2	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-hind2-paired.fastq
2017-05-22 12:25:04,481 SAMPLE_2\REP_3	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-hind2-paired.fastq
2017-05-22 12:25:04,481 SAMPLE_2\REP_4	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-hind1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-hind2-paired.fastq
2017-05-22 12:25:04,481 #########################################################################

2017-05-22 12:25:04,482 start mapping..
2017-05-22 12:25:04,482 mapping the first sample