2017-05-22 12:23:31,318 rMATS version: 3.2.5
2017-05-22 12:23:31,319 Start the program with [RNASeq-MATS.py -s1 /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-cort2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-cort2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-cort2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-cort2-paired.fastq -s2 /cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-cort2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-cort2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-cort2-paired.fastq,/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-cort2-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-cort-ctrl-KO-mm9-frstrand -libType fr-firststrand ]

2017-05-22 12:23:31,401 ################### folder names and associated input files #############
2017-05-22 12:23:31,401 SAMPLE_1\REP_1	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt1-cort2-paired.fastq
2017-05-22 12:23:31,401 SAMPLE_1\REP_2	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt2-cort2-paired.fastq
2017-05-22 12:23:31,402 SAMPLE_1\REP_3	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt3-cort2-paired.fastq
2017-05-22 12:23:31,402 SAMPLE_1\REP_4	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/Wt4-cort2-paired.fastq
2017-05-22 12:23:31,402 SAMPLE_2\REP_1	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO1-cort2-paired.fastq
2017-05-22 12:23:31,402 SAMPLE_2\REP_2	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO2-cort2-paired.fastq
2017-05-22 12:23:31,402 SAMPLE_2\REP_3	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO3-cort2-paired.fastq
2017-05-22 12:23:31,402 SAMPLE_2\REP_4	/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-cort1-paired.fastq:/cbcl/forouzme/Projects/PolyA/embryonicpenn/fixed-data/paired/KO4-cort2-paired.fastq
2017-05-22 12:23:31,402 #########################################################################

2017-05-22 12:23:31,402 start mapping..
2017-05-22 12:23:31,402 mapping the first sample