2017-05-22 12:25:14,283 rMATS version: 3.2.5 2017-05-22 12:25:14,285 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 12:25:14,425 ################### folder names and associated input files ############# 2017-05-22 12:25:14,425 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 12:25:14,426 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 12:25:14,426 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 12:25:14,426 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 12:25:14,426 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 12:25:14,426 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 12:25:14,426 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 12:25:14,426 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 12:25:14,426 ######################################################################### 2017-05-22 12:25:14,426 start mapping.. 2017-05-22 12:25:14,426 mapping the first sample 2017-05-30 14:19:35,088 mapping sample_1, rep_1 is done with status 26624 2017-05-30 14:19:35,089 error in mapping sample_1, rep_1: 26624 2017-05-30 14:19:35,089 error detail: May 22 12:25:14 ..... started STAR run May 22 12:25:14 ..... loading genome May 30 14:14:41 ..... processing annotations GTF May 30 14:15:01 ..... inserting junctions into the genome indices May 30 14:19:34 ..... started mapping EXITING because of FATAL ERROR: could not create output file /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/SAMPLE_1/REP_1/_STARtmp//Chimeric.out.sam.thread0 Solution: check that you have permission to write this file May 30 14:19:34 ...... FATAL ERROR, exiting 2017-05-30 14:19:35,089 There is an exception in mapping 2017-05-30 14:19:35,089 Exception: 2017-05-30 14:19:35,089 Detail: