2017-05-22 12:25:22,777 rMATS version: 3.2.5
2017-05-22 12:25:22,778 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 12:25:22,844 ################### folder names and associated input files #############
2017-05-22 12:25:22,844 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 12:25:22,844 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 12:25:22,844 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 12:25:22,844 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 12:25:22,844 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 12:25:22,844 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 12:25:22,844 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 12:25:22,844 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 12:25:22,844 #########################################################################

2017-05-22 12:25:22,845 start mapping..
2017-05-22 12:25:22,845 mapping the first sample
2017-05-22 12:38:54,349 mapping sample_1, rep_1 is done with status 0
2017-05-22 12:38:54,350 May 22 12:25:22 ..... started STAR run
May 22 12:25:22 ..... loading genome
May 22 12:25:42 ..... processing annotations GTF
May 22 12:25:55 ..... inserting junctions into the genome indices
May 22 12:30:28 ..... started mapping
May 22 12:38:05 ..... started sorting BAM
May 22 12:38:53 ..... finished successfully
2017-05-22 12:50:31,712 mapping sample_1, rep_2 is done with status 0
2017-05-22 12:50:31,712 May 22 12:38:54 ..... started STAR run
May 22 12:38:54 ..... loading genome
May 22 12:39:22 ..... processing annotations GTF
May 22 12:39:41 ..... inserting junctions into the genome indices
May 22 12:44:13 ..... started mapping
May 22 12:49:58 ..... started sorting BAM
May 22 12:50:31 ..... finished successfully
2017-05-22 13:03:04,342 mapping sample_1, rep_3 is done with status 0
2017-05-22 13:03:04,342 May 22 12:50:31 ..... started STAR run
May 22 12:50:31 ..... loading genome
May 22 12:50:57 ..... processing annotations GTF
May 22 12:51:10 ..... inserting junctions into the genome indices
May 22 12:55:52 ..... started mapping
May 22 13:02:22 ..... started sorting BAM
May 22 13:03:03 ..... finished successfully
2017-05-22 13:14:25,002 mapping sample_1, rep_4 is done with status 0
2017-05-22 13:14:25,003 May 22 13:03:04 ..... started STAR run
May 22 13:03:04 ..... loading genome
May 22 13:03:30 ..... processing annotations GTF
May 22 13:03:44 ..... inserting junctions into the genome indices
May 22 13:08:10 ..... started mapping
May 22 13:13:48 ..... started sorting BAM
May 22 13:14:24 ..... finished successfully
2017-05-22 13:14:25,003 mapping the second sample
2017-05-22 13:27:59,925 mapping sample_2, rep_1 is done with status 0
2017-05-22 13:27:59,925 May 22 13:14:25 ..... started STAR run
May 22 13:14:25 ..... loading genome
May 22 13:14:47 ..... processing annotations GTF
May 22 13:15:00 ..... inserting junctions into the genome indices
May 22 13:19:35 ..... started mapping
May 22 13:27:02 ..... started sorting BAM
May 22 13:27:59 ..... finished successfully
2017-05-22 13:38:07,292 mapping sample_2, rep_2 is done with status 0
2017-05-22 13:38:07,293 May 22 13:27:59 ..... started STAR run
May 22 13:27:59 ..... loading genome
May 22 13:28:31 ..... processing annotations GTF
May 22 13:28:45 ..... inserting junctions into the genome indices
May 22 13:33:18 ..... started mapping
May 22 13:37:35 ..... started sorting BAM
May 22 13:38:06 ..... finished successfully
2017-05-22 13:47:47,594 mapping sample_2, rep_3 is done with status 0
2017-05-22 13:47:47,594 May 22 13:38:07 ..... started STAR run
May 22 13:38:07 ..... loading genome
May 22 13:38:32 ..... processing annotations GTF
May 22 13:38:45 ..... inserting junctions into the genome indices
May 22 13:43:36 ..... started mapping
May 22 13:47:18 ..... started sorting BAM
May 22 13:47:47 ..... finished successfully
2017-05-22 14:01:01,859 mapping sample_2, rep_4 is done with status 0
2017-05-22 14:01:01,860 May 22 13:47:47 ..... started STAR run
May 22 13:47:47 ..... loading genome
May 22 13:48:13 ..... processing annotations GTF
May 22 13:48:26 ..... inserting junctions into the genome indices
May 22 13:53:00 ..... started mapping
May 22 14:00:14 ..... started sorting BAM
May 22 14:01:01 ..... finished successfully
2017-05-22 14:01:01,860 done mapping..
2017-05-22 14:01:01,860 indexing bam files to use pysam
2017-05-22 14:01:01,860 getting unique SAM function..
2017-05-22 15:00:21,965 done indexing bam files..
2017-05-22 15:00:22,014 start getting AS events from GTF and BAM files
2017-05-22 15:00:22,014 getting AS events function..
2017-05-22 15:53:53,352 getting AS events is done with status 0
2017-05-22 15:53:53,352 
2017-05-22 15:53:53,352 done getting AS events..
2017-05-22 15:53:53,434 Setting proper string
2017-05-22 15:53:53,987 start making MATS input files from AS events and SAM files
2017-05-22 15:53:53,987 making MATS input function..
2017-05-22 17:11:31,362 making MATS input is done with status 0
2017-05-22 17:11:31,363 
2017-05-22 17:11:31,363 done making MATS input..
2017-05-22 17:11:31,363 start running MATS for each AS event
2017-05-22 17:11:31,363 running MATS for SE. Using Junction Counts only
2017-05-22 20:20:26,967 running MATS for SE using JC is done with status 0
2017-05-22 20:20:26,968 
2017-05-22 20:20:26,968 running MATS for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-22 22:26:20,816 running MATS for SE using JCEC is done with status 0
2017-05-22 22:26:20,816 
2017-05-22 22:26:20,816 running MATS for MXE. Using Junction Counts only
2017-05-22 22:43:30,884 running MATS for MXE using JC is done with status 0
2017-05-22 22:43:30,884 
2017-05-22 22:43:30,884 running MATS for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-22 22:51:11,716 running MATS for MXE using JCEC is done with status 0
2017-05-22 22:51:11,716 
2017-05-22 22:51:11,716 running MATS for A5SS. Using Junction Counts only
2017-05-22 23:49:54,853 running MATS for A5SS using JC is done with status 0
2017-05-22 23:49:54,854 
2017-05-22 23:49:54,854 running MATS for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 00:24:23,286 running MATS for A5SS using JCEC is done with status 0
2017-05-23 00:24:23,287 
2017-05-23 00:24:23,287 running MATS for A3SS. Using Junction Counts only
2017-05-23 01:55:46,321 running MATS for A3SS using JC is done with status 0
2017-05-23 01:55:46,322 
2017-05-23 01:55:46,322 running MATS for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 02:58:23,872 running MATS for A3SS using JCEC is done with status 0
2017-05-23 02:58:23,872 
2017-05-23 02:58:23,872 running MATS for RI. Using Junction Counts only
2017-05-23 03:12:28,085 running MATS for RI using JC is done with status 0
2017-05-23 03:12:28,086 
2017-05-23 03:12:28,086 running MATS for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:39,391 running MATS for RI using JCEC is done with status 0
2017-05-23 03:19:39,391 
2017-05-23 03:19:39,391 done running MATS for all AS event types..
2017-05-23 03:19:39,391 start joining MATS results for each AS event
2017-05-23 03:19:39,391 joining MATS for SE. Using Junction Counts only
2017-05-23 03:19:40,141 joining MATS for SE using JC is done with status 0
2017-05-23 03:19:40,141 
2017-05-23 03:19:40,141 joining MATS for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:40,788 joining MATS for SE using JCEC is done with status 0
2017-05-23 03:19:40,788 
2017-05-23 03:19:40,788 joining MATS for MXE. Using Junction Counts only
2017-05-23 03:19:41,009 joining MATS for MXE using JC is done with status 0
2017-05-23 03:19:41,009 
2017-05-23 03:19:41,010 joining MATS for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:41,208 joining MATS for MXE using JCEC is done with status 0
2017-05-23 03:19:41,208 
2017-05-23 03:19:41,208 joining MATS for A5SS. Using Junction Counts only
2017-05-23 03:19:41,510 joining MATS for A5SS using JC is done with status 0
2017-05-23 03:19:41,511 
2017-05-23 03:19:41,511 joining MATS for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:41,820 joining MATS for A5SS using JCEC is done with status 0
2017-05-23 03:19:41,820 
2017-05-23 03:19:41,820 joining MATS for A3SS. Using Junction Counts only
2017-05-23 03:19:42,272 joining MATS for A3SS using JC is done with status 0
2017-05-23 03:19:42,272 
2017-05-23 03:19:42,272 joining MATS for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:42,645 joining MATS for A3SS using JCEC is done with status 0
2017-05-23 03:19:42,646 
2017-05-23 03:19:42,646 joining MATS for RI. Using Junction Counts only
2017-05-23 03:19:42,870 joining MATS for RI using JC is done with status 0
2017-05-23 03:19:42,870 
2017-05-23 03:19:42,870 joining MATS for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:43,043 joining MATS for RI using JCEC is done with status 0
2017-05-23 03:19:43,044 
2017-05-23 03:19:43,044 done joining MATS results..
2017-05-23 03:19:43,045 ======================= Final Report =============
2017-05-23 03:19:43,045 getting stats for SE. Using Junction Counts only.
2017-05-23 03:19:43,304 getting stats for SE using JC is done with status 0,0 and 0
2017-05-23 03:19:43,304 numLines: 33739 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/SE.MATS.JunctionCountOnly.txt
2017-05-23 03:19:43,304 Upregulated: 71
2017-05-23 03:19:43,304 Downregulated: 62
2017-05-23 03:19:43,305 ========== SE ========
2017-05-23 03:19:43,305 Junction Counts Only: There are 33738 AS events. Of these, 133 events are statistically significant
2017-05-23 03:19:43,305 71 significant events have higher inclusion level for SAMPLE_1 and 62 events for SAMPLE_2
2017-05-23 03:19:43,306 getting stats for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:43,565 getting stats for SE using JCEC is done with status 0,0 and 0
2017-05-23 03:19:43,565 numLines: 34245 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/SE.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 03:19:43,566 Upregulated: 80
2017-05-23 03:19:43,566 Downregulated: 65
2017-05-23 03:19:43,566 Junction Counts and Reads on target Exon Counts: There are 34244 AS events. Of these, 145 events are statistically significant
2017-05-23 03:19:43,566 80 significant events have higher inclusion level for SAMPLE_1 and 65 events for SAMPLE_2
2017-05-23 03:19:43,566 getting stats for MXE. Using Junction Counts only.
2017-05-23 03:19:43,711 getting stats for MXE using JC is done with status 0,0 and 0
2017-05-23 03:19:43,711 numLines: 4999 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/MXE.MATS.JunctionCountOnly.txt
2017-05-23 03:19:43,712 Upregulated: 28
2017-05-23 03:19:43,712 Downregulated: 42
2017-05-23 03:19:43,712 ========== MXE ========
2017-05-23 03:19:43,712 Junction Counts Only: There are 4998 AS events. Of these, 70 events are statistically significant
2017-05-23 03:19:43,712 28 significant events have higher inclusion level for SAMPLE_1 and 42 events for SAMPLE_2
2017-05-23 03:19:43,712 getting stats for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:43,858 getting stats for MXE using JCEC is done with status 0,0 and 0
2017-05-23 03:19:43,859 numLines: 5065 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 03:19:43,859 Upregulated: 50
2017-05-23 03:19:43,859 Downregulated: 64
2017-05-23 03:19:43,859 Junction Counts and Reads on target Exon Counts: There are 5064 AS events. Of these, 114 events are statistically significant
2017-05-23 03:19:43,859 50 significant events have higher inclusion level for SAMPLE_1 and 64 events for SAMPLE_2
2017-05-23 03:19:43,859 getting stats for A5SS. Using Junction Counts only.
2017-05-23 03:19:44,031 getting stats for A5SS using JC is done with status 0,0 and 0
2017-05-23 03:19:44,031 numLines: 12446 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/A5SS.MATS.JunctionCountOnly.txt
2017-05-23 03:19:44,031 Upregulated: 66
2017-05-23 03:19:44,032 Downregulated: 78
2017-05-23 03:19:44,032 ========== A5SS ========
2017-05-23 03:19:44,032 Junction Counts Only: There are 12445 AS events. Of these, 144 events are statistically significant
2017-05-23 03:19:44,032 66 significant events have higher inclusion level for SAMPLE_1 and 78 events for SAMPLE_2
2017-05-23 03:19:44,032 getting stats for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:44,203 getting stats for A5SS using JCEC is done with status 0,0 and 0
2017-05-23 03:19:44,203 numLines: 12468 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 03:19:44,203 Upregulated: 72
2017-05-23 03:19:44,203 Downregulated: 89
2017-05-23 03:19:44,203 Junction Counts and Reads on target Exon Counts: There are 12467 AS events. Of these, 161 events are statistically significant
2017-05-23 03:19:44,203 72 significant events have higher inclusion level for SAMPLE_1 and 89 events for SAMPLE_2
2017-05-23 03:19:44,203 getting stats for A3SS. Using Junction Counts only.
2017-05-23 03:19:44,403 getting stats for A3SS using JC is done with status 0,0 and 0
2017-05-23 03:19:44,403 numLines: 18981 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/A3SS.MATS.JunctionCountOnly.txt
2017-05-23 03:19:44,403 Upregulated: 95
2017-05-23 03:19:44,404 Downregulated: 114
2017-05-23 03:19:44,404 ========== A3SS ========
2017-05-23 03:19:44,404 Junction Counts Only: There are 18980 AS events. Of these, 209 events are statistically significant
2017-05-23 03:19:44,404 95 significant events have higher inclusion level for SAMPLE_1 and 114 events for SAMPLE_2
2017-05-23 03:19:44,404 getting stats for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:44,603 getting stats for A3SS using JCEC is done with status 0,0 and 0
2017-05-23 03:19:44,604 numLines: 19000 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 03:19:44,604 Upregulated: 100
2017-05-23 03:19:44,604 Downregulated: 114
2017-05-23 03:19:44,604 Junction Counts and Reads on target Exon Counts: There are 18999 AS events. Of these, 214 events are statistically significant
2017-05-23 03:19:44,604 100 significant events have higher inclusion level for SAMPLE_1 and 114 events for SAMPLE_2
2017-05-23 03:19:44,604 getting stats for RI. Using Junction Counts only.
2017-05-23 03:19:44,743 getting stats for RI using JC is done with status 0,0 and 0
2017-05-23 03:19:44,743 numLines: 3787 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/RI.MATS.JunctionCountOnly.txt
2017-05-23 03:19:44,743 Upregulated: 66
2017-05-23 03:19:44,743 Downregulated: 56
2017-05-23 03:19:44,743 ========== RI ========
2017-05-23 03:19:44,743 Junction Counts Only: There are 3786 AS events. Of these, 122 events are statistically significant
2017-05-23 03:19:44,744 66 significant events have higher inclusion level for SAMPLE_1 and 56 events for SAMPLE_2
2017-05-23 03:19:44,744 getting stats for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-23 03:19:44,883 getting stats for RI using JCEC is done with status 0,0 and 0
2017-05-23 03:19:44,883 numLines: 3807 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-hind-ctrl-KO-mm9-frstrand/MATS_output/RI.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 03:19:44,883 Upregulated: 66
2017-05-23 03:19:44,883 Downregulated: 68
2017-05-23 03:19:44,884 Junction Counts and Reads on target Exon Counts: There are 3806 AS events. Of these, 134 events are statistically significant
2017-05-23 03:19:44,884 66 significant events have higher inclusion level for SAMPLE_1 and 68 events for SAMPLE_2
2017-05-23 03:19:44,884 done printing out stats..
2017-05-23 03:19:45,028 Temp folder is deleted..
2017-05-23 03:19:45,029 Program ended
2017-05-23 03:19:45,029 Program ran 14:54:22