2017-05-22 12:24:15,243 rMATS version: 3.2.5
2017-05-22 12:24:15,244 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 12:24:15,321 ################### folder names and associated input files #############
2017-05-22 12:24:15,321 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 12:24:15,321 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 12:24:15,321 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 12:24:15,321 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 12:24:15,321 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 12:24:15,321 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 12:24:15,321 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 12:24:15,321 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 12:24:15,321 #########################################################################

2017-05-22 12:24:15,321 start mapping..
2017-05-22 12:24:15,321 mapping the first sample
2017-05-22 12:34:29,182 mapping sample_1, rep_1 is done with status 0
2017-05-22 12:34:29,183 May 22 12:24:15 ..... started STAR run
May 22 12:24:15 ..... loading genome
May 22 12:24:40 ..... processing annotations GTF
May 22 12:24:52 ..... inserting junctions into the genome indices
May 22 12:29:24 ..... started mapping
May 22 12:33:57 ..... started sorting BAM
May 22 12:34:28 ..... finished successfully
2017-05-22 12:46:38,703 mapping sample_1, rep_2 is done with status 0
2017-05-22 12:46:38,704 May 22 12:34:29 ..... started STAR run
May 22 12:34:29 ..... loading genome
May 22 12:34:52 ..... processing annotations GTF
May 22 12:35:06 ..... inserting junctions into the genome indices
May 22 12:39:52 ..... started mapping
May 22 12:46:01 ..... started sorting BAM
May 22 12:46:38 ..... finished successfully
2017-05-22 12:57:12,455 mapping sample_1, rep_3 is done with status 0
2017-05-22 12:57:12,455 May 22 12:46:38 ..... started STAR run
May 22 12:46:38 ..... loading genome
May 22 12:47:01 ..... processing annotations GTF
May 22 12:47:14 ..... inserting junctions into the genome indices
May 22 12:51:43 ..... started mapping
May 22 12:56:38 ..... started sorting BAM
May 22 12:57:11 ..... finished successfully
2017-05-22 13:07:40,105 mapping sample_1, rep_4 is done with status 0
2017-05-22 13:07:40,106 May 22 12:57:12 ..... started STAR run
May 22 12:57:12 ..... loading genome
May 22 12:57:37 ..... processing annotations GTF
May 22 12:57:51 ..... inserting junctions into the genome indices
May 22 13:02:27 ..... started mapping
May 22 13:07:05 ..... started sorting BAM
May 22 13:07:39 ..... finished successfully
2017-05-22 13:07:40,106 mapping the second sample
2017-05-22 13:20:09,531 mapping sample_2, rep_1 is done with status 0
2017-05-22 13:20:09,532 May 22 13:07:40 ..... started STAR run
May 22 13:07:40 ..... loading genome
May 22 13:08:14 ..... processing annotations GTF
May 22 13:08:28 ..... inserting junctions into the genome indices
May 22 13:13:06 ..... started mapping
May 22 13:19:22 ..... started sorting BAM
May 22 13:20:08 ..... finished successfully
2017-05-22 13:31:19,118 mapping sample_2, rep_2 is done with status 0
2017-05-22 13:31:19,118 May 22 13:20:09 ..... started STAR run
May 22 13:20:09 ..... loading genome
May 22 13:20:34 ..... processing annotations GTF
May 22 13:20:49 ..... inserting junctions into the genome indices
May 22 13:25:32 ..... started mapping
May 22 13:30:49 ..... started sorting BAM
May 22 13:31:18 ..... finished successfully
2017-05-22 13:44:12,669 mapping sample_2, rep_3 is done with status 0
2017-05-22 13:44:12,669 May 22 13:31:19 ..... started STAR run
May 22 13:31:19 ..... loading genome
May 22 13:31:45 ..... processing annotations GTF
May 22 13:31:57 ..... inserting junctions into the genome indices
May 22 13:36:23 ..... started mapping
May 22 13:43:28 ..... started sorting BAM
May 22 13:44:11 ..... finished successfully
2017-05-22 14:06:19,691 mapping sample_2, rep_4 is done with status 0
2017-05-22 14:06:19,691 May 22 13:44:12 ..... started STAR run
May 22 13:44:12 ..... loading genome
May 22 13:44:36 ..... processing annotations GTF
May 22 13:44:51 ..... inserting junctions into the genome indices
May 22 13:49:38 ..... started mapping
May 22 14:04:54 ..... started sorting BAM
May 22 14:06:18 ..... finished successfully
2017-05-22 14:06:19,691 done mapping..
2017-05-22 14:06:19,691 indexing bam files to use pysam
2017-05-22 14:06:19,691 getting unique SAM function..
2017-05-22 15:09:56,910 done indexing bam files..
2017-05-22 15:09:56,984 start getting AS events from GTF and BAM files
2017-05-22 15:09:56,984 getting AS events function..
2017-05-22 16:07:27,413 getting AS events is done with status 0
2017-05-22 16:07:27,413 
2017-05-22 16:07:27,414 done getting AS events..
2017-05-22 16:07:27,493 Setting proper string
2017-05-22 16:07:28,034 start making MATS input files from AS events and SAM files
2017-05-22 16:07:28,034 making MATS input function..
2017-05-22 17:36:09,017 making MATS input is done with status 0
2017-05-22 17:36:09,017 
2017-05-22 17:36:09,017 done making MATS input..
2017-05-22 17:36:09,018 start running MATS for each AS event
2017-05-22 17:36:09,018 running MATS for SE. Using Junction Counts only
2017-05-22 21:27:59,152 running MATS for SE using JC is done with status 0
2017-05-22 21:27:59,152 
2017-05-22 21:27:59,152 running MATS for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 00:01:43,200 running MATS for SE using JCEC is done with status 0
2017-05-23 00:01:43,201 
2017-05-23 00:01:43,201 running MATS for MXE. Using Junction Counts only
2017-05-23 00:23:46,024 running MATS for MXE using JC is done with status 0
2017-05-23 00:23:46,025 
2017-05-23 00:23:46,025 running MATS for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 00:32:57,815 running MATS for MXE using JCEC is done with status 0
2017-05-23 00:32:57,816 
2017-05-23 00:32:57,816 running MATS for A5SS. Using Junction Counts only
2017-05-23 01:48:33,653 running MATS for A5SS using JC is done with status 0
2017-05-23 01:48:33,653 
2017-05-23 01:48:33,653 running MATS for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 02:28:14,874 running MATS for A5SS using JCEC is done with status 0
2017-05-23 02:28:14,874 
2017-05-23 02:28:14,874 running MATS for A3SS. Using Junction Counts only
2017-05-23 04:11:26,878 running MATS for A3SS using JC is done with status 0
2017-05-23 04:11:26,878 
2017-05-23 04:11:26,878 running MATS for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:14:21,458 running MATS for A3SS using JCEC is done with status 0
2017-05-23 05:14:21,459 
2017-05-23 05:14:21,459 running MATS for RI. Using Junction Counts only
2017-05-23 05:29:52,147 running MATS for RI using JC is done with status 0
2017-05-23 05:29:52,147 
2017-05-23 05:29:52,147 running MATS for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:44,840 running MATS for RI using JCEC is done with status 0
2017-05-23 05:37:44,840 
2017-05-23 05:37:44,840 done running MATS for all AS event types..
2017-05-23 05:37:44,840 start joining MATS results for each AS event
2017-05-23 05:37:44,840 joining MATS for SE. Using Junction Counts only
2017-05-23 05:37:45,757 joining MATS for SE using JC is done with status 0
2017-05-23 05:37:45,757 
2017-05-23 05:37:45,757 joining MATS for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:46,502 joining MATS for SE using JCEC is done with status 0
2017-05-23 05:37:46,502 
2017-05-23 05:37:46,502 joining MATS for MXE. Using Junction Counts only
2017-05-23 05:37:46,784 joining MATS for MXE using JC is done with status 0
2017-05-23 05:37:46,784 
2017-05-23 05:37:46,784 joining MATS for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:47,028 joining MATS for MXE using JCEC is done with status 0
2017-05-23 05:37:47,028 
2017-05-23 05:37:47,028 joining MATS for A5SS. Using Junction Counts only
2017-05-23 05:37:47,446 joining MATS for A5SS using JC is done with status 0
2017-05-23 05:37:47,447 
2017-05-23 05:37:47,447 joining MATS for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:47,779 joining MATS for A5SS using JCEC is done with status 0
2017-05-23 05:37:47,779 
2017-05-23 05:37:47,779 joining MATS for A3SS. Using Junction Counts only
2017-05-23 05:37:48,268 joining MATS for A3SS using JC is done with status 0
2017-05-23 05:37:48,268 
2017-05-23 05:37:48,268 joining MATS for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:48,678 joining MATS for A3SS using JCEC is done with status 0
2017-05-23 05:37:48,678 
2017-05-23 05:37:48,678 joining MATS for RI. Using Junction Counts only
2017-05-23 05:37:48,878 joining MATS for RI using JC is done with status 0
2017-05-23 05:37:48,879 
2017-05-23 05:37:48,879 joining MATS for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:49,056 joining MATS for RI using JCEC is done with status 0
2017-05-23 05:37:49,057 
2017-05-23 05:37:49,057 done joining MATS results..
2017-05-23 05:37:49,058 ======================= Final Report =============
2017-05-23 05:37:49,058 getting stats for SE. Using Junction Counts only.
2017-05-23 05:37:49,335 getting stats for SE using JC is done with status 0,0 and 0
2017-05-23 05:37:49,336 numLines: 39157 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/SE.MATS.JunctionCountOnly.txt
2017-05-23 05:37:49,336 Upregulated: 199
2017-05-23 05:37:49,336 Downregulated: 95
2017-05-23 05:37:49,337 ========== SE ========
2017-05-23 05:37:49,337 Junction Counts Only: There are 39156 AS events. Of these, 294 events are statistically significant
2017-05-23 05:37:49,337 199 significant events have higher inclusion level for SAMPLE_1 and 95 events for SAMPLE_2
2017-05-23 05:37:49,337 getting stats for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:49,629 getting stats for SE using JCEC is done with status 0,0 and 0
2017-05-23 05:37:49,630 numLines: 39716 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/SE.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 05:37:49,630 Upregulated: 231
2017-05-23 05:37:49,630 Downregulated: 116
2017-05-23 05:37:49,630 Junction Counts and Reads on target Exon Counts: There are 39715 AS events. Of these, 347 events are statistically significant
2017-05-23 05:37:49,630 231 significant events have higher inclusion level for SAMPLE_1 and 116 events for SAMPLE_2
2017-05-23 05:37:49,630 getting stats for MXE. Using Junction Counts only.
2017-05-23 05:37:49,782 getting stats for MXE using JC is done with status 0,0 and 0
2017-05-23 05:37:49,782 numLines: 6275 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/MXE.MATS.JunctionCountOnly.txt
2017-05-23 05:37:49,782 Upregulated: 28
2017-05-23 05:37:49,782 Downregulated: 23
2017-05-23 05:37:49,782 ========== MXE ========
2017-05-23 05:37:49,782 Junction Counts Only: There are 6274 AS events. Of these, 51 events are statistically significant
2017-05-23 05:37:49,782 28 significant events have higher inclusion level for SAMPLE_1 and 23 events for SAMPLE_2
2017-05-23 05:37:49,782 getting stats for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:49,946 getting stats for MXE using JCEC is done with status 0,0 and 0
2017-05-23 05:37:49,946 numLines: 6356 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 05:37:49,946 Upregulated: 38
2017-05-23 05:37:49,946 Downregulated: 26
2017-05-23 05:37:49,946 Junction Counts and Reads on target Exon Counts: There are 6355 AS events. Of these, 64 events are statistically significant
2017-05-23 05:37:49,946 38 significant events have higher inclusion level for SAMPLE_1 and 26 events for SAMPLE_2
2017-05-23 05:37:49,946 getting stats for A5SS. Using Junction Counts only.
2017-05-23 05:37:50,124 getting stats for A5SS using JC is done with status 0,0 and 0
2017-05-23 05:37:50,124 numLines: 13900 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/A5SS.MATS.JunctionCountOnly.txt
2017-05-23 05:37:50,124 Upregulated: 55
2017-05-23 05:37:50,124 Downregulated: 37
2017-05-23 05:37:50,124 ========== A5SS ========
2017-05-23 05:37:50,124 Junction Counts Only: There are 13899 AS events. Of these, 92 events are statistically significant
2017-05-23 05:37:50,125 55 significant events have higher inclusion level for SAMPLE_1 and 37 events for SAMPLE_2
2017-05-23 05:37:50,125 getting stats for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:50,312 getting stats for A5SS using JCEC is done with status 0,0 and 0
2017-05-23 05:37:50,312 numLines: 13933 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 05:37:50,312 Upregulated: 58
2017-05-23 05:37:50,312 Downregulated: 37
2017-05-23 05:37:50,312 Junction Counts and Reads on target Exon Counts: There are 13932 AS events. Of these, 95 events are statistically significant
2017-05-23 05:37:50,312 58 significant events have higher inclusion level for SAMPLE_1 and 37 events for SAMPLE_2
2017-05-23 05:37:50,313 getting stats for A3SS. Using Junction Counts only.
2017-05-23 05:37:50,517 getting stats for A3SS using JC is done with status 0,0 and 0
2017-05-23 05:37:50,518 numLines: 21196 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/A3SS.MATS.JunctionCountOnly.txt
2017-05-23 05:37:50,518 Upregulated: 64
2017-05-23 05:37:50,518 Downregulated: 44
2017-05-23 05:37:50,518 ========== A3SS ========
2017-05-23 05:37:50,518 Junction Counts Only: There are 21195 AS events. Of these, 108 events are statistically significant
2017-05-23 05:37:50,518 64 significant events have higher inclusion level for SAMPLE_1 and 44 events for SAMPLE_2
2017-05-23 05:37:50,518 getting stats for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:50,735 getting stats for A3SS using JCEC is done with status 0,0 and 0
2017-05-23 05:37:50,736 numLines: 21206 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 05:37:50,736 Upregulated: 63
2017-05-23 05:37:50,736 Downregulated: 51
2017-05-23 05:37:50,736 Junction Counts and Reads on target Exon Counts: There are 21205 AS events. Of these, 114 events are statistically significant
2017-05-23 05:37:50,736 63 significant events have higher inclusion level for SAMPLE_1 and 51 events for SAMPLE_2
2017-05-23 05:37:50,736 getting stats for RI. Using Junction Counts only.
2017-05-23 05:37:50,877 getting stats for RI using JC is done with status 0,0 and 0
2017-05-23 05:37:50,877 numLines: 4111 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/RI.MATS.JunctionCountOnly.txt
2017-05-23 05:37:50,877 Upregulated: 23
2017-05-23 05:37:50,877 Downregulated: 28
2017-05-23 05:37:50,877 ========== RI ========
2017-05-23 05:37:50,877 Junction Counts Only: There are 4110 AS events. Of these, 51 events are statistically significant
2017-05-23 05:37:50,877 23 significant events have higher inclusion level for SAMPLE_1 and 28 events for SAMPLE_2
2017-05-23 05:37:50,877 getting stats for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-23 05:37:51,028 getting stats for RI using JCEC is done with status 0,0 and 0
2017-05-23 05:37:51,028 numLines: 4137 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9-frstrand/MATS_output/RI.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-23 05:37:51,028 Upregulated: 34
2017-05-23 05:37:51,028 Downregulated: 34
2017-05-23 05:37:51,029 Junction Counts and Reads on target Exon Counts: There are 4136 AS events. Of these, 68 events are statistically significant
2017-05-23 05:37:51,029 34 significant events have higher inclusion level for SAMPLE_1 and 34 events for SAMPLE_2
2017-05-23 05:37:51,029 done printing out stats..
2017-05-23 05:37:51,120 Temp folder is deleted..
2017-05-23 05:37:51,120 Program ended
2017-05-23 05:37:51,120 Program ran 17:13:35