2017-05-23 10:58:06,581 rMATS version: 3.2.5
2017-05-23 10:58:06,582 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 ]

2017-05-23 10:58:06,659 ################### folder names and associated input files #############
2017-05-23 10:58:06,659 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
2017-05-23 10:58:06,659 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
2017-05-23 10:58:06,659 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
2017-05-23 10:58:06,659 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
2017-05-23 10:58:06,659 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
2017-05-23 10:58:06,659 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
2017-05-23 10:58:06,659 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
2017-05-23 10:58:06,659 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
2017-05-23 10:58:06,659 #########################################################################

2017-05-23 10:58:06,659 start mapping..
2017-05-23 10:58:06,659 mapping the first sample
2017-05-23 11:08:25,335 mapping sample_1, rep_1 is done with status 0
2017-05-23 11:08:25,335 May 23 10:58:06 ..... started STAR run
May 23 10:58:06 ..... loading genome
May 23 10:58:30 ..... processing annotations GTF
May 23 10:58:43 ..... inserting junctions into the genome indices
May 23 11:03:16 ..... started mapping
May 23 11:07:51 ..... started sorting BAM
May 23 11:08:24 ..... finished successfully
2017-05-23 11:20:32,813 mapping sample_1, rep_2 is done with status 0
2017-05-23 11:20:32,813 May 23 11:08:25 ..... started STAR run
May 23 11:08:25 ..... loading genome
May 23 11:08:52 ..... processing annotations GTF
May 23 11:09:07 ..... inserting junctions into the genome indices
May 23 11:13:38 ..... started mapping
May 23 11:19:51 ..... started sorting BAM
May 23 11:20:32 ..... finished successfully
2017-05-23 11:31:32,453 mapping sample_1, rep_3 is done with status 0
2017-05-23 11:31:32,453 May 23 11:20:32 ..... started STAR run
May 23 11:20:32 ..... loading genome
May 23 11:21:00 ..... processing annotations GTF
May 23 11:21:21 ..... inserting junctions into the genome indices
May 23 11:25:56 ..... started mapping
May 23 11:30:58 ..... started sorting BAM
May 23 11:31:31 ..... finished successfully
2017-05-23 11:42:06,103 mapping sample_1, rep_4 is done with status 0
2017-05-23 11:42:06,103 May 23 11:31:32 ..... started STAR run
May 23 11:31:32 ..... loading genome
May 23 11:31:59 ..... processing annotations GTF
May 23 11:32:13 ..... inserting junctions into the genome indices
May 23 11:36:55 ..... started mapping
May 23 11:41:31 ..... started sorting BAM
May 23 11:42:05 ..... finished successfully
2017-05-23 11:42:06,103 mapping the second sample
2017-05-23 11:54:34,669 mapping sample_2, rep_1 is done with status 0
2017-05-23 11:54:34,669 May 23 11:42:06 ..... started STAR run
May 23 11:42:06 ..... loading genome
May 23 11:42:33 ..... processing annotations GTF
May 23 11:42:48 ..... inserting junctions into the genome indices
May 23 11:47:25 ..... started mapping
May 23 11:53:45 ..... started sorting BAM
May 23 11:54:33 ..... finished successfully
2017-05-23 12:05:38,597 mapping sample_2, rep_2 is done with status 0
2017-05-23 12:05:38,598 May 23 11:54:34 ..... started STAR run
May 23 11:54:34 ..... loading genome
May 23 11:55:03 ..... processing annotations GTF
May 23 11:55:17 ..... inserting junctions into the genome indices
May 23 11:59:56 ..... started mapping
May 23 12:05:08 ..... started sorting BAM
May 23 12:05:38 ..... finished successfully
2017-05-23 12:19:05,759 mapping sample_2, rep_3 is done with status 0
2017-05-23 12:19:05,759 May 23 12:05:38 ..... started STAR run
May 23 12:05:38 ..... loading genome
May 23 12:06:07 ..... processing annotations GTF
May 23 12:06:22 ..... inserting junctions into the genome indices
May 23 12:11:10 ..... started mapping
May 23 12:18:18 ..... started sorting BAM
May 23 12:19:05 ..... finished successfully
2017-05-23 12:41:04,789 mapping sample_2, rep_4 is done with status 0
2017-05-23 12:41:04,790 May 23 12:19:05 ..... started STAR run
May 23 12:19:05 ..... loading genome
May 23 12:19:34 ..... processing annotations GTF
May 23 12:19:48 ..... inserting junctions into the genome indices
May 23 12:24:24 ..... started mapping
May 23 12:39:40 ..... started sorting BAM
May 23 12:41:03 ..... finished successfully
2017-05-23 12:41:04,790 done mapping..
2017-05-23 12:41:04,790 indexing bam files to use pysam
2017-05-23 12:41:04,790 getting unique SAM function..
2017-05-23 13:44:42,126 done indexing bam files..
2017-05-23 13:44:42,172 start getting AS events from GTF and BAM files
2017-05-23 13:44:42,172 getting AS events function..
2017-05-23 14:43:30,541 getting AS events is done with status 0
2017-05-23 14:43:30,542 
2017-05-23 14:43:30,542 done getting AS events..
2017-05-23 14:43:30,622 Setting proper string
2017-05-23 14:43:31,196 start making MATS input files from AS events and SAM files
2017-05-23 14:43:31,196 making MATS input function..
2017-05-23 16:08:56,797 making MATS input is done with status 0
2017-05-23 16:08:56,798 
2017-05-23 16:08:56,798 done making MATS input..
2017-05-23 16:08:56,798 start running MATS for each AS event
2017-05-23 16:08:56,798 running MATS for SE. Using Junction Counts only
2017-05-23 19:53:26,265 running MATS for SE using JC is done with status 0
2017-05-23 19:53:26,266 
2017-05-23 19:53:26,266 running MATS for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 22:37:51,391 running MATS for SE using JCEC is done with status 0
2017-05-23 22:37:51,392 
2017-05-23 22:37:51,392 running MATS for MXE. Using Junction Counts only
2017-05-23 22:58:33,551 running MATS for MXE using JC is done with status 0
2017-05-23 22:58:33,551 
2017-05-23 22:58:33,551 running MATS for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-23 23:08:22,353 running MATS for MXE using JCEC is done with status 0
2017-05-23 23:08:22,353 
2017-05-23 23:08:22,353 running MATS for A5SS. Using Junction Counts only
2017-05-24 00:20:09,334 running MATS for A5SS using JC is done with status 0
2017-05-24 00:20:09,334 
2017-05-24 00:20:09,334 running MATS for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-24 00:59:05,669 running MATS for A5SS using JCEC is done with status 0
2017-05-24 00:59:05,669 
2017-05-24 00:59:05,670 running MATS for A3SS. Using Junction Counts only
2017-05-24 02:41:52,559 running MATS for A3SS using JC is done with status 0
2017-05-24 02:41:52,560 
2017-05-24 02:41:52,560 running MATS for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-24 03:42:50,294 running MATS for A3SS using JCEC is done with status 0
2017-05-24 03:42:50,295 
2017-05-24 03:42:50,295 running MATS for RI. Using Junction Counts only
2017-05-24 03:57:01,087 running MATS for RI using JC is done with status 0
2017-05-24 03:57:01,088 
2017-05-24 03:57:01,088 running MATS for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:51,082 running MATS for RI using JCEC is done with status 0
2017-05-24 04:04:51,082 
2017-05-24 04:04:51,082 done running MATS for all AS event types..
2017-05-24 04:04:51,082 start joining MATS results for each AS event
2017-05-24 04:04:51,082 joining MATS for SE. Using Junction Counts only
2017-05-24 04:04:52,231 joining MATS for SE using JC is done with status 0
2017-05-24 04:04:52,231 
2017-05-24 04:04:52,231 joining MATS for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:53,105 joining MATS for SE using JCEC is done with status 0
2017-05-24 04:04:53,105 
2017-05-24 04:04:53,105 joining MATS for MXE. Using Junction Counts only
2017-05-24 04:04:53,489 joining MATS for MXE using JC is done with status 0
2017-05-24 04:04:53,489 
2017-05-24 04:04:53,489 joining MATS for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:53,805 joining MATS for MXE using JCEC is done with status 0
2017-05-24 04:04:53,806 
2017-05-24 04:04:53,806 joining MATS for A5SS. Using Junction Counts only
2017-05-24 04:04:54,280 joining MATS for A5SS using JC is done with status 0
2017-05-24 04:04:54,280 
2017-05-24 04:04:54,281 joining MATS for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:54,765 joining MATS for A5SS using JCEC is done with status 0
2017-05-24 04:04:54,766 
2017-05-24 04:04:54,766 joining MATS for A3SS. Using Junction Counts only
2017-05-24 04:04:55,382 joining MATS for A3SS using JC is done with status 0
2017-05-24 04:04:55,382 
2017-05-24 04:04:55,382 joining MATS for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:55,943 joining MATS for A3SS using JCEC is done with status 0
2017-05-24 04:04:55,943 
2017-05-24 04:04:55,943 joining MATS for RI. Using Junction Counts only
2017-05-24 04:04:56,349 joining MATS for RI using JC is done with status 0
2017-05-24 04:04:56,350 
2017-05-24 04:04:56,350 joining MATS for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:56,536 joining MATS for RI using JCEC is done with status 0
2017-05-24 04:04:56,537 
2017-05-24 04:04:56,537 done joining MATS results..
2017-05-24 04:04:56,539 ======================= Final Report =============
2017-05-24 04:04:56,539 getting stats for SE. Using Junction Counts only.
2017-05-24 04:04:56,857 getting stats for SE using JC is done with status 0,0 and 0
2017-05-24 04:04:56,857 numLines: 39157 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/SE.MATS.JunctionCountOnly.txt
2017-05-24 04:04:56,857 Upregulated: 199
2017-05-24 04:04:56,857 Downregulated: 95
2017-05-24 04:04:56,876 ========== SE ========
2017-05-24 04:04:56,876 Junction Counts Only: There are 39156 AS events. Of these, 294 events are statistically significant
2017-05-24 04:04:56,876 199 significant events have higher inclusion level for SAMPLE_1 and 95 events for SAMPLE_2
2017-05-24 04:04:56,876 getting stats for SE. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:57,289 getting stats for SE using JCEC is done with status 0,0 and 0
2017-05-24 04:04:57,289 numLines: 39740 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/SE.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-24 04:04:57,290 Upregulated: 230
2017-05-24 04:04:57,290 Downregulated: 120
2017-05-24 04:04:57,290 Junction Counts and Reads on target Exon Counts: There are 39739 AS events. Of these, 350 events are statistically significant
2017-05-24 04:04:57,290 230 significant events have higher inclusion level for SAMPLE_1 and 120 events for SAMPLE_2
2017-05-24 04:04:57,290 getting stats for MXE. Using Junction Counts only.
2017-05-24 04:04:57,485 getting stats for MXE using JC is done with status 0,0 and 0
2017-05-24 04:04:57,485 numLines: 6275 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/MXE.MATS.JunctionCountOnly.txt
2017-05-24 04:04:57,485 Upregulated: 28
2017-05-24 04:04:57,485 Downregulated: 23
2017-05-24 04:04:57,485 ========== MXE ========
2017-05-24 04:04:57,486 Junction Counts Only: There are 6274 AS events. Of these, 51 events are statistically significant
2017-05-24 04:04:57,486 28 significant events have higher inclusion level for SAMPLE_1 and 23 events for SAMPLE_2
2017-05-24 04:04:57,486 getting stats for MXE. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:57,647 getting stats for MXE using JCEC is done with status 0,0 and 0
2017-05-24 04:04:57,648 numLines: 6359 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-24 04:04:57,648 Upregulated: 39
2017-05-24 04:04:57,648 Downregulated: 26
2017-05-24 04:04:57,648 Junction Counts and Reads on target Exon Counts: There are 6358 AS events. Of these, 65 events are statistically significant
2017-05-24 04:04:57,648 39 significant events have higher inclusion level for SAMPLE_1 and 26 events for SAMPLE_2
2017-05-24 04:04:57,648 getting stats for A5SS. Using Junction Counts only.
2017-05-24 04:04:57,883 getting stats for A5SS using JC is done with status 0,0 and 0
2017-05-24 04:04:57,884 numLines: 13929 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/A5SS.MATS.JunctionCountOnly.txt
2017-05-24 04:04:57,884 Upregulated: 55
2017-05-24 04:04:57,884 Downregulated: 44
2017-05-24 04:04:57,884 ========== A5SS ========
2017-05-24 04:04:57,884 Junction Counts Only: There are 13928 AS events. Of these, 99 events are statistically significant
2017-05-24 04:04:57,884 55 significant events have higher inclusion level for SAMPLE_1 and 44 events for SAMPLE_2
2017-05-24 04:04:57,884 getting stats for A5SS. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:58,076 getting stats for A5SS using JCEC is done with status 0,0 and 0
2017-05-24 04:04:58,076 numLines: 13954 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-24 04:04:58,076 Upregulated: 61
2017-05-24 04:04:58,076 Downregulated: 47
2017-05-24 04:04:58,077 Junction Counts and Reads on target Exon Counts: There are 13953 AS events. Of these, 108 events are statistically significant
2017-05-24 04:04:58,077 61 significant events have higher inclusion level for SAMPLE_1 and 47 events for SAMPLE_2
2017-05-24 04:04:58,077 getting stats for A3SS. Using Junction Counts only.
2017-05-24 04:04:58,289 getting stats for A3SS using JC is done with status 0,0 and 0
2017-05-24 04:04:58,290 numLines: 21229 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/A3SS.MATS.JunctionCountOnly.txt
2017-05-24 04:04:58,290 Upregulated: 64
2017-05-24 04:04:58,290 Downregulated: 52
2017-05-24 04:04:58,290 ========== A3SS ========
2017-05-24 04:04:58,290 Junction Counts Only: There are 21228 AS events. Of these, 116 events are statistically significant
2017-05-24 04:04:58,290 64 significant events have higher inclusion level for SAMPLE_1 and 52 events for SAMPLE_2
2017-05-24 04:04:58,290 getting stats for A3SS. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:58,501 getting stats for A3SS using JCEC is done with status 0,0 and 0
2017-05-24 04:04:58,501 numLines: 21239 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-24 04:04:58,501 Upregulated: 63
2017-05-24 04:04:58,501 Downregulated: 54
2017-05-24 04:04:58,502 Junction Counts and Reads on target Exon Counts: There are 21238 AS events. Of these, 117 events are statistically significant
2017-05-24 04:04:58,502 63 significant events have higher inclusion level for SAMPLE_1 and 54 events for SAMPLE_2
2017-05-24 04:04:58,502 getting stats for RI. Using Junction Counts only.
2017-05-24 04:04:58,645 getting stats for RI using JC is done with status 0,0 and 0
2017-05-24 04:04:58,646 numLines: 4130 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/RI.MATS.JunctionCountOnly.txt
2017-05-24 04:04:58,646 Upregulated: 18
2017-05-24 04:04:58,646 Downregulated: 13
2017-05-24 04:04:58,646 ========== RI ========
2017-05-24 04:04:58,646 Junction Counts Only: There are 4129 AS events. Of these, 31 events are statistically significant
2017-05-24 04:04:58,646 18 significant events have higher inclusion level for SAMPLE_1 and 13 events for SAMPLE_2
2017-05-24 04:04:58,646 getting stats for RI. Using Junction Counts and Reads on target Exon Counts
2017-05-24 04:04:58,800 getting stats for RI using JCEC is done with status 0,0 and 0
2017-05-24 04:04:58,800 numLines: 4156 /dfs2/cbcl/forouzme/Projects/PolyA/rMATS/rMATS.3.2.5/colleen-cort-ctrl-KO-mm9/MATS_output/RI.MATS.ReadsOnTargetAndJunctionCounts.txt
2017-05-24 04:04:58,800 Upregulated: 25
2017-05-24 04:04:58,800 Downregulated: 24
2017-05-24 04:04:58,800 Junction Counts and Reads on target Exon Counts: There are 4155 AS events. Of these, 49 events are statistically significant
2017-05-24 04:04:58,800 25 significant events have higher inclusion level for SAMPLE_1 and 24 events for SAMPLE_2
2017-05-24 04:04:58,800 done printing out stats..
2017-05-24 04:04:58,992 Temp folder is deleted..
2017-05-24 04:04:58,992 Program ended
2017-05-24 04:04:58,992 Program ran 17:06:52