2014-10-28 22:47:47,174 MATS version: 3.0.8 2014-10-28 22:47:47,174 Start the program with [/sb/software/areas/ircm/tools/MATS.3.0.8/RNASeq-MATS.py -b1 ../../results/tophat/Emb9_FANCI_ko/Emb9_FANCI_ko_picard_sorted_accepted_hits.bam -b2 ../../results/tophat/Emb2_FANCI_wt/Emb2_FANCI_wt_picard_sorted_accepted_hits.bam -gtf /sb/project/afb-431-ac/genomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/Mus_musculus.GRCm38.77.gtf -o ../../results/test -keepTemp -r1 166 -sd1 72 -r2 175 -sd2 85 -t paired -len 50 -a 8 -c 0.0001 -analysis U -expressionChange 10000.0 ] 2014-10-28 22:47:47,194 ################### folder names and associated input files ############# 2014-10-28 22:47:47,195 SAMPLE_1\REP_1 ../../results/tophat/Emb9_FANCI_ko/Emb9_FANCI_ko_picard_sorted_accepted_hits.bam 2014-10-28 22:47:47,195 SAMPLE_2\REP_1 ../../results/tophat/Emb2_FANCI_wt/Emb2_FANCI_wt_picard_sorted_accepted_hits.bam 2014-10-28 22:47:47,195 ######################################################################### 2014-10-28 22:47:47,195 start mapping.. 2014-10-28 22:47:47,195 bam files are provided. skip mapping.. 2014-10-28 22:47:47,195 done mapping.. 2014-10-28 22:47:47,195 getting uniquely mapped reads or pairs 2014-10-28 22:47:47,195 getting unique SAM function.. 2014-10-29 00:54:36,936 getting uniquely mapped reads or pairs for sample_1, rep_1 is done with status 0 2014-10-29 00:54:36,936 2014-10-29 03:02:51,850 getting uniquely mapped reads or pairs for sample_2, rep_1 is done with status 0 2014-10-29 03:02:51,850 2014-10-29 03:02:51,850 done getting unique SAM files.. 2014-10-29 03:02:51,854 start getting AS events from GTF and SAM files 2014-10-29 03:02:51,854 getting AS events function.. 2014-10-29 05:46:19,218 getting AS events is done with status 0 2014-10-29 05:46:19,218 2014-10-29 05:46:19,218 done getting AS events.. 2014-10-29 05:46:19,276 Setting proper string 2014-10-29 05:46:19,339 start making MATS input files from AS events and SAM files 2014-10-29 05:46:19,340 making MATS input function.. 2014-10-29 06:26:01,845 making MATS input is done with status 0 2014-10-29 06:26:01,845 2014-10-29 06:26:01,845 done making MATS input.. 2014-10-29 06:26:01,845 start getting gene expression count 2014-10-29 06:26:01,845 getting gene expression count function.. 2014-10-29 06:26:01,845 Getting total number of mapped reads for the first sample 2014-10-29 06:26:01,845 getting total number of mapped reads for /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/SAMPLE_1/REP_1/unique.S1.sam 2014-10-29 06:26:56,869 getting total number of mapped reads for /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/SAMPLE_1/REP_1/unique.S1.sam is done. Num lines: 131753506 2014-10-29 06:26:56,869 Getting total number of mapped reads for the second sample 2014-10-29 06:26:56,869 getting total number of mapped reads for /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/SAMPLE_2/REP_1/unique.S2.sam 2014-10-29 06:27:42,526 getting total number of mapped reads for /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/SAMPLE_2/REP_1/unique.S2.sam is done. Num lines: 130860514 2014-10-29 06:27:42,526 Running gene expression program 2014-10-29 07:32:22,565 running gene expression program is done with 0 2014-10-29 07:32:22,565 2014-10-29 07:32:22,565 done getting gene expression count.. 2014-10-29 07:32:22,565 start filtering using gene expression count.. 2014-10-29 07:32:22,565 filtering gene expression count.. 2014-10-29 07:32:23,111 filtering JC SE input using gene expression count is done with 0 2014-10-29 07:32:23,111 2014-10-29 07:32:23,637 filtering JCEC SE input using gene expression count is done with 0 2014-10-29 07:32:23,637 2014-10-29 07:32:23,992 filtering JC MXE input using gene expression count is done with 0 2014-10-29 07:32:23,992 2014-10-29 07:32:24,348 filtering JCEC MXE input using gene expression count is done with 0 2014-10-29 07:32:24,348 2014-10-29 07:32:24,724 filtering JC A5SS input using gene expression count is done with 0 2014-10-29 07:32:24,724 2014-10-29 07:32:25,099 filtering JCEC A5SS input using gene expression count is done with 0 2014-10-29 07:32:25,099 2014-10-29 07:32:25,494 filtering JC A3SS input using gene expression count is done with 0 2014-10-29 07:32:25,495 2014-10-29 07:32:25,890 filtering JCEC A3SS input using gene expression count is done with 0 2014-10-29 07:32:25,890 2014-10-29 07:32:26,279 filtering JC RI input using gene expression count is done with 0 2014-10-29 07:32:26,280 2014-10-29 07:32:26,669 filtering JCEC RI input using gene expression count is done with 0 2014-10-29 07:32:26,669 2014-10-29 07:32:26,670 done filtering using gene expression count.. 2014-10-29 07:32:26,670 start running MATS for each AS event 2014-10-29 07:32:26,670 running MATS for SE. Using Junction Counts only 2014-10-29 07:33:46,486 running MATS for SE using JC is done with status 0 2014-10-29 07:33:46,486 2014-10-29 07:33:46,486 running MATS for SE. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:35:10,248 running MATS for SE using JCEC is done with status 0 2014-10-29 07:35:10,248 2014-10-29 07:35:10,248 running MATS for MXE. Using Junction Counts only 2014-10-29 07:35:14,734 running MATS for MXE using JC is done with status 0 2014-10-29 07:35:14,734 2014-10-29 07:35:14,734 running MATS for MXE. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:35:19,623 running MATS for MXE using JCEC is done with status 0 2014-10-29 07:35:19,624 2014-10-29 07:35:19,624 running MATS for A5SS. Using Junction Counts only 2014-10-29 07:35:32,798 running MATS for A5SS using JC is done with status 0 2014-10-29 07:35:32,798 2014-10-29 07:35:32,798 running MATS for A5SS. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:35:46,684 running MATS for A5SS using JCEC is done with status 0 2014-10-29 07:35:46,685 2014-10-29 07:35:46,685 running MATS for A3SS. Using Junction Counts only 2014-10-29 07:36:10,629 running MATS for A3SS using JC is done with status 0 2014-10-29 07:36:10,629 2014-10-29 07:36:10,629 running MATS for A3SS. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:36:35,183 running MATS for A3SS using JCEC is done with status 0 2014-10-29 07:36:35,183 2014-10-29 07:36:35,183 running MATS for RI. Using Junction Counts only 2014-10-29 07:36:56,639 running MATS for RI using JC is done with status 0 2014-10-29 07:36:56,639 2014-10-29 07:36:56,639 running MATS for RI. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:19,534 running MATS for RI using JCEC is done with status 0 2014-10-29 07:37:19,534 2014-10-29 07:37:19,534 done running MATS for all AS event types.. 2014-10-29 07:37:19,534 start joining MATS results for each AS event 2014-10-29 07:37:19,534 joining MATS for SE. Using Junction Counts only 2014-10-29 07:37:19,786 joining MATS for SE using JC is done with status 0 2014-10-29 07:37:19,787 2014-10-29 07:37:19,787 joining MATS for SE. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,014 joining MATS for SE using JCEC is done with status 0 2014-10-29 07:37:20,014 2014-10-29 07:37:20,014 joining MATS for MXE. Using Junction Counts only 2014-10-29 07:37:20,092 joining MATS for MXE using JC is done with status 0 2014-10-29 07:37:20,092 2014-10-29 07:37:20,092 joining MATS for MXE. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,169 joining MATS for MXE using JCEC is done with status 0 2014-10-29 07:37:20,170 2014-10-29 07:37:20,170 joining MATS for A5SS. Using Junction Counts only 2014-10-29 07:37:20,262 joining MATS for A5SS using JC is done with status 0 2014-10-29 07:37:20,262 2014-10-29 07:37:20,262 joining MATS for A5SS. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,355 joining MATS for A5SS using JCEC is done with status 0 2014-10-29 07:37:20,356 2014-10-29 07:37:20,356 joining MATS for A3SS. Using Junction Counts only 2014-10-29 07:37:20,469 joining MATS for A3SS using JC is done with status 0 2014-10-29 07:37:20,469 2014-10-29 07:37:20,469 joining MATS for A3SS. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,583 joining MATS for A3SS using JCEC is done with status 0 2014-10-29 07:37:20,584 2014-10-29 07:37:20,584 joining MATS for RI. Using Junction Counts only 2014-10-29 07:37:20,689 joining MATS for RI using JC is done with status 0 2014-10-29 07:37:20,689 2014-10-29 07:37:20,689 joining MATS for RI. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,797 joining MATS for RI using JCEC is done with status 0 2014-10-29 07:37:20,797 2014-10-29 07:37:20,797 done joining MATS results.. 2014-10-29 07:37:20,797 ======================= Final Report ============= 2014-10-29 07:37:20,797 getting stats for SE. Using Junction Counts only. 2014-10-29 07:37:20,835 getting stats for SE using JC is done with status 0,0 and 0 2014-10-29 07:37:20,835 numLines: 8062 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/SE.MATS.JunctionCountOnly.txt 2014-10-29 07:37:20,835 Upregulated: 223 2014-10-29 07:37:20,835 Downregulated: 341 2014-10-29 07:37:20,835 ========== SE ======== 2014-10-29 07:37:20,835 Junction Counts Only: There are 8061 AS events. Of these, 564 events are statistically significant 2014-10-29 07:37:20,835 223 significant events have higher inclusion level for SAMPLE_1 and 341 events for SAMPLE_2 2014-10-29 07:37:20,835 getting stats for SE. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,873 getting stats for SE using JCEC is done with status 0,0 and 0 2014-10-29 07:37:20,873 numLines: 8463 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/SE.MATS.ReadsOnTargetAndJunctionCounts.txt 2014-10-29 07:37:20,873 Upregulated: 282 2014-10-29 07:37:20,873 Downregulated: 447 2014-10-29 07:37:20,873 Junction Counts and Reads on target Exon Counts: There are 8462 AS events. Of these, 729 events are statistically significant 2014-10-29 07:37:20,873 282 significant events have higher inclusion level for SAMPLE_1 and 447 events for SAMPLE_2 2014-10-29 07:37:20,874 getting stats for MXE. Using Junction Counts only. 2014-10-29 07:37:20,886 getting stats for MXE using JC is done with status 0,0 and 0 2014-10-29 07:37:20,886 numLines: 400 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/MXE.MATS.JunctionCountOnly.txt 2014-10-29 07:37:20,886 Upregulated: 22 2014-10-29 07:37:20,887 Downregulated: 16 2014-10-29 07:37:20,887 ========== MXE ======== 2014-10-29 07:37:20,887 Junction Counts Only: There are 399 AS events. Of these, 38 events are statistically significant 2014-10-29 07:37:20,887 22 significant events have higher inclusion level for SAMPLE_1 and 16 events for SAMPLE_2 2014-10-29 07:37:20,887 getting stats for MXE. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,900 getting stats for MXE using JCEC is done with status 0,0 and 0 2014-10-29 07:37:20,900 numLines: 435 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/MXE.MATS.ReadsOnTargetAndJunctionCounts.txt 2014-10-29 07:37:20,900 Upregulated: 38 2014-10-29 07:37:20,900 Downregulated: 29 2014-10-29 07:37:20,900 Junction Counts and Reads on target Exon Counts: There are 434 AS events. Of these, 67 events are statistically significant 2014-10-29 07:37:20,900 38 significant events have higher inclusion level for SAMPLE_1 and 29 events for SAMPLE_2 2014-10-29 07:37:20,900 getting stats for A5SS. Using Junction Counts only. 2014-10-29 07:37:20,916 getting stats for A5SS using JC is done with status 0,0 and 0 2014-10-29 07:37:20,916 numLines: 1302 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/A5SS.MATS.JunctionCountOnly.txt 2014-10-29 07:37:20,916 Upregulated: 22 2014-10-29 07:37:20,916 Downregulated: 17 2014-10-29 07:37:20,916 ========== A5SS ======== 2014-10-29 07:37:20,916 Junction Counts Only: There are 1301 AS events. Of these, 39 events are statistically significant 2014-10-29 07:37:20,916 22 significant events have higher inclusion level for SAMPLE_1 and 17 events for SAMPLE_2 2014-10-29 07:37:20,916 getting stats for A5SS. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,932 getting stats for A5SS using JCEC is done with status 0,0 and 0 2014-10-29 07:37:20,932 numLines: 1354 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt 2014-10-29 07:37:20,932 Upregulated: 26 2014-10-29 07:37:20,932 Downregulated: 24 2014-10-29 07:37:20,932 Junction Counts and Reads on target Exon Counts: There are 1353 AS events. Of these, 50 events are statistically significant 2014-10-29 07:37:20,932 26 significant events have higher inclusion level for SAMPLE_1 and 24 events for SAMPLE_2 2014-10-29 07:37:20,933 getting stats for A3SS. Using Junction Counts only. 2014-10-29 07:37:20,951 getting stats for A3SS using JC is done with status 0,0 and 0 2014-10-29 07:37:20,951 numLines: 2420 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/A3SS.MATS.JunctionCountOnly.txt 2014-10-29 07:37:20,952 Upregulated: 16 2014-10-29 07:37:20,952 Downregulated: 14 2014-10-29 07:37:20,952 ========== A3SS ======== 2014-10-29 07:37:20,952 Junction Counts Only: There are 2419 AS events. Of these, 30 events are statistically significant 2014-10-29 07:37:20,952 16 significant events have higher inclusion level for SAMPLE_1 and 14 events for SAMPLE_2 2014-10-29 07:37:20,952 getting stats for A3SS. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:20,971 getting stats for A3SS using JCEC is done with status 0,0 and 0 2014-10-29 07:37:20,971 numLines: 2471 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt 2014-10-29 07:37:20,971 Upregulated: 20 2014-10-29 07:37:20,971 Downregulated: 21 2014-10-29 07:37:20,972 Junction Counts and Reads on target Exon Counts: There are 2470 AS events. Of these, 41 events are statistically significant 2014-10-29 07:37:20,972 20 significant events have higher inclusion level for SAMPLE_1 and 21 events for SAMPLE_2 2014-10-29 07:37:20,972 getting stats for RI. Using Junction Counts only. 2014-10-29 07:37:20,989 getting stats for RI using JC is done with status 0,0 and 0 2014-10-29 07:37:20,989 numLines: 2088 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/RI.MATS.JunctionCountOnly.txt 2014-10-29 07:37:20,990 Upregulated: 21 2014-10-29 07:37:20,990 Downregulated: 69 2014-10-29 07:37:20,990 ========== RI ======== 2014-10-29 07:37:20,990 Junction Counts Only: There are 2087 AS events. Of these, 90 events are statistically significant 2014-10-29 07:37:20,990 21 significant events have higher inclusion level for SAMPLE_1 and 69 events for SAMPLE_2 2014-10-29 07:37:20,990 getting stats for RI. Using Junction Counts and Reads on target Exon Counts 2014-10-29 07:37:21,008 getting stats for RI using JCEC is done with status 0,0 and 0 2014-10-29 07:37:21,008 numLines: 2215 /sb/project/afb-431/BIF/MAS/MAS-BIF-P1/results/test/MATS_output/RI.MATS.ReadsOnTargetAndJunctionCounts.txt 2014-10-29 07:37:21,008 Upregulated: 80 2014-10-29 07:37:21,009 Downregulated: 191 2014-10-29 07:37:21,009 Junction Counts and Reads on target Exon Counts: There are 2214 AS events. Of these, 271 events are statistically significant 2014-10-29 07:37:21,009 80 significant events have higher inclusion level for SAMPLE_1 and 191 events for SAMPLE_2 2014-10-29 07:37:21,009 done printing out stats.. 2014-10-29 07:37:21,009 Program ended 2014-10-29 07:37:21,009 Program ran 08:49:33