STAR version=2.7.3a STAR compilation time,server,dir=Tue Oct 8 14:26:19 EDT 2019 vega:/home/dobin/data/STAR/STARcode/STAR.master/source ##### Command Line: STAR --genomeDir /media/data1/genome/HG19/STAR-index/2.7.3a --sjdbGTFfile /media/data1/genome/HG19/annotation.gtf --readFilesIn /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz --outSAMtype BAM Unsorted --outFilterType BySJout --outSJfilterCountUniqueMin -1 2 2 2 --outSJfilterCountTotalMin -1 2 2 2 --outFilterIntronMotifs RemoveNoncanonical --twopassMode Basic --outSAMattributes NH NM MD --outSAMunmapped Within --outSAMmapqUnique 50 --limitBAMsortRAM 24000000000 --outFileNamePrefix KO_GAQ3/STAR/ --readFilesCommand zcat --runThreadN 8 --quantMode GeneCounts ##### Initial USER parameters from Command Line: outFileNamePrefix KO_GAQ3/STAR/ ###### All USER parameters from Command Line: genomeDir /media/data1/genome/HG19/STAR-index/2.7.3a ~RE-DEFINED sjdbGTFfile /media/data1/genome/HG19/annotation.gtf ~RE-DEFINED readFilesIn /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz ~RE-DEFINED outSAMtype BAM Unsorted ~RE-DEFINED outFilterType BySJout ~RE-DEFINED outSJfilterCountUniqueMin -1 2 2 2 ~RE-DEFINED outSJfilterCountTotalMin -1 2 2 2 ~RE-DEFINED outFilterIntronMotifs RemoveNoncanonical ~RE-DEFINED twopassMode Basic ~RE-DEFINED outSAMattributes NH NM MD ~RE-DEFINED outSAMunmapped Within ~RE-DEFINED outSAMmapqUnique 50 ~RE-DEFINED limitBAMsortRAM 24000000000 ~RE-DEFINED outFileNamePrefix KO_GAQ3/STAR/ ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED runThreadN 8 ~RE-DEFINED quantMode GeneCounts ~RE-DEFINED ##### Finished reading parameters from all sources ##### Final user re-defined parameters-----------------: runThreadN 8 genomeDir /media/data1/genome/HG19/STAR-index/2.7.3a readFilesIn /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz readFilesCommand zcat limitBAMsortRAM 24000000000 outFileNamePrefix KO_GAQ3/STAR/ outSAMtype BAM Unsorted outSAMattributes NH NM MD outSAMunmapped Within outSAMmapqUnique 50 outSJfilterCountUniqueMin -1 2 2 2 outSJfilterCountTotalMin -1 2 2 2 outFilterType BySJout outFilterIntronMotifs RemoveNoncanonical sjdbGTFfile /media/data1/genome/HG19/annotation.gtf quantMode GeneCounts twopassMode Basic ------------------------------- ##### Final effective command line: STAR --runThreadN 8 --genomeDir /media/data1/genome/HG19/STAR-index/2.7.3a --readFilesIn /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz --readFilesCommand zcat --limitBAMsortRAM 24000000000 --outFileNamePrefix KO_GAQ3/STAR/ --outSAMtype BAM Unsorted --outSAMattributes NH NM MD --outSAMunmapped Within --outSAMmapqUnique 50 --outSJfilterCountUniqueMin -1 2 2 2 --outSJfilterCountTotalMin -1 2 2 2 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonical --sjdbGTFfile /media/data1/genome/HG19/annotation.gtf --quantMode GeneCounts --twopassMode Basic ---------------------------------------- Input read files for mate 1, from input string /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz -rwxrwxrwx 1 ramn 100 1387285503 Jun 24 19:40 /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz readsCommandsFile: exec > "KO_GAQ3/STAR/_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "/home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz" Finished loading and checking parameters Reading genome generation parameters: ### STAR --runMode genomeGenerate --runThreadN 8 --genomeDir 2.7.3a --genomeFastaFiles ../GRCh37.primary_assembly.genome.fa --sjdbGTFfile ../gencode.v27lift37.annotation.gtf --sjdbOverhang 100 ### GstrandBit=32 versionGenome 2.7.1a ~RE-DEFINED genomeFastaFiles ../GRCh37.primary_assembly.genome.fa ~RE-DEFINED genomeSAindexNbases 14 ~RE-DEFINED genomeChrBinNbits 18 ~RE-DEFINED genomeSAsparseD 1 ~RE-DEFINED sjdbOverhang 100 ~RE-DEFINED sjdbFileChrStartEnd - ~RE-DEFINED sjdbGTFfile ../gencode.v27lift37.annotation.gtf ~RE-DEFINED sjdbGTFchrPrefix - ~RE-DEFINED sjdbGTFfeatureExon exon ~RE-DEFINED sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED sjdbGTFtagExonParentGene gene_id ~RE-DEFINED sjdbInsertSave Basic ~RE-DEFINED genomeFileSizes 3186586660 24219091152 ~RE-DEFINED Genome version is compatible with current STAR Number of real (reference) chromosomes= 84 1 chr1 249250621 0 2 chr10 135534747 249298944 3 chr11 135006516 385089536 4 chr12 133851895 520355840 5 chr13 115169878 654311424 6 chr14 107349540 769654784 7 chr15 102531392 877133824 8 chr16 90354753 979894272 9 chr17 81195210 1070333952 10 chr18 78077248 1151598592 11 chr19 59128983 1229717504 12 chr2 243199373 1288962048 13 chr20 63025520 1532231680 14 chr21 48129895 1595408384 15 chr22 51304566 1643642880 16 chr3 198022430 1695023104 17 chr4 191154276 1893203968 18 chr5 180915260 2084569088 19 chr6 171115067 2265710592 20 chr7 159138663 2436890624 21 chr8 146364022 2596274176 22 chr9 141213431 2742812672 23 chrM 16569 2884108288 24 chrX 155270560 2884370432 25 chrY 59373566 3039821824 26 GL000192.1 547496 3099328512 27 GL000225.1 211173 3100114944 28 GL000194.1 191469 3100377088 29 GL000193.1 189789 3100639232 30 GL000200.1 187035 3100901376 31 GL000222.1 186861 3101163520 32 GL000212.1 186858 3101425664 33 GL000195.1 182896 3101687808 34 GL000223.1 180455 3101949952 35 GL000224.1 179693 3102212096 36 GL000219.1 179198 3102474240 37 GL000205.1 174588 3102736384 38 GL000215.1 172545 3102998528 39 GL000216.1 172294 3103260672 40 GL000217.1 172149 3103522816 41 GL000199.1 169874 3103784960 42 GL000211.1 166566 3104047104 43 GL000213.1 164239 3104309248 44 GL000220.1 161802 3104571392 45 GL000218.1 161147 3104833536 46 GL000209.1 159169 3105095680 47 GL000221.1 155397 3105357824 48 GL000214.1 137718 3105619968 49 GL000228.1 129120 3105882112 50 GL000227.1 128374 3106144256 51 GL000191.1 106433 3106406400 52 GL000208.1 92689 3106668544 53 GL000198.1 90085 3106930688 54 GL000204.1 81310 3107192832 55 GL000233.1 45941 3107454976 56 GL000237.1 45867 3107717120 57 GL000230.1 43691 3107979264 58 GL000242.1 43523 3108241408 59 GL000243.1 43341 3108503552 60 GL000241.1 42152 3108765696 61 GL000236.1 41934 3109027840 62 GL000240.1 41933 3109289984 63 GL000206.1 41001 3109552128 64 GL000232.1 40652 3109814272 65 GL000234.1 40531 3110076416 66 GL000202.1 40103 3110338560 67 GL000238.1 39939 3110600704 68 GL000244.1 39929 3110862848 69 GL000248.1 39786 3111124992 70 GL000196.1 38914 3111387136 71 GL000249.1 38502 3111649280 72 GL000246.1 38154 3111911424 73 GL000203.1 37498 3112173568 74 GL000197.1 37175 3112435712 75 GL000245.1 36651 3112697856 76 GL000247.1 36422 3112960000 77 GL000201.1 36148 3113222144 78 GL000235.1 34474 3113484288 79 GL000239.1 33824 3113746432 80 GL000210.1 27682 3114008576 81 GL000231.1 27386 3114270720 82 GL000229.1 19913 3114532864 83 GL000226.1 15008 3114795008 84 GL000207.1 4262 3115057152 --sjdbOverhang = 100 taken from the generated genome Started loading the genome: Wed Jul 14 15:32:00 2021 Genome: size given as a parameter = 3186586660 SA: size given as a parameter = 24219091152 SAindex: size given as a parameter = 1 Read from SAindex: pGe.gSAindexNbases=14 nSAi=357913940 nGenome=3186586660; nSAbyte=24219091152 GstrandBit=32 SA number of indices=5871294824 Shared memory is not used for genomes. Allocated a private copy of the genome. Genome file size: 3186586660 bytes; state: good=1 eof=0 fail=0 bad=0 Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 3186586660 bytes SA file size: 24219091152 bytes; state: good=1 eof=0 fail=0 bad=0 Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 24219091152 bytes Loading SAindex ... done: 1565873619 bytes Finished loading the genome: Wed Jul 14 15:33:43 2021 Processing splice junctions database sjdbN=354564, pGe.sjdbOverhang=100 alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824 Jul 14 15:33:43 Loaded database junctions from the generated genome /media/data1/genome/HG19/STAR-index/2.7.3a/sjdbList.out.tab: 354564 total junctions Jul 14 15:33:43 ..... processing annotations GTF WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 1570603 1570918 chr1 1570919 1570922 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 1570919 1570922 chr1 1570923 1571218 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 1592939 1594199 chr1 1594200 1594840 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 1592940 1594199 chr1 1594200 1594840 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 7442548 7442597 chr1 7442598 7442783 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 10446161 10446921 chr1 10446922 10447207 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 12568947 12570579 chr1 12570580 12572099 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 12568947 12570579 chr1 12570580 12572099 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 12568947 12570579 chr1 12570580 12572099 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 12568947 12570579 chr1 12570580 12572099 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 12822305 12822498 chr1 12822499 12823036 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 27730730 27732103 chr1 27732104 27734840 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 144610815 144610985 chr1 144610986 144612647 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145115735 145116148 chr1 145116149 145116310 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145138424 145139089 chr1 145139090 145139613 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145139025 145139089 chr1 145139090 145139569 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145290781 145291615 chr1 145291616 145291654 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145281955 145284171 chr1 145284172 145285912 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145382056 145382201 chr1 145382202 145382434 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145382056 145382201 chr1 145382202 145382397 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145382056 145382201 chr1 145382202 145382378 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145382056 145382201 chr1 145382202 145382362 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145472122 145472451 chr1 145472452 145472569 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145500513 145500921 chr1 145500922 145501670 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145509166 145511796 chr1 145511797 145513536 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145514174 145514214 chr1 145514215 145514276 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 145688683 145695506 chr1 145695507 145696218 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 147228332 147229643 chr1 147229644 147231379 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 147228333 147229643 chr1 147229644 147231379 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 147229426 147229643 chr1 147229644 147229879 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 149910685 149911936 chr1 149911937 149916964 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 150192510 150192565 chr1 150192566 150193063 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 150192510 150192565 chr1 150192566 150193063 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 150192510 150192565 chr1 150192566 150193063 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 155160639 155161248 chr1 155161249 155161488 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 155161249 155161488 chr1 155161489 155161620 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 155161489 155161620 chr1 155161621 155162074 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 174968300 174968530 chr1 174968531 174968825 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr1 181767428 181776078 chr1 181776079 181777219 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 24387068 24387178 chr2 24387179 24387204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 24387068 24387178 chr2 24387179 24387204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 24387068 24387178 chr2 24387179 24387204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 24387068 24387178 chr2 24387179 24387204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 24387068 24387178 chr2 24387179 24387204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 24387126 24387178 chr2 24387179 24387204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 24387068 24387178 chr2 24387179 24387204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 27535274 27535311 chr2 27535312 27535320 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 27535082 27535311 chr2 27535312 27535456 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 27533941 27535311 chr2 27535312 27536254 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 27534798 27535311 chr2 27535312 27535456 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 27535082 27535311 chr2 27535312 27535456 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 27535116 27535311 chr2 27535312 27535456 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 27535168 27535311 chr2 27535312 27535456 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 31805690 31805880 chr2 31805881 31806136 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302923 38303017 chr2 38303018 38303323 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302919 38303017 chr2 38303018 38303218 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302923 38303017 chr2 38303018 38303296 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302791 38303017 chr2 38303018 38303210 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302810 38303017 chr2 38303018 38303210 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302843 38303017 chr2 38303018 38303210 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302843 38303017 chr2 38303018 38303210 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302843 38303017 chr2 38303018 38303210 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 38302843 38303017 chr2 38303018 38303210 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 39102929 39103032 chr2 39103033 39103049 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 39102929 39103032 chr2 39103033 39103066 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 39102929 39103032 chr2 39103033 39103075 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 55844280 55844616 chr2 55844617 55844749 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 55844280 55844616 chr2 55844617 55844743 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 55844280 55844616 chr2 55844617 55844723 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 55844280 55844616 chr2 55844617 55845113 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 73675090 73675227 chr2 73675228 73681194 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 73675090 73675227 chr2 73675228 73681194 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 73675090 73675227 chr2 73675228 73681194 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 88751415 88751751 chr2 88751752 88752174 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 89100616 89103058 chr2 89103059 89104394 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 96778623 96780988 chr2 96780989 96781984 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 103512092 103512153 chr2 103512154 103512180 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 172821355 172821358 chr2 172821359 172822038 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 232225466 232225535 chr2 232225536 232225594 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr2 232225466 232225535 chr2 232225536 232225594 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 14561618 14561627 chr3 14561628 14561786 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 14561618 14561627 chr3 14561628 14561786 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 14561618 14561627 chr3 14561628 14561786 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 50306593 50306752 chr3 50306753 50306780 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 50306593 50306752 chr3 50306753 50306780 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 50306306 50306752 chr3 50306753 50306780 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 50306438 50306752 chr3 50306753 50306780 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 50306597 50306752 chr3 50306753 50306780 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 50306601 50306752 chr3 50306753 50306780 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 50306646 50306752 chr3 50306753 50306780 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 53317448 53318546 chr3 53318547 53321678 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 124646379 124646705 chr3 124646706 124646837 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 133969267 133969437 chr3 133969438 133969487 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 133969438 133969487 chr3 133969488 133969586 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 133969267 133969437 chr3 133969438 133969487 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr3 133969438 133969487 chr3 133969488 133969586 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 48991 49445 chr4 49446 49850 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 85622 85997 chr4 85998 86017 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 85998 86017 chr4 86018 86032 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 86045 86101 chr4 86102 87276 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 87278 87313 chr4 87314 87604 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 87314 87604 chr4 87605 88099 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 85622 85997 chr4 85998 86017 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 85998 86017 chr4 86018 86032 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 86045 86101 chr4 86102 87276 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 87278 87313 chr4 87314 87412 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 85622 85997 chr4 85998 86017 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 85998 86017 chr4 86018 86032 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 86045 86101 chr4 86102 87276 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 87278 87313 chr4 87314 87410 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 124420 124905 chr4 124906 124930 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr4 9471182 9471212 chr4 9471213 9471221 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 35055802 35058665 chr5 35058666 35058727 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 35058666 35058727 chr5 35058728 35058804 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 35058728 35058804 chr5 35058805 35066204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 35055802 35058665 chr5 35058666 35058727 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 35058666 35058727 chr5 35058728 35058804 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 35058728 35058804 chr5 35058805 35066204 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 58460774 58460844 chr5 58460845 58460876 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 72742083 72743299 chr5 72743300 72744352 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 77745757 77745853 chr5 77745854 77745857 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 77745757 77745853 chr5 77745854 77745857 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 77745757 77745853 chr5 77745854 77745857 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 102512568 102512570 chr5 102512571 102512611 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 102512568 102512570 chr5 102512571 102512611 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 102512568 102512570 chr5 102512571 102512611 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 131695773 131695801 chr5 131695802 131695808 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 131695773 131695801 chr5 131695802 131695828 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 135513026 135513085 chr5 135513086 135518420 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 135513026 135513085 chr5 135513086 135518422 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 140474163 140474190 chr5 140474191 140478287 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 140560980 140561176 chr5 140561177 140563573 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 140566701 140568034 chr5 140568035 140571114 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 140567853 140568034 chr5 140568035 140568320 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 156721792 156721863 chr5 156721864 156721868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 175810941 175811094 chr5 175811095 175811099 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 175810949 175811094 chr5 175811095 175811284 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 175810949 175811094 chr5 175811095 175811375 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 175810961 175811094 chr5 175811095 175811287 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr5 175810984 175811094 chr5 175811095 175811287 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 958563 958803 chr6 958804 958828 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 28239632 28239932 chr6 28239933 28240116 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 28239632 28239932 chr6 28239933 28240113 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 28239632 28239932 chr6 28239933 28240113 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 28239632 28239932 chr6 28239933 28240116 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 43501091 43501580 chr6 43501581 43501744 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 49325859 49325994 chr6 49325995 49326569 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 70916851 70917559 chr6 70917560 70919679 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 114178541 114178831 chr6 114178832 114179023 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr6 114182784 114183162 chr6 114183163 114183593 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 2515304 2515382 chr7 2515383 2515462 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 2515065 2515382 chr7 2515383 2515462 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 17832466 17835124 chr7 17835125 17836562 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 20821903 20822304 chr7 20822305 20824947 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 28997499 28997596 chr7 28997597 28997908 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552557 36552729 chr7 36552730 36552790 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552730 36552790 chr7 36552791 36552986 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552607 36552729 chr7 36552730 36552790 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552730 36552790 chr7 36552791 36552986 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552610 36552729 chr7 36552730 36552790 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552730 36552790 chr7 36552791 36552986 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552610 36552729 chr7 36552730 36552790 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552730 36552790 chr7 36552791 36552986 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552611 36552729 chr7 36552730 36552790 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 36552730 36552790 chr7 36552791 36552986 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 65112457 65112524 chr7 65112525 65112954 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 65150572 65150713 chr7 65150714 65150776 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 65150572 65150713 chr7 65150714 65150776 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 72663923 72664015 chr7 72664016 72664105 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 72663923 72664015 chr7 72664016 72664105 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 72663923 72664015 chr7 72664016 72664105 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 74016692 74016918 chr7 74016919 74016930 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 74016692 74016918 chr7 74016919 74016927 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 74617274 74617342 chr7 74617343 74617435 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 75914933 75914934 chr7 75914935 75916603 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 75914933 75914934 chr7 75914935 75916605 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 100472733 100472932 chr7 100472933 100472949 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 100472748 100472932 chr7 100472933 100472949 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 100472748 100472932 chr7 100472933 100472949 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 100472785 100472932 chr7 100472933 100472949 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 100472807 100472932 chr7 100472933 100472949 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 100472810 100472932 chr7 100472933 100472949 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 100494174 100494222 chr7 100494223 100494594 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 101200651 101200669 chr7 101200670 101202304 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 101200651 101200669 chr7 101200670 101202304 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 101200651 101200669 chr7 101200670 101200913 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 128533445 128533514 chr7 128533515 128533529 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 128533445 128533514 chr7 128533515 128533529 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 128533445 128533514 chr7 128533515 128533529 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 128533445 128533514 chr7 128533515 128533529 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 128533445 128533514 chr7 128533515 128533529 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 128533445 128533514 chr7 128533515 128533529 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 130416063 130417497 chr7 130417498 130418688 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 141989465 141989554 chr7 141989555 141989609 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 142561724 142562051 chr7 142562052 142562504 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 142561724 142562051 chr7 142562052 142562504 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 142561724 142562051 chr7 142562052 142562504 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 142561724 142562051 chr7 142562052 142562504 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 142561724 142562051 chr7 142562052 142562504 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 142576023 142576435 chr7 142576436 142583134 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 148920904 148921866 chr7 148921867 148923339 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 149426279 149426305 chr7 149426306 149426460 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 149426279 149426305 chr7 149426306 149426460 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 149476623 149476666 chr7 149476667 149476774 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 149476623 149476666 chr7 149476667 149476774 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 150713776 150713902 chr7 150713903 150713908 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 150713776 150713902 chr7 150713903 150713908 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 150713776 150713902 chr7 150713903 150713908 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 150713776 150713902 chr7 150713903 150713908 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 150713776 150713902 chr7 150713903 150713908 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 150892662 150892684 chr7 150892685 150892744 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 150892662 150892684 chr7 150892685 150892744 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr7 158488833 158489052 chr7 158489053 158489342 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 1248649 1249714 chr8 1249715 1250630 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 1249715 1250630 chr8 1250631 1250766 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 8175258 8176387 chr8 8176388 8176818 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 8233763 8234870 chr8 8234871 8235588 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 8175259 8176387 chr8 8176388 8176818 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 8233763 8234870 chr8 8234871 8235588 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 30620790 30620840 chr8 30620841 30620863 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 30620790 30620840 chr8 30620841 30620863 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 30620790 30620840 chr8 30620841 30620863 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 30620790 30620840 chr8 30620841 30620863 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 30620790 30620840 chr8 30620841 30620863 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 30620790 30620840 chr8 30620841 30620863 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 30620663 30620840 chr8 30620841 30620863 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 48805700 48805816 chr8 48805817 48805947 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 48805700 48805816 chr8 48805817 48805947 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64100303 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64100303 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64100303 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64100303 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64100303 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64100303 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64099057 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64098819 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64099029 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64100303 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64098918 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 64098706 64098729 chr8 64098730 64100303 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86124392 86126830 chr8 86126831 86128536 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86126311 86126830 chr8 86126831 86126860 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86126312 86126830 chr8 86126831 86126860 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86126722 86126830 chr8 86126831 86126860 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86126737 86126830 chr8 86126831 86126860 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86126737 86126830 chr8 86126831 86126860 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86126737 86126830 chr8 86126831 86126860 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86126738 86126830 chr8 86126831 86126860 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 86126791 86126830 chr8 86126831 86126860 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 87526656 87526691 chr8 87526692 87526769 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 87526666 87526691 chr8 87526692 87526769 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 87526667 87526691 chr8 87526692 87526769 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 87526672 87526691 chr8 87526692 87526769 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 87526675 87526691 chr8 87526692 87526769 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 87526688 87526691 chr8 87526692 87526801 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143738874 143739805 chr8 143739806 143741374 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143738874 143739805 chr8 143739806 143741374 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143739778 143739805 chr8 143739806 143740356 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143857324 143857441 chr8 143857442 143857537 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143857324 143857441 chr8 143857442 143857537 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143857324 143857441 chr8 143857442 143857537 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143857324 143857441 chr8 143857442 143857537 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143857324 143857441 chr8 143857442 143857537 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 143857324 143857441 chr8 143857442 143857537 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 144297134 144298159 chr8 144298160 144299044 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 144940082 144940300 chr8 144940301 144940437 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 144940301 144940437 chr8 144940438 144947466 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 144940082 144940300 chr8 144940301 144940437 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 144940301 144940437 chr8 144940438 144947434 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr8 145554228 145556063 chr8 145556064 145557778 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 42338767 42338804 chr9 42338805 42338937 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 42359212 42359231 chr9 42359232 42359290 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 42470357 42472055 chr9 42472056 42474239 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 42506229 42506791 chr9 42506792 42506814 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 44821627 44821655 chr9 44821656 44821689 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 44821656 44821689 chr9 44821690 44821755 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 46390110 46390233 chr9 46390234 46390265 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 70941179 70942321 chr9 70942322 70943606 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr9 139235327 139235824 chr9 139235825 139236288 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 61122159 61122268 chr10 61122269 61122308 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 61122159 61122268 chr10 61122269 61122352 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 61122159 61122268 chr10 61122269 61122305 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 61122159 61122268 chr10 61122269 61122322 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 61122159 61122268 chr10 61122269 61122348 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 61122159 61122268 chr10 61122269 61122352 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 61122159 61122268 chr10 61122269 61122280 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 97915954 97920099 chr10 97920100 97922498 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 97915954 97920099 chr10 97920100 97923508 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 97915954 97920099 chr10 97920100 97923508 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 97915954 97920099 chr10 97920100 97923517 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 116930795 116931101 chr10 116931102 116931125 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 116930795 116931101 chr10 116931102 116931132 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 118383457 118383463 chr10 118383464 118383610 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 118383457 118383463 chr10 118383464 118383624 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 118383457 118383463 chr10 118383464 118383610 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 118383457 118383463 chr10 118383464 118383610 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr10 118383457 118383463 chr10 118383464 118383610 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 159455 159865 chr11 159866 159980 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 14101446 14101493 chr11 14101494 14101567 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67765146 67765163 chr11 67765164 67765269 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67765146 67765163 chr11 67765164 67765269 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67765029 67765163 chr11 67765164 67765269 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67785997 67786064 chr11 67786065 67786106 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67788954 67789293 chr11 67789294 67789339 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67795217 67795378 chr11 67795379 67796163 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67785997 67786064 chr11 67786065 67786106 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67782767 67786064 chr11 67786065 67786106 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67788954 67789293 chr11 67789294 67789339 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67795217 67795378 chr11 67795379 67796749 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67785997 67786064 chr11 67786065 67786106 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67788954 67789293 chr11 67789294 67789339 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67795217 67795378 chr11 67795379 67795624 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67785997 67786064 chr11 67786065 67786106 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67788954 67789293 chr11 67789294 67789339 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67795217 67795378 chr11 67795379 67796743 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67788954 67789293 chr11 67789294 67789339 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67795217 67795378 chr11 67795379 67796161 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67785997 67786064 chr11 67786065 67786106 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67785997 67786064 chr11 67786065 67786106 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67789223 67789293 chr11 67789294 67789339 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67795217 67795378 chr11 67795379 67795577 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67786051 67786064 chr11 67786065 67786106 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 67788954 67789293 chr11 67789294 67789320 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 71850007 71850156 chr11 71850157 71850193 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 71849879 71850156 chr11 71850157 71850193 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 71850007 71850156 chr11 71850157 71850193 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 71850007 71850156 chr11 71850157 71850193 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 94699460 94699507 chr11 94699508 94699577 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 94699460 94699507 chr11 94699508 94699577 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 94699460 94699507 chr11 94699508 94699577 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 94800361 94800902 chr11 94800903 94804387 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 111853064 111853106 chr11 111853107 111853211 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 111853064 111853106 chr11 111853107 111853211 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 111853064 111853106 chr11 111853107 111853211 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 111852942 111853106 chr11 111853107 111853211 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112831969 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112831969 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112831969 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112831969 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112831997 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832090 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832090 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832124 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832124 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832147 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832157 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832158 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832159 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832161 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 112832202 112832308 chr11 112832309 112832340 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118494801 118495216 chr11 118495217 118495227 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118529018 118529044 chr11 118529045 118529077 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118529018 118529044 chr11 118529045 118529077 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118529018 118529044 chr11 118529045 118529077 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118620718 118621889 chr11 118621890 118622806 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118620718 118621889 chr11 118621890 118622806 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118620718 118621889 chr11 118621890 118622614 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118926991 118927013 chr11 118927014 118927129 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118926991 118927013 chr11 118927014 118927116 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118926991 118927013 chr11 118927014 118927129 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118939907 118939939 chr11 118939940 118940054 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118939884 118939939 chr11 118939940 118940054 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 118939909 118939939 chr11 118939940 118940054 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 119031591 119031841 chr11 119031842 119033362 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 119031591 119031841 chr11 119031842 119032145 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 119031591 119031841 chr11 119031842 119032357 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 124120407 124121286 chr11 124121287 124122018 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 125452242 125452300 chr11 125452301 125452315 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 125452242 125452300 chr11 125452301 125452315 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 125452242 125452300 chr11 125452301 125452315 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 125452242 125452300 chr11 125452301 125452315 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 125452242 125452300 chr11 125452301 125452315 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 125452242 125452300 chr11 125452301 125452315 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr11 125452242 125452300 chr11 125452301 125452315 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr12 6937575 6938023 chr12 6938024 6938102 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr12 7090456 7090659 chr12 7090660 7090793 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr12 86349445 86372640 chr12 86372641 86374208 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr12 86372516 86372640 chr12 86372641 86374208 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr12 86372524 86372640 chr12 86372641 86374208 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr12 86372524 86372640 chr12 86372641 86374208 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr12 108925141 108925300 chr12 108925301 108925744 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr13 20659962 20664042 chr13 20664043 20665968 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr13 20659962 20664042 chr13 20664043 20665968 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr13 86929483 86929508 chr13 86929509 86929524 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 19500239 19500274 chr14 19500275 19500332 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 19563122 19563209 chr14 19563210 19563254 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 19880209 19880408 chr14 19880409 19880919 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 19882159 19882463 chr14 19882464 19884029 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 19889804 19889902 chr14 19889903 19890067 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 19891059 19891075 chr14 19891076 19891695 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 19969314 19969408 chr14 19969409 19969433 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 19969409 19969433 chr14 19969434 19969977 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 20105463 20105495 chr14 20105496 20105503 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21964704 21965671 chr14 21965672 21965677 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21965672 21965677 chr14 21965678 21967319 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21964704 21965671 chr14 21965672 21965677 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21965672 21965677 chr14 21965678 21967315 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21963388 21964191 chr14 21964192 21964385 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21989232 21989475 chr14 21989476 21989706 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21989476 21989706 chr14 21989707 21993788 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21989234 21989475 chr14 21989476 21989706 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21989476 21989706 chr14 21989707 21990378 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 21989673 21989706 chr14 21989707 21990378 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 22136154 22136698 chr14 22136699 22138553 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 22141306 22141815 chr14 22141816 22142033 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 23020550 23020688 chr14 23020689 23020821 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 24646350 24646406 chr14 24646407 24646428 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 24646350 24646406 chr14 24646407 24646428 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 24646350 24646406 chr14 24646407 24646428 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 24646350 24646406 chr14 24646407 24646428 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 24646350 24646406 chr14 24646407 24646428 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 63784361 63784407 chr14 63784408 63784564 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 63784361 63784407 chr14 63784408 63784563 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 73957669 73957981 chr14 73957982 73960096 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 74100365 74100524 chr14 74100525 74100644 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582191 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582176 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94582127 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 94581857 94582131 chr14 94582132 94582279 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106627439 106627699 chr14 106627700 106627741 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636283 106636324 chr14 106636325 106636348 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636325 106636348 chr14 106636349 106636364 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636349 106636364 chr14 106636365 106636370 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636365 106636370 chr14 106636371 106636375 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636371 106636375 chr14 106636376 106636385 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636376 106636385 chr14 106636386 106636397 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636386 106636397 chr14 106636398 106636434 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636398 106636434 chr14 106636435 106636453 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636435 106636453 chr14 106636454 106636487 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636454 106636487 chr14 106636488 106636662 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636488 106636662 chr14 106636663 106636709 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636663 106636709 chr14 106636710 106636724 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636710 106636724 chr14 106636725 106636731 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636725 106636731 chr14 106636732 106636736 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636732 106636736 chr14 106636737 106636742 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636737 106636742 chr14 106636743 106636751 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636743 106636751 chr14 106636752 106636766 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106636752 106636766 chr14 106636767 106636820 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106744810 106744834 chr14 106744835 106745422 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106744810 106744834 chr14 106744835 106744966 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106899044 106899121 chr14 106899122 106899345 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106928715 106928857 chr14 106928858 106928923 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106937431 106937467 chr14 106937468 106937712 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 106960402 106960440 chr14 106960441 106960747 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 107057488 107057605 chr14 107057606 107057656 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 107275873 107276110 chr14 107276111 107276167 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 107280994 107281145 chr14 107281146 107281216 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 107281146 107281216 chr14 107281217 107281251 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr14 107281217 107281251 chr14 107281252 107281265 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22082361 22082663 chr15 22082664 22083194 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22082361 22082663 chr15 22082664 22082818 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22082361 22082663 chr15 22082664 22083141 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22742655 22743074 chr15 22743075 22743166 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22743179 22743199 chr15 22743200 22743283 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22744255 22745802 chr15 22745803 22746002 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22742655 22743074 chr15 22743075 22743166 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22743075 22743166 chr15 22743167 22743178 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22743167 22743178 chr15 22743179 22743199 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22743179 22743199 chr15 22743200 22743406 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22743200 22743406 chr15 22743407 22743598 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 22744255 22745802 chr15 22745803 22745998 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 40699837 40700006 chr15 40700007 40700011 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 65243544 65243569 chr15 65243570 65243582 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 65243586 65243590 chr15 65243591 65243641 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 65243591 65243641 chr15 65243642 65243670 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 83192743 83192942 chr15 83192943 83193062 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 83192943 83193062 chr15 83193063 83193313 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 83193063 83193313 chr15 83193314 83193331 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 83193314 83193331 chr15 83193332 83193409 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 99645241 99646107 chr15 99646108 99646214 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 99645286 99646107 chr15 99646108 99646214 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 99645286 99646107 chr15 99646108 99646214 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 102029579 102029685 chr15 102029686 102030042 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 102029579 102029685 chr15 102029686 102029947 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 102029579 102029685 chr15 102029686 102029947 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 102029579 102029685 chr15 102029686 102029947 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 102029579 102029685 chr15 102029686 102029900 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 102029579 102029685 chr15 102029686 102029900 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr15 102029579 102029685 chr15 102029686 102030187 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 138697 138772 chr16 138773 141084 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 138697 138772 chr16 138773 138888 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 138697 138772 chr16 138773 138888 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 138697 138772 chr16 138773 138888 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 138697 138772 chr16 138773 138888 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 138697 138772 chr16 138773 138888 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 11493329 11493346 chr16 11493347 11493456 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 11493329 11493346 chr16 11493347 11493456 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 47005261 47006160 chr16 47006161 47006854 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 71981395 71981414 chr16 71981415 71981490 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 76311176 76311602 chr16 76311603 76311644 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 76311176 76311602 chr16 76311603 76311644 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 76311176 76311602 chr16 76311603 76311644 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr16 76311561 76311602 chr16 76311603 76311644 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 6555038 6555546 chr17 6555547 6556792 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 6555191 6555546 chr17 6555547 6555913 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 6555484 6555546 chr17 6555547 6555913 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 8725164 8725214 chr17 8725215 8725253 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 8725164 8725214 chr17 8725215 8725253 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 8725164 8725214 chr17 8725215 8725253 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 8725164 8725214 chr17 8725215 8725253 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 18498035 18498059 chr17 18498060 18498175 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 18498035 18498059 chr17 18498060 18498175 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 18498035 18498059 chr17 18498060 18498175 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 18498035 18498059 chr17 18498060 18498175 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 21156472 21156530 chr17 21156531 21156722 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 26684395 26684529 chr17 26684530 26684545 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 26687758 26687898 chr17 26687899 26688130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 26692143 26692224 chr17 26692225 26692265 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 26699207 26699367 chr17 26699368 26699521 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 26723176 26724874 chr17 26724875 26727721 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 26723176 26724874 chr17 26724875 26725179 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 26721775 26724874 chr17 26724875 26726729 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 26722695 26724874 chr17 26724875 26726729 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 34100185 34100350 chr17 34100351 34100408 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 34100185 34100350 chr17 34100351 34100408 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 34100185 34100350 chr17 34100351 34100408 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 34859790 34860752 chr17 34860753 34861016 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 34860742 34860752 chr17 34860753 34861243 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 35294210 35294340 chr17 35294341 35294542 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 35970177 35970339 chr17 35970340 35974398 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 36338141 36338150 chr17 36338151 36338594 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 38333748 38334359 chr17 38334360 38334633 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 38334115 38334359 chr17 38334360 38334633 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 40976173 40976311 chr17 40976312 40976396 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 43192462 43192549 chr17 43192550 43192611 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 43192462 43192549 chr17 43192550 43192710 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 43192511 43192549 chr17 43192550 43192611 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 43192462 43192549 chr17 43192550 43192611 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 43363798 43364293 chr17 43364294 43364411 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 43363798 43364293 chr17 43364294 43364411 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 43363798 43364293 chr17 43364294 43364411 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 46115033 46115074 chr17 46115075 46115084 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 46115075 46115084 chr17 46115085 46115122 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 46115085 46115122 chr17 46115123 46115144 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 46115033 46115074 chr17 46115075 46115084 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 46115075 46115084 chr17 46115085 46115122 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 46115085 46115122 chr17 46115123 46115135 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 48226508 48227384 chr17 48227385 48227403 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 48227385 48227403 chr17 48227404 48227991 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 72889504 72889677 chr17 72889678 72889708 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 72889504 72889677 chr17 72889678 72889879 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73232694 73234010 chr17 73234011 73234470 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73232694 73234010 chr17 73234011 73234470 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73232694 73234010 chr17 73234011 73234470 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73232694 73234010 chr17 73234011 73234470 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73232695 73234010 chr17 73234011 73234470 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73232697 73234010 chr17 73234011 73234470 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73612605 73612642 chr17 73612643 73612865 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73612605 73612642 chr17 73612643 73612865 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73612605 73612642 chr17 73612643 73612865 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 73612393 73612642 chr17 73612643 73612759 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 77682281 77682786 chr17 77682787 77683390 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr17 77683430 77683981 chr17 77683982 77686081 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr18 43833663 43833701 chr18 43833702 43833786 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr18 43833663 43833701 chr18 43833702 43833786 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr18 74401986 74403378 chr18 74403379 74403929 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr18 74402046 74403378 chr18 74403379 74403499 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 2340075 2340154 chr19 2340155 2340170 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 4954662 4954679 chr19 4954680 4954833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 4954662 4954679 chr19 4954680 4954833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 4954662 4954679 chr19 4954680 4954833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 4954662 4954679 chr19 4954680 4954833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 4954662 4954679 chr19 4954680 4954833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 4954662 4954679 chr19 4954680 4954833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 4954662 4954679 chr19 4954680 4954833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 7938305 7938306 chr19 7938307 7938581 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 7938305 7938306 chr19 7938307 7938482 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 11526623 11526892 chr19 11526893 11526908 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 15730446 15730498 chr19 15730499 15730572 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 15730301 15730498 chr19 15730499 15730572 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 15728811 15730498 chr19 15730499 15730572 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 15730446 15730498 chr19 15730499 15730572 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 18897342 18897526 chr19 18897527 18897844 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 35842455 35844679 chr19 35844680 35844764 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41122795 41123093 chr19 41123094 41123102 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 41123006 41123093 chr19 41123094 41123130 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 42347645 42347973 chr19 42347974 42348736 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 45170227 45170572 chr19 45170573 45170589 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 45170227 45170572 chr19 45170573 45170589 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 45170227 45170572 chr19 45170573 45170589 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 51676233 51676684 chr19 51676685 51676780 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 51676233 51676684 chr19 51676685 51676756 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 51675323 51676684 chr19 51676685 51676778 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 51676233 51676684 chr19 51676685 51676685 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 54663846 54663896 chr19 54663897 54664111 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 54663846 54663896 chr19 54663897 54664111 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 54663846 54663896 chr19 54663897 54664111 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 54663846 54663896 chr19 54663897 54664111 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 54676734 54676814 chr19 54676815 54676865 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 54676734 54676814 chr19 54676815 54676944 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 54676734 54676814 chr19 54676815 54676854 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 54869615 54870006 chr19 54870007 54870232 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 55056656 55057022 chr19 55057023 55057053 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 55049184 55049597 chr19 55049598 55049868 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 55098668 55100683 chr19 55100684 55101752 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 56052023 56052337 chr19 56052338 56052892 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr19 58718087 58718360 chr19 58718361 58718455 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21186130 21186161 chr20 21186162 21186222 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21186130 21186161 chr20 21186162 21186222 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21186130 21186161 chr20 21186162 21186222 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21186130 21186161 chr20 21186162 21186222 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21186130 21186161 chr20 21186162 21186222 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21186130 21186161 chr20 21186162 21186222 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21186130 21186161 chr20 21186162 21186222 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21186130 21186161 chr20 21186162 21186168 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 21174683 21176014 chr20 21176015 21179443 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34130571 34131762 chr20 34131763 34132550 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34147111 34147281 chr20 34147282 34147394 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34147111 34147281 chr20 34147282 34147394 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34152290 34152587 chr20 34152588 34152834 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34147111 34147281 chr20 34147282 34148405 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34152290 34152587 chr20 34152588 34152834 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34147111 34147281 chr20 34147282 34147394 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34152290 34152587 chr20 34152588 34152834 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34146926 34147281 chr20 34147282 34147394 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 34147111 34147281 chr20 34147282 34147394 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 60511795 60512339 chr20 60512340 60515673 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62329995 62331335 chr20 62331336 62331882 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62329996 62331335 chr20 62331336 62331882 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62329996 62331335 chr20 62331336 62332054 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62329996 62331335 chr20 62331336 62331882 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62330809 62331335 chr20 62331336 62331882 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62330809 62331335 chr20 62331336 62331882 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62330809 62331335 chr20 62331336 62331882 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62330831 62331335 chr20 62331336 62332054 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62330850 62331335 chr20 62331336 62331882 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr20 62330865 62331335 chr20 62331336 62332054 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 14415535 14416337 chr21 14416338 14416438 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 15048216 15048731 chr21 15048732 15049653 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 17979314 17981988 chr21 17981989 17982094 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 34224059 34224412 chr21 34224413 34224779 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 35339584 35339763 chr21 35339764 35339819 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 35339326 35339763 chr21 35339764 35339819 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 35819064 35819995 chr21 35819996 35821982 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 35819064 35819995 chr21 35819996 35821982 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 44514765 44514969 chr21 44514970 44516053 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 44514765 44514969 chr21 44514970 44516500 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 44517756 44520034 chr21 44520035 44521542 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr21 44589711 44589920 chr21 44589921 44589963 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 18032535 18035852 chr22 18035853 18036387 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 20779948 20779973 chr22 20779974 20780025 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 20779948 20779973 chr22 20779974 20780025 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22393836 22394291 chr22 22394292 22394463 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22618984 22626577 chr22 22626578 22627402 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22640241 22640282 chr22 22640283 22640354 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22838767 22840125 chr22 22840126 22841789 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22840126 22841789 chr22 22841790 22841833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22841790 22841833 chr22 22841834 22841840 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22839204 22840125 chr22 22840126 22840320 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22841203 22841789 chr22 22841790 22841833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22841790 22841833 chr22 22841834 22841840 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22839219 22840125 chr22 22840126 22840320 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22841203 22841789 chr22 22841790 22841833 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 22841790 22841833 chr22 22841834 22841840 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 23165153 23165242 chr22 23165243 23165360 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 27061421 27062698 chr22 27062699 27062900 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 27061495 27062698 chr22 27062699 27062900 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 27061495 27062698 chr22 27062699 27062900 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 27061421 27062698 chr22 27062699 27062900 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 29707452 29707639 chr22 29707640 29708774 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 29706817 29707639 chr22 29707640 29708083 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 29707452 29707639 chr22 29707640 29708774 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 29707452 29707639 chr22 29707640 29708774 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 29707452 29707639 chr22 29707640 29708774 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 30818266 30819615 chr22 30819616 30821305 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 30818266 30819615 chr22 30819616 30819826 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 30818266 30819615 chr22 30819616 30819828 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 30818266 30819615 chr22 30819616 30819826 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 30822705 30822920 chr22 30822921 30823179 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 36585172 36587845 chr22 36587846 36587958 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 36585177 36587845 chr22 36587846 36587958 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 36585177 36587845 chr22 36587846 36587958 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 36586845 36587845 chr22 36587846 36587958 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 36587307 36587845 chr22 36587846 36587958 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 37243415 37243537 chr22 37243538 37244059 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 37600278 37602583 chr22 37602584 37603878 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 37602520 37602583 chr22 37602584 37603878 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 38694586 38694588 chr22 38694589 38694939 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 45810203 45810278 chr22 45810279 45810283 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 45810204 45810278 chr22 45810279 45810283 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 51042270 51042513 chr22 51042514 51043492 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chr22 51042270 51042513 chr22 51042514 51043492 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 46917569 46918916 chrX 46918917 46918950 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 46918917 46918950 chrX 46918951 46918957 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 46918951 46918957 chrX 46918958 46918974 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 46918958 46918974 chrX 46918975 46919651 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 46917569 46918916 chrX 46918917 46918950 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 46918917 46918950 chrX 46918951 46918957 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 46918951 46918957 chrX 46918958 46918974 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 46918958 46918974 chrX 46918975 46919651 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 47925699 47925715 chrX 47925716 47925971 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 49022413 49024806 chrX 49024807 49024820 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 49040112 49040115 chrX 49040116 49040370 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 49040049 49040115 chrX 49040116 49040370 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 50121097 50121146 chrX 50121147 50121230 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 52985471 52987539 chrX 52987540 52987681 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 52986286 52987539 chrX 52987540 52987611 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 53713533 53713584 chrX 53713585 53713629 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 53713533 53713584 chrX 53713585 53713629 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 76849166 76851914 chrX 76851915 76852344 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 85224092 85224121 chrX 85224122 85226590 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 103029314 103029329 chrX 103029330 103029383 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 103172033 103172240 chrX 103172241 103172808 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 103343898 103348397 chrX 103348398 103349971 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 114659426 114659662 chrX 114659663 114660070 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 122318371 122318386 chrX 122318387 122318496 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 122336488 122336600 chrX 122336601 122336633 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 122318096 122318386 chrX 122318387 122318496 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 122318152 122318386 chrX 122318387 122318496 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 122336488 122336600 chrX 122336601 122336633 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 122318224 122318386 chrX 122318387 122318496 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 122318336 122318386 chrX 122318387 122318496 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 122318336 122318386 chrX 122318387 122318496 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 142712353 142714379 chrX 142714380 142715896 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 148615540 148615567 chrX 148615568 148615906 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 148615540 148615567 chrX 148615568 148615960 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 148615540 148615567 chrX 148615568 148615906 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 148713226 148713418 chrX 148713419 148713568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 148713226 148713418 chrX 148713419 148713568 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864420 152864480 chrX 152864481 152864513 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864481 152864513 chrX 152864514 152864609 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864514 152864609 chrX 152864610 152864641 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864424 152864480 chrX 152864481 152864488 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864424 152864480 chrX 152864481 152864513 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864481 152864513 chrX 152864514 152864573 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864420 152864480 chrX 152864481 152864513 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864481 152864513 chrX 152864514 152864573 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864424 152864480 chrX 152864481 152864513 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864481 152864513 chrX 152864514 152864573 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864420 152864480 chrX 152864481 152864511 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864420 152864480 chrX 152864481 152864513 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 152864481 152864513 chrX 152864514 152864572 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 153149319 153149708 chrX 153149709 153149960 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 153149403 153149708 chrX 153149709 153149727 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 153360425 153362757 chrX 153362758 153362980 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 153700933 153702655 chrX 153702656 153703118 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 153702656 153703118 chrX 153703119 153703438 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 153703119 153703438 chrX 153703439 153704796 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: chrX 153704798 153706040 chrX 153706041 153706118 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000220.1 153803 154481 GL000220.1 154482 154617 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000195.1 45410 45519 GL000195.1 45520 45717 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000195.1 52090 52278 GL000195.1 52279 52580 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000195.1 52279 52580 GL000195.1 52581 52708 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000195.1 45414 45519 GL000195.1 45520 45591 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000195.1 140970 141239 GL000195.1 141240 141288 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000195.1 140970 141239 GL000195.1 141240 141288 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000195.1 140970 141239 GL000195.1 141240 141288 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000204.1 43956 43976 GL000204.1 43977 43996 WARNING: while processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf: overlapping or touching exons: GL000204.1 43998 44311 GL000204.1 44312 47993 Processing pGe.sjdbGTFfile=/media/data1/genome/HG19/annotation.gtf, found: 202697 transcripts 1206031 exons (non-collapsed) 354658 collapsed junctions Jul 14 15:33:54 ..... finished GTF processing Jul 14 15:33:54 Loaded database junctions from the GTF file: /media/data1/genome/HG19/annotation.gtf: 709222 total junctions WARNING: long repeat for junction # 117708 : chr15 89398753 89398809; left shift = 14; right shift = 255 WARNING: long repeat for junction # 472294 : chr15 89398753 89398809; left shift = 14; right shift = 255 Jul 14 15:33:54 Finished preparing junctions Jul 14 15:33:54 ..... inserting junctions into the genome indices Jul 14 15:33:55 Finished SA search: number of new junctions=0, old junctions=354564 Jul 14 15:33:55 Finished sorting SA indicesL nInd=0 Genome size with junctions=3186586660 3115319296 71267364 GstrandBit1=32 GstrandBit=32 Jul 14 15:35:02 Finished inserting junction indices Jul 14 15:35:06 Finished SAi Jul 14 15:35:06 ..... finished inserting junctions into genome Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Starting to map file # 0 mate 1: /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz Created thread # 6 Created thread # 7 Thread #0 end of input stream, nextChar=-1 Completed: thread #4 Completed: thread #5 Completed: thread #7 Completed: thread #6 Completed: thread #0 Completed: thread #1 Joined thread # 1 Completed: thread #3 Completed: thread #2 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Jul 14 15:41:59 Loaded database junctions from the 1st pass file: KO_GAQ3/STAR/_STARpass1//SJ.out.tab: 766217 total junctions WARNING: long repeat for junction # 117708 : chr15 89398753 89398809; left shift = 14; right shift = 255 WARNING: long repeat for junction # 472294 : chr15 89398753 89398809; left shift = 14; right shift = 255 Jul 14 15:41:59 Finished preparing junctions Jul 14 15:41:59 ..... inserting junctions into the genome indices Jul 14 15:42:01 Finished SA search: number of new junctions=1266, old junctions=354564 Jul 14 15:42:01 Finished sorting SA indicesL nInd=506400 Genome size with junctions=3186841126 3115319296 71521830 GstrandBit1=32 GstrandBit=32 Jul 14 15:43:07 Finished inserting junction indices Jul 14 15:43:12 Finished SAi Jul 14 15:43:12 ..... finished inserting junctions into genome Input read files for mate 1, from input string /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz -rwxrwxrwx 1 ramn 100 1387285503 Jun 24 19:40 /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz readsCommandsFile: exec > "KO_GAQ3/STAR/_STARtmp/tmp.fifo.read1" echo FILE 0 zcat "/home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz" Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread0 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread1 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread2 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread3 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread4 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread5 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread6 ... ok Opening the file: KO_GAQ3/STAR/_STARtmp//FilterBySJoutFiles.mate1.thread7 ... ok Created thread # 1 Created thread # 2 Created thread # 3 Starting to map file # 0 mate 1: /home/malhusayan/workdir/Media/WORK2/Collab/RogerGreenberg/RNA-Seq/KO_GAQ3/KO_GAQ3_S17_R1_001.fastq.gz Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Thread #0 end of input stream, nextChar=-1 Completed: thread #7 Completed: thread #1 Completed: thread #2 Completed: thread #5 Completed: thread #6 Completed: thread #0 Joined thread # 1 Joined thread # 2 Completed: thread #3 Joined thread # 3 Completed: thread #4 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 Completed stage 1 mapping of outFilterBySJout mapping Detected 21 novel junctions that passed filtering, will proceed to filter reads that contained unannotated junctions Created thread # 1 Created thread # 2 Created thread # 3 Created thread # 4 Created thread # 5 Created thread # 6 Created thread # 7 Completed: thread #5 Completed: thread #4 Completed: thread #0 Completed: thread #7 Completed: thread #2 Completed: thread #6 Completed: thread #3 Completed: thread #1 Joined thread # 1 Joined thread # 2 Joined thread # 3 Joined thread # 4 Joined thread # 5 Joined thread # 6 Joined thread # 7 ALL DONE!