Error, strand conflict in gtf info for chr1 ENSEMBL exon 218541690 218541899 . - . gene_id "U3^ENSG00000212610.2"; transcript_id "ENST00000391308.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.29-201"; exon_number 1; exon_id "ENSE00001509092.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212610.2"; orig_coord_info "chr1,218541690,218541899,-";
Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 75627950 75628168 . + . gene_id "U3^ENSG00000221638.2"; transcript_id "ENST00000408711.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.40-201"; exon_number 1; exon_id "ENSE00001565346.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221638.2"; orig_coord_info "chr2,75627950,75628168,+";
Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 114005440 114005655 . - . gene_id "U3^ENSG00000212182.2"; transcript_id "ENST00000390880.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.17-201"; exon_number 1; exon_id "ENSE00001508664.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212182.2"; orig_coord_info "chr2,114005440,114005655,-";
Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 240289216 240289443 . + . gene_id "U3^ENSG00000276366.1"; transcript_id "ENST00000611947.1"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.49-201"; exon_number 1; exon_id "ENSE00003712639.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000276366.1"; orig_coord_info "chr2,240289216,240289443,+";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 30304321 30304536 . - . gene_id "U3^ENSG00000281710.1"; transcript_id "ENST00000628922.1"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.52-201"; exon_number 1; exon_id "ENSE00003765285.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000281710.1"; orig_coord_info "chr3,30304321,30304536,-";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 45255409 45255620 . - . gene_id "U3^ENSG00000202268.2"; transcript_id "ENST00000365398.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.14-201"; exon_number 1; exon_id "ENSE00001440161.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000202268.2"; orig_coord_info "chr3,45255409,45255620,-";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 60856389 60856605 . - . gene_id "U3^ENSG00000212211.2"; transcript_id "ENST00000390909.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.19-201"; exon_number 1; exon_id "ENSE00001508693.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212211.2"; orig_coord_info "chr3,60856389,60856605,-";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 64071807 64072019 . - . gene_id "U3^ENSG00000200222.2"; transcript_id "ENST00000363352.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.4-201"; exon_number 1; exon_id "ENSE00001438115.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200222.2"; orig_coord_info "chr3,64071807,64072019,-";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 90030284 90030495 . + . gene_id "U3^ENSG00000212598.2"; transcript_id "ENST00000391296.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.28-201"; exon_number 1; exon_id "ENSE00001509080.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212598.2"; orig_coord_info "chr3,90030284,90030495,+";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 109018909 109019116 . - . gene_id "U3^ENSG00000221633.2"; transcript_id "ENST00000408706.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.39-201"; exon_number 1; exon_id "ENSE00001565341.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221633.2"; orig_coord_info "chr3,109018909,109019116,-";
Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 158700691 158700909 . + . gene_id "U3^ENSG00000271817.2"; transcript_id "ENST00000607547.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.44-201"; exon_number 1; exon_id "ENSE00003695581.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000271817.2"; orig_coord_info "chr4,158700691,158700909,+";
Error, chr discrepancy in gtf info for chr5 ENSEMBL exon 35429064 35429277 . + . gene_id "U3^ENSG00000201368.2"; transcript_id "ENST00000364498.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.11-201"; exon_number 1; exon_id "ENSE00001439261.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000201368.2"; orig_coord_info "chr5,35429064,35429277,+";
Error, chr discrepancy in gtf info for chr5 ENSEMBL exon 149695748 149695959 . - . gene_id "U3^ENSG00000221043.2"; transcript_id "ENST00000408116.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.31-201"; exon_number 1; exon_id "ENSE00001564751.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221043.2"; orig_coord_info "chr5,149695748,149695959,-";
Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 28015568 28015777 . + . gene_id "U3^ENSG00000199851.2"; transcript_id "ENST00000362981.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.2-201"; exon_number 1; exon_id "ENSE00001437744.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000199851.2"; orig_coord_info "chr6,28015568,28015777,+";
Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 71126893 71127105 . - . gene_id "U3^ENSG00000221345.2"; transcript_id "ENST00000408418.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.35-201"; exon_number 1; exon_id "ENSE00001565053.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221345.2"; orig_coord_info "chr6,71126893,71127105,-";
Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 75398860 75399067 . - . gene_id "U3^ENSG00000221332.2"; transcript_id "ENST00000408405.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.34-201"; exon_number 1; exon_id "ENSE00001565040.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221332.2"; orig_coord_info "chr6,75398860,75399067,-";
Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 92119423 92119633 . + . gene_id "U3^ENSG00000200492.2"; transcript_id "ENST00000363622.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.5-201"; exon_number 1; exon_id "ENSE00001438385.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200492.2"; orig_coord_info "chr6,92119423,92119633,+";
Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 92790453 92790665 . + . gene_id "U3^ENSG00000221455.2"; transcript_id "ENST00000408528.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.36-201"; exon_number 1; exon_id "ENSE00001565163.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221455.2"; orig_coord_info "chr6,92790453,92790665,+";
Error, chr discrepancy in gtf info for chr7 ENSEMBL exon 10222797 10223011 . + . gene_id "U3^ENSG00000212422.2"; transcript_id "ENST00000391120.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.21-201"; exon_number 1; exon_id "ENSE00001508904.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212422.2"; orig_coord_info "chr7,10222797,10223011,+";
Error, chr discrepancy in gtf info for chr7 ENSEMBL exon 25264656 25264882 . + . gene_id "U3^ENSG00000202233.2"; transcript_id "ENST00000365363.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.13-201"; exon_number 1; exon_id "ENSE00001440126.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000202233.2"; orig_coord_info "chr7,25264656,25264882,+";
Error, chr discrepancy in gtf info for chr7 ENSEMBL exon 107999791 107999982 . - . gene_id "U3^ENSG00000238297.2"; transcript_id "ENST00000458938.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.43-201"; exon_number 1; exon_id "ENSE00001809260.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000238297.2"; orig_coord_info "chr7,107999791,107999982,-";
Error, chr discrepancy in gtf info for chr7 ENSEMBL exon 148389645 148389859 . + . gene_id "U3^ENSG00000199370.2"; transcript_id "ENST00000362500.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.1-201"; exon_number 1; exon_id "ENSE00001437263.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000199370.2"; orig_coord_info "chr7,148389645,148389859,+";
Error, chr discrepancy in gtf info for chr8 ENSEMBL exon 43378297 43378510 . + . gene_id "U3^ENSG00000201329.2"; transcript_id "ENST00000364459.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.9-201"; exon_number 1; exon_id "ENSE00001439222.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000201329.2"; orig_coord_info "chr8,43378297,43378510,+";
Error, chr discrepancy in gtf info for chr8 ENSEMBL exon 123180310 123180525 . - . gene_id "U3^ENSG00000221461.2"; transcript_id "ENST00000408534.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.37-201"; exon_number 1; exon_id "ENSE00001565169.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221461.2"; orig_coord_info "chr8,123180310,123180525,-";
Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 19598247 19598463 . + . gene_id "U3^ENSG00000200545.2"; transcript_id "ENST00000363675.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.7-201"; exon_number 1; exon_id "ENSE00001438438.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200545.2"; orig_coord_info "chr10,19598247,19598463,+";
Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 28408039 28408251 . - . gene_id "U3^ENSG00000222666.2"; transcript_id "ENST00000410734.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.42-201"; exon_number 1; exon_id "ENSE00001590552.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000222666.2"; orig_coord_info "chr10,28408039,28408251,-";
Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 32081764 32081973 . + . gene_id "U3^ENSG00000212551.2"; transcript_id "ENST00000391249.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.27-201"; exon_number 1; exon_id "ENSE00001509033.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212551.2"; orig_coord_info "chr11,32081764,32081973,+";
Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 63651296 63651499 . - . gene_id "U3^ENSG00000200693.2"; transcript_id "ENST00000363823.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.8-201"; exon_number 1; exon_id "ENSE00001438586.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200693.2"; orig_coord_info "chr14,63651296,63651499,-";
Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 91714915 91715130 . - . gene_id "U3^ENSG00000275154.1"; transcript_id "ENST00000363172.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.47-201"; exon_number 1; exon_id "ENSE00001807572.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000275154.1"; orig_coord_info "chr14,91714915,91715130,-";
Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 101145480 101145695 . - . gene_id "U3^ENSG00000277754.1"; transcript_id "ENST00000384034.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.51-201"; exon_number 1; exon_id "ENSE00001808913.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000277754.1"; orig_coord_info "chr14,101145480,101145695,-";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 36852640 36852859 . + . gene_id "U3^ENSG00000212511.2"; transcript_id "ENST00000391209.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.24-201"; exon_number 1; exon_id "ENSE00001508993.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212511.2"; orig_coord_info "chr15,36852640,36852859,+";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 69457941 69458149 . - . gene_id "U3^ENSG00000207119.2"; transcript_id "ENST00000384391.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.15-201"; exon_number 1; exon_id "ENSE00001499400.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000207119.2"; orig_coord_info "chr15,69457941,69458149,-";
Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 44025020 44025223 . - . gene_id "U3^ENSG00000221044.2"; transcript_id "ENST00000408117.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.32-201"; exon_number 1; exon_id "ENSE00001977749.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221044.2"; orig_coord_info "chr17,44025020,44025223,-";
Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 44303965 44304203 . + . gene_id "U3^ENSG00000221496.2"; transcript_id "ENST00000408569.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.38-201"; exon_number 1; exon_id "ENSE00001565204.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221496.2"; orig_coord_info "chr17,44303965,44304203,+";
Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 48382371 48382586 . - . gene_id "U3^ENSG00000200538.2"; transcript_id "ENST00000363668.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.6-201"; exon_number 1; exon_id "ENSE00001807711.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200538.2"; orig_coord_info "chr17,48382371,48382586,-";
Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 58631641 58631836 . - . gene_id "U3^ENSG00000212195.2"; transcript_id "ENST00000390893.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.18-201"; exon_number 1; exon_id "ENSE00001508677.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212195.2"; orig_coord_info "chr17,58631641,58631836,-";
Error, chr discrepancy in gtf info for chr18 ENSEMBL exon 7995570 7995785 . + . gene_id "U3^ENSG00000199856.2"; transcript_id "ENST00000362986.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.3-201"; exon_number 1; exon_id "ENSE00001437749.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000199856.2"; orig_coord_info "chr18,7995570,7995785,+";
Error, chr discrepancy in gtf info for chr18 ENSEMBL exon 26689316 26689529 . - . gene_id "U3^ENSG00000275900.1"; transcript_id "ENST00000391065.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.48-201"; exon_number 1; exon_id "ENSE00001508849.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000275900.1"; orig_coord_info "chr18,26689316,26689529,-";
Error, chr discrepancy in gtf info for chr18 ENSEMBL exon 56957270 56957469 . + . gene_id "U3^ENSG00000212539.2"; transcript_id "ENST00000391237.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.26-201"; exon_number 1; exon_id "ENSE00001509021.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212539.2"; orig_coord_info "chr18,56957270,56957469,+";
Error, chr discrepancy in gtf info for chr19 ENSEMBL exon 49949316 49949527 . - . gene_id "U3^ENSG00000221125.2"; transcript_id "ENST00000408198.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.33-201"; exon_number 1; exon_id "ENSE00001564833.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221125.2"; orig_coord_info "chr19,49949316,49949527,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 3384229 3384440 . + . gene_id "U3^ENSG00000201346.2"; transcript_id "ENST00000364476.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.10-201"; exon_number 1; exon_id "ENSE00001439239.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000201346.2"; orig_coord_info "chr20,3384229,3384440,+";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 16982831 16983033 . - . gene_id "U3^ENSG00000212165.2"; transcript_id "ENST00000390863.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.16-201"; exon_number 1; exon_id "ENSE00001508647.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212165.2"; orig_coord_info "chr20,16982831,16983033,-";
Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 29180425 29180639 . - . gene_id "U3^ENSG00000212479.2"; transcript_id "ENST00000391177.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.23-201"; exon_number 1; exon_id "ENSE00001508961.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212479.2"; orig_coord_info "chr21,29180425,29180639,-";
Error, chr discrepancy in gtf info for chrX ENSEMBL exon 69692956 69693155 . + . gene_id "U3^ENSG00000212434.2"; transcript_id "ENST00000391132.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.22-201"; exon_number 1; exon_id "ENSE00001508916.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212434.2"; orig_coord_info "chrX,69692956,69693155,+";
Error, chr discrepancy in gtf info for chrX ENSEMBL exon 72726122 72726337 . - . gene_id "U3^ENSG00000273788.1"; transcript_id "ENST00000365612.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.45-201"; exon_number 1; exon_id "ENSE00001806856.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000273788.1"; orig_coord_info "chrX,72726122,72726337,-";
Error, chr discrepancy in gtf info for chrX ENSEMBL exon 113944186 113944399 . - . gene_id "U3^ENSG00000201674.2"; transcript_id "ENST00000364804.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.12-201"; exon_number 1; exon_id "ENSE00001439567.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000201674.2"; orig_coord_info "chrX,113944186,113944399,-";
Error, chr discrepancy in gtf info for chrX ENSEMBL exon 122840426 122840645 . + . gene_id "U3^ENSG00000212321.2"; transcript_id "ENST00000391019.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.20-201"; exon_number 1; exon_id "ENSE00001508803.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212321.2"; orig_coord_info "chrX,122840426,122840645,+";
Error - no gene spans 100M bases in length.... likely problem at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 589.
main::get_gene_span_info("chr1\x{9}ENSEMBL\x{9}exon\x{9}116278606\x{9}116278821\x{9}.\x{9}+\x{9}.\x{9}gene_id \"U3^ENSG0"...) called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 417
main::get_gene_contig_gtf("chr1\x{9}ENSEMBL\x{9}exon\x{9}116278606\x{9}116278821\x{9}.\x{9}+\x{9}.\x{9}gene_id \"U3^ENSG0"..., "/tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir/ref_genome.fa") called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 214
eval {...} called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 210
Done.
-parsing GTF file: /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
10:48:43 : INFO : Done.
-parsing GTF file: /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[1400000] -done parsing /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 18,
'small anchor length' => 23,
'low complexity anchor region' => 2,
'excessive soft clipping' => 8478,
'per_id < 96' => 4188,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 88,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
'num genes matched < 2' => 8,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8,
' ** passed ** ' => 3021
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[401000] -fusion SPANNING read extraction for scaff: PRPF8--BEST1
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[63000] -fusion SPANNING read extraction for scaff: SH3GLB2--CDC27
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[14000] -fusion SPANNING read extraction for scaff: SLC39A11--LINC00511
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[96000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[115000] -fusion SPANNING read extraction for scaff: TAS1R2--ARHGEF10L
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[27000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[96000] -fusion SPANNING read extraction for scaff: TP53--CLDN7
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 10188
};
EM: Starting log likelihood: -4340.079626
EM: Round [1] log likelihood: -4340.072222
EM: Round [2] log likelihood: -4340.072196
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -4235.082197
EM: Round [1] log likelihood: -4235.074794
EM: Round [2] log likelihood: -4235.074767
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 274831184
Warning - not locating file: /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000253787.1]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
ls: cannot access 'IGV_inputs': No such file or directory