Error, chr discrepancy in gtf info for chrY HAVANA exon 386368 386907 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 1; exon_id "ENSE00001912068.2"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,386368,386907,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 386368 386691 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 1; exon_id "ENSE00001912068.2"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,386368,386691,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 361405 361590 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 2; exon_id "ENSE00003653358.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 361405 361590 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 2; exon_id "ENSE00003653358.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347590 347693 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 3; exon_id "ENSE00003509428.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 347590 347693 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 3; exon_id "ENSE00003509428.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347336 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 4; exon_id "ENSE00003492683.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 347234 347336 . - 1 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 4; exon_id "ENSE00003492683.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346701 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 5; exon_id "ENSE00003489026.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346701,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 346701 346775 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 5; exon_id "ENSE00003489026.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346701,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346174 346260 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 6; exon_id "ENSE00003574906.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346260,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 346174 346260 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 6; exon_id "ENSE00003574906.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346260,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345672 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 7; exon_id "ENSE00003687848.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 345516 345672 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 7; exon_id "ENSE00003687848.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341883 341931 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 8; exon_id "ENSE00003511595.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341883,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 341883 341931 . - 2 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 8; exon_id "ENSE00003511595.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341883,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341396 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 9; exon_id "ENSE00003587700.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341396,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 341307 341396 . - 1 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 9; exon_id "ENSE00003587700.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341396,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 10; exon_id "ENSE00003668507.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 340765 340940 . - 1 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 10; exon_id "ENSE00003668507.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338778 338896 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 11; exon_id "ENSE00003622978.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338778,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 338778 338896 . - 2 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 11; exon_id "ENSE00003622978.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338778,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338604 338710 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 12; exon_id "ENSE00003501875.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338604,338710,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 338604 338710 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 12; exon_id "ENSE00003501875.1"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338604,338710,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 333933 334517 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 13; exon_id "ENSE00001844596.2"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,333933,334517,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 334370 334517 . - 1 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000390665.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-202"; exon_number 13; exon_id "ENSE00001844596.2"; level 2; protein_id "ENSP00000375080.3"; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14104.1"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055577.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,334370,334517,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341711 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 1; exon_id "ENSE00001918099.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341711,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 2; exon_id "ENSE00003553826.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338778 338896 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 3; exon_id "ENSE00003592960.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338778,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338604 338710 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 4; exon_id "ENSE00003534283.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338604,338710,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 334235 334517 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000479438.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-208"; exon_number 5; exon_id "ENSE00001489278.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354555.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,334235,334517,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347324 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 1; exon_id "ENSE00001716328.2"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347324,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346701 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 2; exon_id "ENSE00003571094.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346701,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346174 346260 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 3; exon_id "ENSE00003477290.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346260,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345672 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 4; exon_id "ENSE00003641725.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341931 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 5; exon_id "ENSE00001915623.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 6; exon_id "ENSE00003553826.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338778 338896 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 7; exon_id "ENSE00003592960.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338778,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 334239 338710 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477110.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-206"; exon_number 8; exon_id "ENSE00001815257.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055583.2"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,334239,338710,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345629 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 1; exon_id "ENSE00001890387.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345629,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341883 341931 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 2; exon_id "ENSE00003555172.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341883,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341396 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 3; exon_id "ENSE00003689816.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341396,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 4; exon_id "ENSE00003553826.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 338613 338896 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000468169.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-204"; exon_number 5; exon_id "ENSE00001951758.1"; level 2; transcript_support_level "3"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055585.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,338613,338896,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345626 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000484364.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-209"; exon_number 1; exon_id "ENSE00001888244.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055580.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345626,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341883 342237 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000484364.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-209"; exon_number 2; exon_id "ENSE00001815626.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055580.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341883,342237,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341307 341396 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000484364.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-209"; exon_number 3; exon_id "ENSE00003689816.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055580.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341307,341396,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 340765 340940 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000484364.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-209"; exon_number 4; exon_id "ENSE00003553826.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055580.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,340765,340940,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346174 346514 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477636.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-207"; exon_number 1; exon_id "ENSE00001896157.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055581.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346514,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 345516 345672 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477636.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-207"; exon_number 2; exon_id "ENSE00003641725.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055581.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,345516,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 341911 341931 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000477636.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-207"; exon_number 3; exon_id "ENSE00001911121.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055581.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,341911,341931,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 386368 386955 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 1; exon_id "ENSE00001912680.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,386368,386955,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 362255 362332 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 2; exon_id "ENSE00001847312.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,362255,362332,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 361405 361590 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 3; exon_id "ENSE00003585491.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347590 347693 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 4; exon_id "ENSE00003475055.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347336 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 5; exon_id "ENSE00003606316.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346701 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 6; exon_id "ENSE00003571094.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346701,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346174 346260 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 7; exon_id "ENSE00003477290.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346174,346260,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 344896 345672 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000445792.7_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-203"; exon_number 8; exon_id "ENSE00001950030.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354554.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,344896,345672,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 361405 361516 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000496630.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-210"; exon_number 1; exon_id "ENSE00001916804.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354557.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361516,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347590 347693 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000496630.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-210"; exon_number 2; exon_id "ENSE00003475055.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354557.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347336 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000496630.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-210"; exon_number 3; exon_id "ENSE00003606316.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354557.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346637 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000496630.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-210"; exon_number 4; exon_id "ENSE00001851476.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354557.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346637,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347590 347838 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000475859.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-205"; exon_number 1; exon_id "ENSE00001843788.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354556.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347590,347838,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347234 347336 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000475859.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-205"; exon_number 2; exon_id "ENSE00003606316.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354556.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347234,347336,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 346720 346775 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000475859.6_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "retained_intron"; transcript_name "PPP2R3B-205"; exon_number 3; exon_id "ENSE00001849084.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:13417"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000354556.1"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,346720,346775,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 373532 374044 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 1; exon_id "ENSE00001489321.3"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,373532,374044,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 373532 373771 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 1; exon_id "ENSE00001489321.3"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,373532,373771,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 361405 361590 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 2; exon_id "ENSE00003653358.1"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 361405 361590 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 2; exon_id "ENSE00003653358.1"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,361405,361590,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 347611 347693 . - . gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 3; exon_id "ENSE00001877883.1"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347611,347693,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 347611 347693 . - 0 gene_id "PPP2R3B^ENSG00000167393.18_PAR_Y"; transcript_id "ENST00000381625.9_PAR_Y"; gene_type "protein_coding"; gene_name "PPP2R3B"; transcript_type "protein_coding"; transcript_name "PPP2R3B-201"; exon_number 3; exon_id "ENSE00001877883.1"; level 2; protein_id "ENSP00000371038.4"; transcript_support_level "5"; hgnc_id "HGNC:13417"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021052.4"; havana_transcript "OTTHUMT00000055578.3"; FI_gene_label "PPP2R3B^ENSG00000167393.18_PAR_Y"; orig_coord_info "chrY,347611,347693,-";
Done.
-parsing GTF file: /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.i8pHKUuplb/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.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_cTi-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_cTi-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:11:51 : INFO : Done.
-parsing GTF file: /tmp/nxf.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[2520000] -done parsing /tmp/nxf.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 19445,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
'per_id < 96' => 9791,
'low complexity anchor region' => 6,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 48,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 62,
'num genes matched < 2' => 222,
'small anchor length' => 190,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 24,
'exons hit < 2' => 1,
'excessive soft clipping' => 18131,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 350,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 9,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
'seq-similar region overlap' => 241,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 72,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 10
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2
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[442000] -fusion SPANNING read extraction for scaff: CPSF6--TMBIM4
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[109000] -fusion SPANNING read extraction for scaff: EEF1AKMT3--CTDSP2
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[4000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[42000] -fusion SPANNING read extraction for scaff: MARCHF9--GRIP1
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[20000] -fusion SPANNING read extraction for scaff: MARCHF9--AC023141.7
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[20000] -fusion SPANNING read extraction for scaff: MARCHF9--AC128676.1
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[21000] -fusion SPANNING read extraction for scaff: MRPS35--TMTC1
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[304000] -fusion SPANNING read extraction for scaff: NCOA4--GLUD1P2
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[15000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[17000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[14000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8
[1000]
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4
[1000]
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7
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[64000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[64000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
[1000]
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[14000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[15000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[64000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[64000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[13000] -fusion SPANNING read extraction for scaff: PPP2R3B--TMLHE
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[153000] -fusion SPANNING read extraction for scaff: RAP1B--SRGAP1
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[47000] -fusion SPANNING read extraction for scaff: SAV1--SOS2
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[86000] -fusion SPANNING read extraction for scaff: SRGAP1--GRIP1
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[56000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[29000] -fusion SPANNING read extraction for scaff: TMEM243--AC020637.1
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[26000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[42000] -fusion SPANNING read extraction for scaff: TYW1--VKORC1L1
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[64000] -fusion SPANNING read extraction for scaff: VGLL4--ATG7
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 22551,
'seq similar region alignment' => 173673
};
EM: Starting log likelihood: -9194.742835
EM: Round [1] log likelihood: -9191.308153
EM: Round [2] log likelihood: -9190.216930
EM: Round [3] log likelihood: -9189.287521
EM: Round [4] log likelihood: -9188.461947
EM: Round [5] log likelihood: -9187.722357
EM: Round [6] log likelihood: -9187.055317
EM: Round [7] log likelihood: -9186.450083
EM: Round [8] log likelihood: -9185.897990
EM: Round [9] log likelihood: -9185.391994
EM: Round [10] log likelihood: -9184.926324
EM: Round [11] log likelihood: -9184.496212
EM: Round [12] log likelihood: -9184.097683
EM: Round [13] log likelihood: -9183.727391
EM: Round [14] log likelihood: -9183.382494
EM: Round [15] log likelihood: -9183.060556
EM: Round [16] log likelihood: -9182.759467
EM: Round [17] log likelihood: -9182.477387
EM: Round [18] log likelihood: -9182.212695
EM: Round [19] log likelihood: -9181.963954
EM: Round [20] log likelihood: -9181.729880
EM: Round [21] log likelihood: -9181.509322
EM: Round [22] log likelihood: -9181.301240
EM: Round [23] log likelihood: -9181.104692
EM: Round [24] log likelihood: -9180.918822
EM: Round [25] log likelihood: -9180.742846
EM: Round [26] log likelihood: -9180.576051
EM: Round [27] log likelihood: -9180.417780
EM: Round [28] log likelihood: -9180.267433
EM: Round [29] log likelihood: -9180.124456
EM: Round [30] log likelihood: -9179.988340
EM: Round [31] log likelihood: -9179.858618
EM: Round [32] log likelihood: -9179.734857
EM: Round [33] log likelihood: -9179.616658
EM: Round [34] log likelihood: -9179.503656
EM: Round [35] log likelihood: -9179.395511
EM: Round [36] log likelihood: -9179.291909
EM: Round [37] log likelihood: -9179.192562
EM: Round [38] log likelihood: -9179.097203
EM: Round [39] log likelihood: -9179.005584
EM: Round [40] log likelihood: -9178.917477
EM: Round [41] log likelihood: -9178.832671
EM: Round [42] log likelihood: -9178.750970
EM: Round [43] log likelihood: -9178.672193
EM: Round [44] log likelihood: -9178.596173
EM: Round [45] log likelihood: -9178.522755
EM: Round [46] log likelihood: -9178.451793
EM: Round [47] log likelihood: -9178.383154
EM: Round [48] log likelihood: -9178.316714
EM: Round [49] log likelihood: -9178.252358
EM: Round [50] log likelihood: -9178.189977
EM: Round [51] log likelihood: -9178.129473
EM: Round [52] log likelihood: -9178.070753
EM: Round [53] log likelihood: -9178.013729
EM: Round [54] log likelihood: -9177.958320
EM: Round [55] log likelihood: -9177.904452
EM: Round [56] log likelihood: -9177.852054
EM: Round [57] log likelihood: -9177.801059
EM: Round [58] log likelihood: -9177.751406
EM: Round [59] log likelihood: -9177.703038
EM: Round [60] log likelihood: -9177.655898
EM: Round [61] log likelihood: -9177.609938
EM: Round [62] log likelihood: -9177.565109
EM: Round [63] log likelihood: -9177.521365
EM: Round [64] log likelihood: -9177.478664
EM: Round [65] log likelihood: -9177.436966
EM: Round [66] log likelihood: -9177.396234
EM: Round [67] log likelihood: -9177.356432
EM: Round [68] log likelihood: -9177.317525
EM: Round [69] log likelihood: -9177.279483
EM: Round [70] log likelihood: -9177.242274
EM: Round [71] log likelihood: -9177.205870
EM: Round [72] log likelihood: -9177.170244
EM: Round [73] log likelihood: -9177.135370
EM: Round [74] log likelihood: -9177.101223
EM: Round [75] log likelihood: -9177.067780
EM: Round [76] log likelihood: -9177.035018
EM: Round [77] log likelihood: -9177.002916
EM: Round [78] log likelihood: -9176.971454
EM: Round [79] log likelihood: -9176.940613
EM: Round [80] log likelihood: -9176.910373
EM: Round [81] log likelihood: -9176.880718
EM: Round [82] log likelihood: -9176.851629
EM: Round [83] log likelihood: -9176.823091
EM: Round [84] log likelihood: -9176.795088
EM: Round [85] log likelihood: -9176.767605
EM: Round [86] log likelihood: -9176.740628
EM: Round [87] log likelihood: -9176.714143
EM: Round [88] log likelihood: -9176.688137
EM: Round [89] log likelihood: -9176.662596
EM: Round [90] log likelihood: -9176.637508
EM: Round [91] log likelihood: -9176.612863
EM: Round [92] log likelihood: -9176.588647
EM: Round [93] log likelihood: -9176.564851
EM: Round [94] log likelihood: -9176.541463
EM: Round [95] log likelihood: -9176.518474
EM: Round [96] log likelihood: -9176.495873
EM: Round [97] log likelihood: -9176.473651
EM: Round [98] log likelihood: -9176.451798
EM: Round [99] log likelihood: -9176.430306
EM: Round [100] log likelihood: -9176.409166
EM: Round [101] log likelihood: -9176.388370
EM: Round [102] log likelihood: -9176.367910
EM: Round [103] log likelihood: -9176.347777
EM: Round [104] log likelihood: -9176.327964
EM: Round [105] log likelihood: -9176.308465
EM: Round [106] log likelihood: -9176.289271
EM: Round [107] log likelihood: -9176.270375
EM: Round [108] log likelihood: -9176.251772
EM: Round [109] log likelihood: -9176.233455
EM: Round [110] log likelihood: -9176.215416
EM: Round [111] log likelihood: -9176.197651
EM: Round [112] log likelihood: -9176.180153
EM: Round [113] log likelihood: -9176.162917
EM: Round [114] log likelihood: -9176.145936
EM: Round [115] log likelihood: -9176.129206
EM: Round [116] log likelihood: -9176.112721
EM: Round [117] log likelihood: -9176.096476
EM: Round [118] log likelihood: -9176.080466
EM: Round [119] log likelihood: -9176.064685
EM: Round [120] log likelihood: -9176.049131
EM: Round [121] log likelihood: -9176.033797
EM: Round [122] log likelihood: -9176.018679
EM: Round [123] log likelihood: -9176.003773
EM: Round [124] log likelihood: -9175.989074
EM: Round [125] log likelihood: -9175.974579
EM: Round [126] log likelihood: -9175.960284
EM: Round [127] log likelihood: -9175.946184
EM: Round [128] log likelihood: -9175.932276
EM: Round [129] log likelihood: -9175.918555
EM: Round [130] log likelihood: -9175.905019
EM: Round [131] log likelihood: -9175.891664
EM: Round [132] log likelihood: -9175.878486
EM: Round [133] log likelihood: -9175.865482
EM: Round [134] log likelihood: -9175.852649
EM: Round [135] log likelihood: -9175.839983
EM: Round [136] log likelihood: -9175.827482
EM: Round [137] log likelihood: -9175.815141
EM: Round [138] log likelihood: -9175.802960
EM: Round [139] log likelihood: -9175.790933
EM: Round [140] log likelihood: -9175.779059
EM: Round [141] log likelihood: -9175.767335
EM: Round [142] log likelihood: -9175.755758
EM: Round [143] log likelihood: -9175.744326
EM: Round [144] log likelihood: -9175.733035
EM: Round [145] log likelihood: -9175.721884
EM: Round [146] log likelihood: -9175.710870
EM: Round [147] log likelihood: -9175.699990
EM: Round [148] log likelihood: -9175.689242
EM: Round [149] log likelihood: -9175.678625
EM: Round [150] log likelihood: -9175.668134
EM: Round [151] log likelihood: -9175.657770
EM: Round [152] log likelihood: -9175.647528
EM: Round [153] log likelihood: -9175.637408
EM: Round [154] log likelihood: -9175.627407
EM: Round [155] log likelihood: -9175.617523
EM: Round [156] log likelihood: -9175.607754
EM: Round [157] log likelihood: -9175.598099
EM: Round [158] log likelihood: -9175.588555
EM: Round [159] log likelihood: -9175.579120
EM: Round [160] log likelihood: -9175.569794
EM: Round [161] log likelihood: -9175.560573
EM: Round [162] log likelihood: -9175.551456
EM: Round [163] log likelihood: -9175.542443
EM: Round [164] log likelihood: -9175.533530
EM: Round [165] log likelihood: -9175.524716
EM: Round [166] log likelihood: -9175.516001
EM: Round [167] log likelihood: -9175.507381
EM: Round [168] log likelihood: -9175.498856
EM: Round [169] log likelihood: -9175.490425
EM: Round [170] log likelihood: -9175.482085
EM: Round [171] log likelihood: -9175.473836
EM: Round [172] log likelihood: -9175.465675
EM: Round [173] log likelihood: -9175.457603
EM: Round [174] log likelihood: -9175.449616
EM: Round [175] log likelihood: -9175.441715
EM: Round [176] log likelihood: -9175.433897
EM: Round [177] log likelihood: -9175.426162
EM: Round [178] log likelihood: -9175.418507
EM: Round [179] log likelihood: -9175.410933
EM: Round [180] log likelihood: -9175.403438
EM: Round [181] log likelihood: -9175.396020
EM: Round [182] log likelihood: -9175.388679
EM: Round [183] log likelihood: -9175.381413
EM: Round [184] log likelihood: -9175.374221
EM: Round [185] log likelihood: -9175.367103
EM: Round [186] log likelihood: -9175.360057
EM: Round [187] log likelihood: -9175.353082
EM: Round [188] log likelihood: -9175.346177
EM: Round [189] log likelihood: -9175.339341
EM: Round [190] log likelihood: -9175.332574
EM: Round [191] log likelihood: -9175.325873
EM: Round [192] log likelihood: -9175.319239
EM: Round [193] log likelihood: -9175.312671
EM: Round [194] log likelihood: -9175.306166
EM: Round [195] log likelihood: -9175.299726
EM: Round [196] log likelihood: -9175.293347
EM: Round [197] log likelihood: -9175.287031
EM: Round [198] log likelihood: -9175.280776
EM: Round [199] log likelihood: -9175.274581
EM: Round [200] log likelihood: -9175.268445
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EM: Round [660] log likelihood: -9174.482504
EM: Round [661] log likelihood: -9174.482182
EM: Round [662] log likelihood: -9174.481862
EM: Round [663] log likelihood: -9174.481544
EM: Round [664] log likelihood: -9174.481227
EM: Round [665] log likelihood: -9174.480912
EM: Round [666] log likelihood: -9174.480598
EM: Round [667] log likelihood: -9174.480286
EM: Round [668] log likelihood: -9174.479976
EM: Round [669] log likelihood: -9174.479667
EM: Round [670] log likelihood: -9174.479359
EM: Round [671] log likelihood: -9174.479054
EM: Round [672] log likelihood: -9174.478750
EM: Round [673] log likelihood: -9174.478447
EM: Round [674] log likelihood: -9174.478146
EM: Round [675] log likelihood: -9174.477846
EM: Round [676] log likelihood: -9174.477548
EM: Round [677] log likelihood: -9174.477252
EM: Round [678] log likelihood: -9174.476957
EM: Round [679] log likelihood: -9174.476663
EM: Round [680] log likelihood: -9174.476371
EM: Round [681] log likelihood: -9174.476081
EM: Round [682] log likelihood: -9174.475792
EM: Round [683] log likelihood: -9174.475504
EM: Round [684] log likelihood: -9174.475218
EM: Round [685] log likelihood: -9174.474933
EM: Round [686] log likelihood: -9174.474650
EM: Round [687] log likelihood: -9174.474368
EM: Round [688] log likelihood: -9174.474088
EM: Round [689] log likelihood: -9174.473809
EM: Round [690] log likelihood: -9174.473531
EM: Round [691] log likelihood: -9174.473255
EM: Round [692] log likelihood: -9174.472980
EM: Round [693] log likelihood: -9174.472707
EM: Round [694] log likelihood: -9174.472435
EM: Round [695] log likelihood: -9174.472164
EM: Round [696] log likelihood: -9174.471895
EM: Round [697] log likelihood: -9174.471627
EM: Round [698] log likelihood: -9174.471360
EM: Round [699] log likelihood: -9174.471095
EM: Round [700] log likelihood: -9174.470831
EM: Round [701] log likelihood: -9174.470568
EM: Round [702] log likelihood: -9174.470307
EM: Round [703] log likelihood: -9174.470047
EM: Round [704] log likelihood: -9174.469788
EM: Round [705] log likelihood: -9174.469531
EM: Round [706] log likelihood: -9174.469275
EM: Round [707] log likelihood: -9174.469020
EM: Round [708] log likelihood: -9174.468767
EM: Round [709] log likelihood: -9174.468514
EM: Round [710] log likelihood: -9174.468264
EM: Round [711] log likelihood: -9174.468014
EM: Round [712] log likelihood: -9174.467765
EM: Round [713] log likelihood: -9174.467518
EM: Round [714] log likelihood: -9174.467272
EM: Round [715] log likelihood: -9174.467027
EM: Round [716] log likelihood: -9174.466784
EM: Round [717] log likelihood: -9174.466542
EM: Round [718] log likelihood: -9174.466300
EM: Round [719] log likelihood: -9174.466061
EM: Round [720] log likelihood: -9174.465822
EM: Round [721] log likelihood: -9174.465584
EM: Round [722] log likelihood: -9174.465348
EM: Round [723] log likelihood: -9174.465113
EM: Round [724] log likelihood: -9174.464879
EM: Round [725] log likelihood: -9174.464646
EM: Round [726] log likelihood: -9174.464414
EM: Round [727] log likelihood: -9174.464184
EM: Round [728] log likelihood: -9174.463955
EM: Round [729] log likelihood: -9174.463726
EM: Round [730] log likelihood: -9174.463499
EM: Round [731] log likelihood: -9174.463273
EM: Round [732] log likelihood: -9174.463049
EM: Round [733] log likelihood: -9174.462825
EM: Round [734] log likelihood: -9174.462602
EM: Round [735] log likelihood: -9174.462381
EM: Round [736] log likelihood: -9174.462161
EM: Round [737] log likelihood: -9174.461941
EM: Round [738] log likelihood: -9174.461723
EM: Round [739] log likelihood: -9174.461506
EM: Round [740] log likelihood: -9174.461290
EM: Round [741] log likelihood: -9174.461075
EM: Round [742] log likelihood: -9174.460861
EM: Round [743] log likelihood: -9174.460648
EM: Round [744] log likelihood: -9174.460436
EM: Round [745] log likelihood: -9174.460226
EM: Round [746] log likelihood: -9174.460016
EM: Round [747] log likelihood: -9174.459807
EM: Round [748] log likelihood: -9174.459600
EM: Round [749] log likelihood: -9174.459393
EM: Round [750] log likelihood: -9174.459188
EM: Round [751] log likelihood: -9174.458983
EM: Round [752] log likelihood: -9174.458780
EM: Round [753] log likelihood: -9174.458577
EM: Round [754] log likelihood: -9174.458376
EM: Round [755] log likelihood: -9174.458175
EM: Round [756] log likelihood: -9174.457975
EM: Round [757] log likelihood: -9174.457777
EM: Round [758] log likelihood: -9174.457579
EM: Round [759] log likelihood: -9174.457383
EM: Round [760] log likelihood: -9174.457187
EM: Round [761] log likelihood: -9174.456992
EM: Round [762] log likelihood: -9174.456799
EM: Round [763] log likelihood: -9174.456606
EM: Round [764] log likelihood: -9174.456414
EM: Round [765] log likelihood: -9174.456223
EM: Round [766] log likelihood: -9174.456033
EM: Round [767] log likelihood: -9174.455844
EM: Round [768] log likelihood: -9174.455656
EM: Round [769] log likelihood: -9174.455469
EM: Round [770] log likelihood: -9174.455283
EM: Round [771] log likelihood: -9174.455098
EM: Round [772] log likelihood: -9174.454913
EM: Round [773] log likelihood: -9174.454730
EM: Round [774] log likelihood: -9174.454547
EM: Round [775] log likelihood: -9174.454366
EM: Round [776] log likelihood: -9174.454185
EM: Round [777] log likelihood: -9174.454005
EM: Round [778] log likelihood: -9174.453826
EM: Round [779] log likelihood: -9174.453648
EM: Round [780] log likelihood: -9174.453471
EM: Round [781] log likelihood: -9174.453294
EM: Round [782] log likelihood: -9174.453119
EM: Round [783] log likelihood: -9174.452944
EM: Round [784] log likelihood: -9174.452770
EM: Round [785] log likelihood: -9174.452597
EM: Round [786] log likelihood: -9174.452425
EM: Round [787] log likelihood: -9174.452254
EM: Round [788] log likelihood: -9174.452084
EM: Round [789] log likelihood: -9174.451914
EM: Round [790] log likelihood: -9174.451745
EM: Round [791] log likelihood: -9174.451577
EM: Round [792] log likelihood: -9174.451410
EM: Round [793] log likelihood: -9174.451244
EM: Round [794] log likelihood: -9174.451079
EM: Round [795] log likelihood: -9174.450914
EM: Round [796] log likelihood: -9174.450750
EM: Round [797] log likelihood: -9174.450587
EM: Round [798] log likelihood: -9174.450425
EM: Round [799] log likelihood: -9174.450263
EM: Round [800] log likelihood: -9174.450103
EM: Round [801] log likelihood: -9174.449943
EM: Round [802] log likelihood: -9174.449784
EM: Round [803] log likelihood: -9174.449625
EM: Round [804] log likelihood: -9174.449468
EM: Round [805] log likelihood: -9174.449311
EM: Round [806] log likelihood: -9174.449155
EM: Round [807] log likelihood: -9174.449000
EM: Round [808] log likelihood: -9174.448845
EM: Round [809] log likelihood: -9174.448691
EM: Round [810] log likelihood: -9174.448538
EM: Round [811] log likelihood: -9174.448386
EM: Round [812] log likelihood: -9174.448234
EM: Round [813] log likelihood: -9174.448084
EM: Round [814] log likelihood: -9174.447934
EM: Round [815] log likelihood: -9174.447784
EM: Round [816] log likelihood: -9174.447636
EM: Round [817] log likelihood: -9174.447488
EM: Round [818] log likelihood: -9174.447341
EM: Round [819] log likelihood: -9174.447194
EM: Round [820] log likelihood: -9174.447049
EM: Round [821] log likelihood: -9174.446904
EM: Round [822] log likelihood: -9174.446759
EM: Round [823] log likelihood: -9174.446616
EM: Round [824] log likelihood: -9174.446473
EM: Round [825] log likelihood: -9174.446331
EM: Round [826] log likelihood: -9174.446189
EM: Round [827] log likelihood: -9174.446048
EM: Round [828] log likelihood: -9174.445908
EM: Round [829] log likelihood: -9174.445769
EM: Round [830] log likelihood: -9174.445630
EM: Round [831] log likelihood: -9174.445492
EM: Round [832] log likelihood: -9174.445354
EM: Round [833] log likelihood: -9174.445217
EM: Round [834] log likelihood: -9174.445081
EM: Round [835] log likelihood: -9174.444946
EM: Round [836] log likelihood: -9174.444811
EM: Round [837] log likelihood: -9174.444677
EM: Round [838] log likelihood: -9174.444543
EM: Round [839] log likelihood: -9174.444411
EM: Round [840] log likelihood: -9174.444278
EM: Round [841] log likelihood: -9174.444147
EM: Round [842] log likelihood: -9174.444016
EM: Round [843] log likelihood: -9174.443886
EM: Round [844] log likelihood: -9174.443756
EM: Round [845] log likelihood: -9174.443627
EM: Round [846] log likelihood: -9174.443498
EM: Round [847] log likelihood: -9174.443371
EM: Round [848] log likelihood: -9174.443244
EM: Round [849] log likelihood: -9174.443117
EM: Round [850] log likelihood: -9174.442991
EM: Round [851] log likelihood: -9174.442866
EM: Round [852] log likelihood: -9174.442741
EM: Round [853] log likelihood: -9174.442617
EM: Round [854] log likelihood: -9174.442493
EM: Round [855] log likelihood: -9174.442370
EM: Round [856] log likelihood: -9174.442248
EM: Round [857] log likelihood: -9174.442126
EM: Round [858] log likelihood: -9174.442005
EM: Round [859] log likelihood: -9174.441885
EM: Round [860] log likelihood: -9174.441765
EM: Round [861] log likelihood: -9174.441645
EM: Round [862] log likelihood: -9174.441526
EM: Round [863] log likelihood: -9174.441408
EM: Round [864] log likelihood: -9174.441290
EM: Round [865] log likelihood: -9174.441173
EM: Round [866] log likelihood: -9174.441057
EM: Round [867] log likelihood: -9174.440941
EM: Round [868] log likelihood: -9174.440825
EM: Round [869] log likelihood: -9174.440710
EM: Round [870] log likelihood: -9174.440596
EM: Round [871] log likelihood: -9174.440482
EM: Round [872] log likelihood: -9174.440369
EM: Round [873] log likelihood: -9174.440256
EM: Round [874] log likelihood: -9174.440144
EM: Round [875] log likelihood: -9174.440033
EM: Round [876] log likelihood: -9174.439922
EM: Round [877] log likelihood: -9174.439811
EM: Round [878] log likelihood: -9174.439701
EM: Round [879] log likelihood: -9174.439592
EM: Round [880] log likelihood: -9174.439483
EM: Round [881] log likelihood: -9174.439374
EM: Round [882] log likelihood: -9174.439266
EM: Round [883] log likelihood: -9174.439159
EM: Round [884] log likelihood: -9174.439052
EM: Round [885] log likelihood: -9174.438946
EM: Round [886] log likelihood: -9174.438840
EM: Round [887] log likelihood: -9174.438735
EM: Round [888] log likelihood: -9174.438630
EM: Round [889] log likelihood: -9174.438526
EM: Round [890] log likelihood: -9174.438422
EM: Round [891] log likelihood: -9174.438318
EM: Round [892] log likelihood: -9174.438216
EM: Round [893] log likelihood: -9174.438113
EM: Round [894] log likelihood: -9174.438011
EM: Round [895] log likelihood: -9174.437910
EM: Round [896] log likelihood: -9174.437809
EM: Round [897] log likelihood: -9174.437709
EM: Round [898] log likelihood: -9174.437609
EM: Stopping iterations at round 898 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_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.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_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.i8pHKUuplb/fi_workdir/659_cTi-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -7386.602576
EM: Round [1] log likelihood: -7386.502208
EM: Round [2] log likelihood: -7386.501941
EM: Round [3] log likelihood: -7386.501941
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295326606
Warning - not locating file: /tmp/nxf.i8pHKUuplb/659_cTi-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000266356.1]
WARNING, no entry stored in dbm for [ENSG00000213650.3]
WARNING, no entry stored in dbm for [ENSG00000266356.1]
WARNING, no entry stored in dbm for [ENSG00000213650.3]
WARNING, no entry stored in dbm for [ENSG00000266356.1]
WARNING, no entry stored in dbm for [ENSG00000213650.3]
WARNING, no entry stored in dbm for [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000258231.5]
WARNING, no entry stored in dbm for [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000265366.6]
ls: cannot access 'IGV_inputs': No such file or directory