Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/0281707304675ac77d260ee8a80a87/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/0281707304675ac77d260ee8a80a87/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e70c49c2e6aadb702c7e955a758580/659_cTi-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/cdf3b2751513048996e56055280585/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e70c49c2e6aadb702c7e955a758580/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
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.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.oIY8PCx2yB/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.oIY8PCx2yB/cytoBand.txt
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed
-parsing GTF file: /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_cTi-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.oIY8PCx2yB/fi_workdir --reads "/tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.oIY8PCx2yB/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.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:08:15 ..... started STAR run
Jun 08 10:08:15 ..... loading genome
Jun 08 10:09:54 ... generating Suffix Array index
Jun 08 10:13:34 ... completed Suffix Array index
Jun 08 10:13:34 ..... processing annotations GTF
Jun 08 10:13:35 ..... inserting junctions into the genome indices
Jun 08 10:14:35 ..... started mapping
Jun 08 11:10:25 ..... finished mapping
Jun 08 11:10:27 ..... started sorting BAM
Jun 08 11:10:27 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
Execution Time = 62.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_cTi-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.oIY8PCx2yB/fi_workdir --reads "/tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:10:32 : INFO : Done.
Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/mark_dups_reads.index.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
[10000]
[20000]
[30000]
[40000]
[50000]
[60000]
[70000]
[80000]
[90000]
[100000]
[110000]
[120000]
[130000]
[140000]
[150000]
[160000]
[170000]
[180000]
[190000]
[200000]
[210000]
[220000]
[230000]
[240000]
[250000]
[260000]
[270000]
[280000]
[290000]
[300000]
[310000]
[320000]
[330000]
[340000]
[350000]
[360000]
[370000]
[380000]
[390000]
[400000]
[410000]
[420000]
[430000]
[440000]
[450000]
[460000]
[470000]
[480000]
[490000]
[500000]
[510000]
[520000]
[530000]
[540000]
[550000]
[560000]
[570000]
[580000]
[590000]
[600000]
[610000]
[620000]
[630000]
[640000]
[650000]
[660000]
[670000]
[680000]
[690000] -done parsing /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 10,
'excessive soft clipping' => 4898,
'num genes matched < 2' => 168,
'seq-similar region overlap' => 21,
'per_id < 96' => 2740,
'low complexity anchor region' => 2,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 63,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 22,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
' ** passed ** ' => 1339
};
-writing fusion junction support info.
Execution Time = 0.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[38000] -fusion SPANNING read extraction for scaff: AC083805.1--TSFM
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[20000] -fusion SPANNING read extraction for scaff: AC093890.1--SOS2
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[20000] -fusion SPANNING read extraction for scaff: CCNY--AL353600.1
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[98000] -fusion SPANNING read extraction for scaff: CCNY--NRP1
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[97000] -fusion SPANNING read extraction for scaff: EEF1AKMT3--CTDSP2
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[17000] -fusion SPANNING read extraction for scaff: MRPS35--TMTC1
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[11000] -fusion SPANNING read extraction for scaff: PPP2R3B--TMLHE
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[114000] -fusion SPANNING read extraction for scaff: RAP1B--SRGAP1
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[28000] -fusion SPANNING read extraction for scaff: SAV1--SOS2
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[65000] -fusion SPANNING read extraction for scaff: SRGAP1--GRIP1
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[4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[20000] -fusion SPANNING read extraction for scaff: TMEM243--AC020637.1
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[20000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[31000] -fusion SPANNING read extraction for scaff: TYW1--VKORC1L1
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[48000] -fusion SPANNING read extraction for scaff: VGLL4--ATG7
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 15024,
'seq similar region alignment' => 495
};
Execution Time = 1.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -2164.405859
EM: Round [1] log likelihood: -2163.761580
EM: Round [2] log likelihood: -2163.359857
EM: Round [3] log likelihood: -2163.041851
EM: Round [4] log likelihood: -2162.784548
EM: Round [5] log likelihood: -2162.574075
EM: Round [6] log likelihood: -2162.400463
EM: Round [7] log likelihood: -2162.256305
EM: Round [8] log likelihood: -2162.135965
EM: Round [9] log likelihood: -2162.035072
EM: Round [10] log likelihood: -2161.950185
EM: Round [11] log likelihood: -2161.878554
EM: Round [12] log likelihood: -2161.817962
EM: Round [13] log likelihood: -2161.766604
EM: Round [14] log likelihood: -2161.722999
EM: Round [15] log likelihood: -2161.685924
EM: Round [16] log likelihood: -2161.654362
EM: Round [17] log likelihood: -2161.627467
EM: Round [18] log likelihood: -2161.604529
EM: Round [19] log likelihood: -2161.584951
EM: Round [20] log likelihood: -2161.568230
EM: Round [21] log likelihood: -2161.553943
EM: Round [22] log likelihood: -2161.541729
EM: Round [23] log likelihood: -2161.531284
EM: Round [24] log likelihood: -2161.522348
EM: Round [25] log likelihood: -2161.514701
EM: Round [26] log likelihood: -2161.508156
EM: Round [27] log likelihood: -2161.502553
EM: Round [28] log likelihood: -2161.497756
EM: Round [29] log likelihood: -2161.493647
EM: Round [30] log likelihood: -2161.490128
EM: Round [31] log likelihood: -2161.487114
EM: Round [32] log likelihood: -2161.484531
EM: Round [33] log likelihood: -2161.482319
EM: Round [34] log likelihood: -2161.480424
EM: Round [35] log likelihood: -2161.478799
EM: Round [36] log likelihood: -2161.477408
EM: Round [37] log likelihood: -2161.476215
EM: Round [38] log likelihood: -2161.475193
EM: Round [39] log likelihood: -2161.474317
EM: Round [40] log likelihood: -2161.473567
EM: Round [41] log likelihood: -2161.472924
EM: Round [42] log likelihood: -2161.472372
EM: Round [43] log likelihood: -2161.471900
EM: Round [44] log likelihood: -2161.471495
EM: Round [45] log likelihood: -2161.471148
EM: Round [46] log likelihood: -2161.470850
EM: Round [47] log likelihood: -2161.470595
EM: Round [48] log likelihood: -2161.470377
EM: Round [49] log likelihood: -2161.470189
EM: Round [50] log likelihood: -2161.470029
EM: Round [51] log likelihood: -2161.469891
EM: Round [52] log likelihood: -2161.469773
EM: Round [53] log likelihood: -2161.469672
EM: Round [54] log likelihood: -2161.469586
EM: Stopping iterations at round 54 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/init_EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_igv_extract_junc_reads.ok
Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_igv_sam_frag_coordss.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_igv_pfam_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/prep_igv_seqsim_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_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.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_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.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.oIY8PCx2yB/fi_workdir/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir
-done, see /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -2116.860461
EM: Round [1] log likelihood: -2116.859622
EM: Round [2] log likelihood: -2116.859619
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 294936328
Execution Time = 5.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.oIY8PCx2yB/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.oIY8PCx2yB/fi_workdir/microH.dat
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.oIY8PCx2yB/fi_workdir/microH.dat /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.oIY8PCx2yB/fi_workdir/microH.dat /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.oIY8PCx2yB --json_outfile /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_cTi-T1-TRNA-1_B23WHTKLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.oIY8PCx2yB --json_outfile /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_cTi-T1-TRNA-1_B23WHTKLT4_1
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/create_fi_igvjs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_cTi-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_cTi-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
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 [ENSG00000245651.3]
WARNING, no entry stored in dbm for [ENSG00000245651.3]
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 [ENSG00000258231.5]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.oIY8PCx2yB/ctat_genome_lib_build_dir > /tmp/nxf.oIY8PCx2yB/659_cTi-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.oIY8PCx2yB/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory