.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/246e781f2eb6835f0dd8d9e3529622/.command.log
Size: 189.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:FUSIONINSPECTOR (BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1)
Attempt
Content

  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/72/14363526a35f12ae85e17f872a34b9/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/246e781f2eb6835f0dd8d9e3529622/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/000ebc254bdaf6a39d18d9adb84e02/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusionreport.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/14363526a35f12ae85e17f872a34b9/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/246e781f2eb6835f0dd8d9e3529622/.command.run
==> STAGING COMPLETE (6 inputs)

Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusionreport.tsv --gtf /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1 --shrink_introns --max_intron_length 1000 
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57184101	57184307	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 1; exon_id "ENSE00003693591.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184101,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57184280	57184307	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 1; exon_id "ENSE00003693591.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184280,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189426	57189539	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 2; exon_id "ENSE00001325991.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189426,57189539,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57189426	57189539	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 2; exon_id "ENSE00001325991.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189426,57189539,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189969	57190080	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 3; exon_id "ENSE00001742205.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189969,57190080,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57189969	57190080	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 3; exon_id "ENSE00001742205.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189969,57190080,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57190197	57190375	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 4; exon_id "ENSE00001800113.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190197,57190375,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57190197	57190375	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 4; exon_id "ENSE00001800113.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190197,57190375,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57190940	57191085	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 5; exon_id "ENSE00000846398.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190940,57191085,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57190940	57191085	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 5; exon_id "ENSE00000846398.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190940,57191085,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57191798	57191999	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 6; exon_id "ENSE00001741000.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57191798,57191999,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57191798	57191999	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 6; exon_id "ENSE00001741000.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57191798,57191999,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57192603	57192708	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 7; exon_id "ENSE00001637342.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192603,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57192603	57192708	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 7; exon_id "ENSE00001637342.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192603,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57194043	57194127	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 8; exon_id "ENSE00003659134.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57194043,57194127,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57194043	57194127	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 8; exon_id "ENSE00003659134.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57194043,57194127,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57196336	57197128	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 9; exon_id "ENSE00001614034.2"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57196336,57197128,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57196336	57196926	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 9; exon_id "ENSE00001614034.2"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57196336,57196926,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57184226	57184307	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 1; exon_id "ENSE00001623885.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184226,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57184264	57184307	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 1; exon_id "ENSE00001623885.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184264,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57187928	57188028	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 2; exon_id "ENSE00003491675.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57187928,57188028,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57187928	57188028	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 2; exon_id "ENSE00003491675.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57187928,57188028,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189402	57189539	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 3; exon_id "ENSE00003693534.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189402,57189539,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57189402	57189539	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 3; exon_id "ENSE00003693534.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189402,57189539,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189969	57190080	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 4; exon_id "ENSE00001742205.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189969,57190080,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57189969	57190080	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 4; exon_id "ENSE00001742205.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189969,57190080,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57190204	57190375	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 5; exon_id "ENSE00001320232.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190204,57190375,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57190204	57190375	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 5; exon_id "ENSE00001320232.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190204,57190375,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57190969	57191085	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 6; exon_id "ENSE00001300194.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190969,57191085,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57190969	57191085	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 6; exon_id "ENSE00001300194.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190969,57191085,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57191798	57191999	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 7; exon_id "ENSE00001741000.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57191798,57191999,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57191798	57191999	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 7; exon_id "ENSE00001741000.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57191798,57191999,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57192603	57192708	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 8; exon_id "ENSE00001637342.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192603,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57192603	57192708	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 8; exon_id "ENSE00001637342.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192603,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57196336	57197337	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 9; exon_id "ENSE00003654520.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57196336,57197337,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57196336	57196369	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 9; exon_id "ENSE00003654520.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57196336,57196369,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57184254	57184307	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000489233.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-203"; exon_number 1; exon_id "ENSE00001867387.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058982.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184254,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57187850	57188028	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000489233.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-203"; exon_number 2; exon_id "ENSE00001819281.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058982.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57187850,57188028,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189426	57189490	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000489233.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-203"; exon_number 3; exon_id "ENSE00001903717.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058982.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189426,57189490,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57192634	57192708	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000494962.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-204"; exon_number 1; exon_id "ENSE00001852003.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058984.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192634,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57194043	57194127	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000494962.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-204"; exon_number 2; exon_id "ENSE00003642278.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058984.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57194043,57194127,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57194419	57194566	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000494962.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-204"; exon_number 3; exon_id "ENSE00001810078.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058984.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57194419,57194566,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57184101	57184307	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 1; exon_id "ENSE00003693591.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184101,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57184280	57184307	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 1; exon_id "ENSE00003693591.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184280,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189426	57189539	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 2; exon_id "ENSE00001325991.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189426,57189539,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57189426	57189539	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 2; exon_id "ENSE00001325991.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189426,57189539,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189969	57190080	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 3; exon_id "ENSE00001742205.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189969,57190080,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57189969	57190080	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 3; exon_id "ENSE00001742205.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189969,57190080,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57190197	57190375	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 4; exon_id "ENSE00001800113.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190197,57190375,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57190197	57190375	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 4; exon_id "ENSE00001800113.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190197,57190375,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57190940	57191085	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 5; exon_id "ENSE00000846398.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190940,57191085,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57190940	57191085	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 5; exon_id "ENSE00000846398.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190940,57191085,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57191798	57191999	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 6; exon_id "ENSE00001741000.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57191798,57191999,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57191798	57191999	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 6; exon_id "ENSE00001741000.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57191798,57191999,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57192603	57192708	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 7; exon_id "ENSE00001637342.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192603,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57192603	57192708	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 7; exon_id "ENSE00001637342.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192603,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57194043	57194127	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 8; exon_id "ENSE00003659134.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57194043,57194127,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57194043	57194127	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 8; exon_id "ENSE00003659134.1"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57194043,57194127,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57196336	57197128	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 9; exon_id "ENSE00001614034.2"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57196336,57197128,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57196336	57196926	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000244174.10_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-201"; exon_number 9; exon_id "ENSE00001614034.2"; level 2; protein_id "ENSP00000244174.5"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS14771.4"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058981.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57196336,57196926,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57184226	57184307	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 1; exon_id "ENSE00001623885.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184226,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57184264	57184307	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 1; exon_id "ENSE00001623885.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184264,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57187928	57188028	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 2; exon_id "ENSE00003491675.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57187928,57188028,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57187928	57188028	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 2; exon_id "ENSE00003491675.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57187928,57188028,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189402	57189539	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 3; exon_id "ENSE00003693534.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189402,57189539,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57189402	57189539	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 3; exon_id "ENSE00003693534.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189402,57189539,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189969	57190080	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 4; exon_id "ENSE00001742205.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189969,57190080,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57189969	57190080	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 4; exon_id "ENSE00001742205.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189969,57190080,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57190204	57190375	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 5; exon_id "ENSE00001320232.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190204,57190375,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57190204	57190375	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 5; exon_id "ENSE00001320232.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190204,57190375,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57190969	57191085	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 6; exon_id "ENSE00001300194.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190969,57191085,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57190969	57191085	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 6; exon_id "ENSE00001300194.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57190969,57191085,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57191798	57191999	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 7; exon_id "ENSE00001741000.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57191798,57191999,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57191798	57191999	.	+	0	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 7; exon_id "ENSE00001741000.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57191798,57191999,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57192603	57192708	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 8; exon_id "ENSE00001637342.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192603,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57192603	57192708	.	+	2	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 8; exon_id "ENSE00001637342.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192603,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57196336	57197337	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 9; exon_id "ENSE00003654520.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57196336,57197337,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57196336	57196369	.	+	1	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000369423.7_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "protein_coding"; transcript_name "IL9R-202"; exon_number 9; exon_id "ENSE00003654520.1"; level 2; protein_id "ENSP00000358431.2"; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "basic"; tag "CCDS"; tag "PAR"; ccdsid "CCDS59180.1"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058980.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57196336,57196369,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57184254	57184307	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000489233.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-203"; exon_number 1; exon_id "ENSE00001867387.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058982.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57184254,57184307,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57187850	57188028	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000489233.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-203"; exon_number 2; exon_id "ENSE00001819281.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058982.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57187850,57188028,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57189426	57189490	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000489233.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-203"; exon_number 3; exon_id "ENSE00001903717.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058982.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57189426,57189490,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57192634	57192708	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000494962.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-204"; exon_number 1; exon_id "ENSE00001852003.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058984.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57192634,57192708,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57194043	57194127	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000494962.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-204"; exon_number 2; exon_id "ENSE00003642278.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058984.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57194043,57194127,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57194419	57194566	.	+	.	gene_id "IL9R^ENSG00000124334.17_PAR_Y"; transcript_id "ENST00000494962.6_PAR_Y"; gene_type "protein_coding"; gene_name "IL9R"; transcript_type "processed_transcript"; transcript_name "IL9R-204"; exon_number 3; exon_id "ENSE00001810078.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:6030"; tag "PAR"; havana_gene "OTTHUMG00000022720.1"; havana_transcript "OTTHUMT00000058984.1"; FI_gene_label "IL9R^ENSG00000124334.17_PAR_Y"; orig_coord_info "chrY,57194419,57194566,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57207346	57207668	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000476066.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-207"; exon_number 1; exon_id "ENSE00001885938.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058829.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57207346,57207668,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208026	57208083	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000476066.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-207"; exon_number 2; exon_id "ENSE00001913331.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058829.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208026,57208083,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208214	57208312	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000476066.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-207"; exon_number 3; exon_id "ENSE00003684718.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058829.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208214,57208312,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000476066.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-207"; exon_number 4; exon_id "ENSE00003462616.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058829.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208843	57208935	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000476066.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-207"; exon_number 5; exon_id "ENSE00001952304.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058829.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208843,57208935,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57207481	57207668	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 1; exon_id "ENSE00001676861.2"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57207481,57207668,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57207481	57207668	.	+	0	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 1; exon_id "ENSE00001676861.2"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57207481,57207668,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208201	57208312	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 2; exon_id "ENSE00001793801.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208201,57208312,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57208201	57208312	.	+	1	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 2; exon_id "ENSE00001793801.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208201,57208312,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 3; exon_id "ENSE00003905033.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57208519	57208665	.	+	0	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 3; exon_id "ENSE00003905033.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208843	57208979	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 4; exon_id "ENSE00003905695.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208843,57208979,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57208843	57208979	.	+	0	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 4; exon_id "ENSE00003905695.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208843,57208979,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209219	57209354	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 5; exon_id "ENSE00003909984.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209219,57209354,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57209219	57209354	.	+	1	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 5; exon_id "ENSE00003909984.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209219,57209354,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209733	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 6; exon_id "ENSE00003910082.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209733,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57209532	57209733	.	+	0	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 6; exon_id "ENSE00003910082.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209733,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57209980	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 7; exon_id "ENSE00003908490.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57209980,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57209822	57209980	.	+	2	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 7; exon_id "ENSE00003908490.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57209980,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57210640	57210792	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 8; exon_id "ENSE00003906775.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57210640,57210792,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57210640	57210792	.	+	2	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 8; exon_id "ENSE00003906775.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57210640,57210792,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211552	57211620	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 9; exon_id "ENSE00003905275.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211552,57211620,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57211552	57211620	.	+	2	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 9; exon_id "ENSE00003905275.1"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211552,57211620,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211761	57211894	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 10; exon_id "ENSE00001416295.3"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211761,57211894,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	CDS	57211761	57211891	.	+	2	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000359512.8_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "protein_coding"; transcript_name "WASH6P-202"; exon_number 10; exon_id "ENSE00001416295.3"; level 2; protein_id "ENSP00000504557.1"; transcript_support_level "NA"; hgnc_id "HGNC:31685"; tag "basic"; tag "appris_principal_1"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211761,57211891,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57207848	57209729	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000461007.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-204"; exon_number 1; exon_id "ENSE00001930880.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058840.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57207848,57209729,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57212183	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000461007.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-204"; exon_number 2; exon_id "ENSE00001940208.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058840.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57212183,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57207965	57208312	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000496011.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-214"; exon_number 1; exon_id "ENSE00001911120.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058831.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57207965,57208312,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000496011.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-214"; exon_number 2; exon_id "ENSE00003462616.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058831.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208843	57208979	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000496011.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-214"; exon_number 3; exon_id "ENSE00003614781.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058831.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208843,57208979,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209727	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000496011.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-214"; exon_number 4; exon_id "ENSE00001876909.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058831.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209727,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208197	57208312	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000479401.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-208"; exon_number 1; exon_id "ENSE00001744356.2"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058828.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208197,57208312,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000479401.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-208"; exon_number 2; exon_id "ENSE00003462616.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058828.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208834	57208979	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000479401.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-208"; exon_number 3; exon_id "ENSE00001821116.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058828.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208834,57208979,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209219	57209354	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000479401.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-208"; exon_number 4; exon_id "ENSE00003682647.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058828.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209219,57209354,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209733	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000479401.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-208"; exon_number 5; exon_id "ENSE00003663894.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058828.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209733,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57209855	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000479401.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-208"; exon_number 6; exon_id "ENSE00001868242.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058828.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57209855,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208208	57208312	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000340131.12_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-201"; exon_number 1; exon_id "ENSE00001861535.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058837.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208208,57208312,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000340131.12_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-201"; exon_number 2; exon_id "ENSE00003462616.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058837.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208843	57209354	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000340131.12_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-201"; exon_number 3; exon_id "ENSE00001818153.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058837.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208843,57209354,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209729	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000340131.12_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-201"; exon_number 4; exon_id "ENSE00001909874.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058837.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209729,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57209980	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000340131.12_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-201"; exon_number 5; exon_id "ENSE00003572814.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058837.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57209980,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57210640	57210792	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000340131.12_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-201"; exon_number 6; exon_id "ENSE00003576210.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058837.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57210640,57210792,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211552	57211620	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000340131.12_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-201"; exon_number 7; exon_id "ENSE00003627301.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058837.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211552,57211620,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211761	57212186	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000340131.12_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-201"; exon_number 8; exon_id "ENSE00001956598.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058837.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211761,57212186,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208208	57208312	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000492963.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-213"; exon_number 1; exon_id "ENSE00001861535.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058839.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208208,57208312,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000492963.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-213"; exon_number 2; exon_id "ENSE00003462616.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058839.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208843	57209354	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000492963.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-213"; exon_number 3; exon_id "ENSE00001818153.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058839.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208843,57209354,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209729	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000492963.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-213"; exon_number 4; exon_id "ENSE00001909874.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058839.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209729,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57211620	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000492963.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-213"; exon_number 5; exon_id "ENSE00001952874.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058839.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57211620,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211761	57212186	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000492963.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-213"; exon_number 6; exon_id "ENSE00001956598.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058839.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211761,57212186,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208208	57208312	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000460206.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-203"; exon_number 1; exon_id "ENSE00001861535.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058838.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208208,57208312,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000460206.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-203"; exon_number 2; exon_id "ENSE00003462616.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058838.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208834	57209354	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000460206.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-203"; exon_number 3; exon_id "ENSE00001906282.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058838.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208834,57209354,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209733	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000460206.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-203"; exon_number 4; exon_id "ENSE00003663894.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058838.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209733,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57209980	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000460206.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-203"; exon_number 5; exon_id "ENSE00003572814.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058838.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57209980,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57210640	57210792	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000460206.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-203"; exon_number 6; exon_id "ENSE00003576210.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058838.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57210640,57210792,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211552	57211620	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000460206.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-203"; exon_number 7; exon_id "ENSE00003627301.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058838.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211552,57211620,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211761	57212230	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000460206.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-203"; exon_number 8; exon_id "ENSE00001856109.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "non_canonical_TEC"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058838.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211761,57212230,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208979	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000475594.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-206"; exon_number 1; exon_id "ENSE00001825471.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058832.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208979,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209612	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000475594.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-206"; exon_number 2; exon_id "ENSE00001887004.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058832.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209612,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000482170.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-209"; exon_number 1; exon_id "ENSE00003462616.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058830.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208843	57209059	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000482170.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-209"; exon_number 2; exon_id "ENSE00001951141.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058830.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208843,57209059,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209219	57209354	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000482170.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-209"; exon_number 3; exon_id "ENSE00003682647.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058830.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209219,57209354,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209729	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000482170.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-209"; exon_number 4; exon_id "ENSE00001909874.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058830.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209729,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57209909	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000482170.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-209"; exon_number 5; exon_id "ENSE00001851840.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058830.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57209909,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208519	57208665	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000484415.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-212"; exon_number 1; exon_id "ENSE00003462616.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058825.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208519,57208665,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57208843	57208979	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000484415.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-212"; exon_number 2; exon_id "ENSE00003614781.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058825.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57208843,57208979,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209219	57209354	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000484415.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-212"; exon_number 3; exon_id "ENSE00003682647.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058825.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209219,57209354,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209532	57209729	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000484415.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-212"; exon_number 4; exon_id "ENSE00001909874.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058825.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209532,57209729,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57212183	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000484415.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-212"; exon_number 5; exon_id "ENSE00001940208.1"; level 2; transcript_support_level "5"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058825.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57212183,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209306	57209733	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000483079.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-210"; exon_number 1; exon_id "ENSE00001930440.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058833.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209306,57209733,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209822	57210051	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000483079.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-210"; exon_number 2; exon_id "ENSE00001937341.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058833.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209822,57210051,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57209887	57209980	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000496301.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-215"; exon_number 1; exon_id "ENSE00001846301.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058827.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57209887,57209980,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57210640	57212186	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000496301.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-215"; exon_number 2; exon_id "ENSE00001870442.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058827.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57210640,57212186,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57210344	57210792	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000483286.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-211"; exon_number 1; exon_id "ENSE00001896212.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058834.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57210344,57210792,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211552	57211620	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000483286.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-211"; exon_number 2; exon_id "ENSE00003627301.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058834.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211552,57211620,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211761	57212074	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000483286.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "retained_intron"; transcript_name "WASH6P-211"; exon_number 3; exon_id "ENSE00001531705.3"; level 2; transcript_support_level "1"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058834.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211761,57212074,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57210591	57210792	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000464205.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-205"; exon_number 1; exon_id "ENSE00001942785.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058835.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57210591,57210792,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211552	57211569	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000464205.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-205"; exon_number 2; exon_id "ENSE00003785071.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058835.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211552,57211569,+";
Error, chr discrepancy in gtf info for chrY	HAVANA	exon	57211761	57212074	.	+	.	gene_id "WASH6P^ENSG00000182484.15_PAR_Y"; transcript_id "ENST00000464205.6_PAR_Y"; gene_type "protein_coding"; gene_name "WASH6P"; transcript_type "processed_transcript"; transcript_name "WASH6P-205"; exon_number 3; exon_id "ENSE00001531705.3"; level 2; transcript_support_level "2"; hgnc_id "HGNC:31685"; tag "PAR"; havana_gene "OTTHUMG00000022677.5"; havana_transcript "OTTHUMT00000058835.1"; FI_gene_label "WASH6P^ENSG00000182484.15_PAR_Y"; orig_coord_info "chrY,57211761,57212074,+";
Done.
Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusionreport.tsv --gtf /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1 --shrink_introns --max_intron_length 1000 
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf > /tmp/nxf.rje3eee0F1/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf > /tmp/nxf.rje3eee0F1/cytoBand.txt
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed
-parsing GTF file: /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf --CPU 8 --out_prefix BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star --out_dir /tmp/nxf.rje3eee0F1/fi_workdir --reads "/tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.rje3eee0F1/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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
Jun 08 10:19:56 ..... started STAR run
Jun 08 10:19:56 ..... loading genome
Jun 08 10:21:35 ... generating Suffix Array index
Jun 08 10:25:15 ... completed Suffix Array index
Jun 08 10:25:15 ..... processing annotations GTF
Jun 08 10:25:15 ..... inserting junctions into the genome indices
Jun 08 10:26:16 ..... started mapping
Jun 08 11:14:18 ..... finished mapping
Jun 08 11:14:20 ..... started sorting BAM
Jun 08 11:14:21 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.sortedByCoord.out.bam
Execution Time = 54.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf --CPU 8 --out_prefix BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star --out_dir /tmp/nxf.rje3eee0F1/fi_workdir --reads "/tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
11:14:40 : INFO : Done.
Execution Time = 0.27 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py  -i /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.sortedByCoord.out.bam   -o /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam   --remove_dups 
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf
-parsing /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam

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[3660000]   -done parsing /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 34,
          'num genes matched < 2' => 66,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 80,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12,
          'per_id < 96' => 17908,
          'excessive soft clipping' => 29194,
          'small anchor length' => 86,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 372,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 27,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 24,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 69,
          ' ** passed ** ' => 83074,
          'low complexity anchor region' => 44,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 38
        };
-writing fusion junction support info.
Execution Time = 2.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[27000]   -fusion SPANNING read extraction for scaff: AGPS--AC092640.1

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[3060000]   
[3061000]   
[3062000]   
[3063000]   
[3064000]   
[3065000]   -fusion SPANNING read extraction for scaff: FGFR3--TACC3

[1000]   -fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2

[1000]   
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[8000]   
[9000]   
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[81000]   
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[83000]   
[84000]   
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[88000]   
[89000]   -fusion SPANNING read extraction for scaff: IL9R--WASH4P

[1000]   
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[8000]   
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[95000]   
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[99000]   
[100000]   
[101000]   
[102000]   
[103000]   -fusion SPANNING read extraction for scaff: IL9R--WASH6P

[1000]   -fusion SPANNING read extraction for scaff: LINC00381--NKAIN2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[43000]   
[44000]   
[45000]   
[46000]   
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[49000]   
[50000]   
[51000]   -fusion SPANNING read extraction for scaff: MSI2--SETP3

[1000]   
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[6000]   
[7000]   
[8000]   
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[33000]   
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[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[30000]   
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[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
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[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[91000]   
[92000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

[1000]   
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[6000]   
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[8000]   
[9000]   
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[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

[1000]   
[2000]   
[3000]   
[4000]   
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[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
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[20000]   
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[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 14707
        };
Execution Time = 5.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir   > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1  > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -37836.933091
EM: Round [1] log likelihood: -37766.436694
EM: Round [2] log likelihood: -37744.204593
EM: Round [3] log likelihood: -37732.555299
EM: Round [4] log likelihood: -37726.185087
EM: Round [5] log likelihood: -37722.596512
EM: Round [6] log likelihood: -37720.520519
EM: Round [7] log likelihood: -37719.293630
EM: Round [8] log likelihood: -37718.556429
EM: Round [9] log likelihood: -37718.107461
EM: Round [10] log likelihood: -37717.830881
EM: Round [11] log likelihood: -37717.658797
EM: Round [12] log likelihood: -37717.550799
EM: Round [13] log likelihood: -37717.482506
EM: Round [14] log likelihood: -37717.439031
EM: Round [15] log likelihood: -37717.411194
EM: Round [16] log likelihood: -37717.393276
EM: Round [17] log likelihood: -37717.381689
EM: Round [18] log likelihood: -37717.374164
EM: Round [19] log likelihood: -37717.369260
EM: Round [20] log likelihood: -37717.366052
EM: Round [21] log likelihood: -37717.363947
EM: Round [22] log likelihood: -37717.362563
EM: Round [23] log likelihood: -37717.361650
EM: Round [24] log likelihood: -37717.361047
EM: Round [25] log likelihood: -37717.360647
EM: Round [26] log likelihood: -37717.360382
EM: Round [27] log likelihood: -37717.360206
EM: Round [28] log likelihood: -37717.360088
EM: Round [29] log likelihood: -37717.360010
EM: Stopping iterations at round 29 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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads  > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags  > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa -  | samtools sort -@ 8 - -o /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam || : 
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam --max_insert_size 10000000 
-extracting read coordinates from /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam into /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam.read_coords > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.96 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam --max_insert_size 10000000 
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.FusionJuncSpan
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.Pfam.gff3 
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.Pfam.gff3 > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.Pfam.gff3 > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf  --genome_lib_dir ctat_genome_lib_build_dir  > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.seqsimilar.gff3 
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa > /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl  --fusion_preds /tmp/nxf.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir
-done, see /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -34077.314999
EM: Round [1] log likelihood: -34068.315610
EM: Round [2] log likelihood: -34065.049219
EM: Round [3] log likelihood: -34063.887934
EM: Round [4] log likelihood: -34063.517588
EM: Round [5] log likelihood: -34063.414999
EM: Round [6] log likelihood: -34063.389956
EM: Round [7] log likelihood: -34063.384351
EM: Round [8] log likelihood: -34063.383157
EM: Round [9] log likelihood: -34063.382909
EM: Round [10] log likelihood: -34063.382858
EM: Stopping iterations at round 10 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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_1.fastp.fastq.gz: 295607690
Execution Time = 5.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa --gtf /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf  > /tmp/nxf.rje3eee0F1/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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fa --gtf /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gtf  > /tmp/nxf.rje3eee0F1/fi_workdir/microH.dat
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.rje3eee0F1/fi_workdir/microH.dat /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_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.rje3eee0F1/fi_workdir/microH.dat /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.rje3eee0F1 --json_outfile /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_inspector_web.json --file_prefix BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.rje3eee0F1 --json_outfile /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_inspector_web.json --file_prefix BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1
Running: touch /tmp/nxf.rje3eee0F1/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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_inspector_web.json --input_file_prefix BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1 --html_output /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 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.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_inspector_web.json --input_file_prefix BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1 --html_output /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
WARNING, no entry stored in dbm for [ENSG00000273897.1]
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 [ENSG00000287149.1]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated  --genome_lib_dir /tmp/nxf.rje3eee0F1/ctat_genome_lib_build_dir > /tmp/nxf.rje3eee0F1/BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 
Running: touch /tmp/nxf.rje3eee0F1/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory