Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/3c6f61594707e1d6128627a7fabe13/659_zO-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/d394d6c174eea44435da8b6fa3da36/.command.sh
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/ed/d394d6c174eea44435da8b6fa3da36/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/3c6f61594707e1d6128627a7fabe13/659_zO-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/f77815e5579250f8bcb85bb7061cf7/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_zO-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Error, chr discrepancy in gtf info for chrY HAVANA exon 2500817 2500976 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 1; exon_id "ENSE00001679842.3"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2500817,2500976,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2500817 2500925 . - 0 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 1; exon_id "ENSE00001679842.3"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2500817,2500925,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2425197 2425304 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 2; exon_id "ENSE00003549694.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425304,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2425197 2425304 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 2; exon_id "ENSE00003549694.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425304,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2408745 2408813 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 3; exon_id "ENSE00003638780.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2408745,2408813,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2408745 2408813 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 3; exon_id "ENSE00003638780.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2408745,2408813,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2291502 2291603 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 4; exon_id "ENSE00003532451.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291603,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2291502 2291603 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 4; exon_id "ENSE00003532451.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291603,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2266740 2266947 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 5; exon_id "ENSE00001761946.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2266740,2266947,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2266740 2266947 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 5; exon_id "ENSE00001761946.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2266740,2266947,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2243023 2243230 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 6; exon_id "ENSE00001931920.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2243023,2243230,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2243023 2243230 . - 1 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 6; exon_id "ENSE00001931920.1"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2243023,2243230,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2219506 2221229 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 7; exon_id "ENSE00001487873.2"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2219506,2221229,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2221044 2221229 . - 0 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000334651.11_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-201"; exon_number 7; exon_id "ENSE00001487873.2"; level 2; protein_id "ENSP00000334113.5"; transcript_support_level "1"; hgnc_id "HGNC:18399"; tag "basic"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; tag "PAR"; ccdsid "CCDS35195.1"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055617.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2221044,2221229,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2500817 2500973 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 1; exon_id "ENSE00001766079.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2500817,2500973,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2500817 2500925 . - 0 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 1; exon_id "ENSE00001766079.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2500817,2500925,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2425197 2425304 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 2; exon_id "ENSE00003549694.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425304,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2425197 2425304 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 2; exon_id "ENSE00003549694.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425304,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2291502 2291603 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 3; exon_id "ENSE00003532451.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291603,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2291502 2291603 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 3; exon_id "ENSE00003532451.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291603,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2266740 2266947 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 4; exon_id "ENSE00001761946.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2266740,2266947,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2266740 2266947 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 4; exon_id "ENSE00001761946.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2266740,2266947,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2243062 2243230 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 5; exon_id "ENSE00001855840.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2243062,2243230,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2243062 2243230 . - 1 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000412516.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-202"; exon_number 5; exon_id "ENSE00001855840.1"; level 2; protein_id "ENSP00000391778.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144307.3"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2243062,2243230,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2266740 2266937 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000464935.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-206"; exon_number 1; exon_id "ENSE00001855267.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144306.1"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2266740,2266937,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2261394 2261767 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000464935.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-206"; exon_number 2; exon_id "ENSE00001941233.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000144306.1"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2261394,2261767,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2500311 2500650 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 1; exon_id "ENSE00001487870.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2500311,2500650,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2425197 2425304 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 2; exon_id "ENSE00003508589.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425304,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2425197 2425212 . - 0 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 2; exon_id "ENSE00003508589.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425212,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2408745 2408813 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 3; exon_id "ENSE00003638780.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2408745,2408813,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2408745 2408813 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 3; exon_id "ENSE00003638780.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2408745,2408813,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2291502 2291603 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 4; exon_id "ENSE00003532451.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291603,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2291502 2291603 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 4; exon_id "ENSE00003532451.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291603,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2266770 2266947 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 5; exon_id "ENSE00001689320.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2266770,2266947,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2266770 2266947 . - 2 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000444280.6_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-205"; exon_number 5; exon_id "ENSE00001689320.1"; level 2; protein_id "ENSP00000402741.1"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000055618.4"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2266770,2266947,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2502761 2502805 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000441131.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-204"; exon_number 1; exon_id "ENSE00001932007.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354624.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2502761,2502805,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2425197 2425304 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000441131.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-204"; exon_number 2; exon_id "ENSE00003524028.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354624.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425304,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2408745 2408813 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000441131.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-204"; exon_number 3; exon_id "ENSE00003683335.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354624.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2408745,2408813,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2392354 2392474 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000441131.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-204"; exon_number 4; exon_id "ENSE00001866858.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354624.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2392354,2392474,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2291502 2291603 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000441131.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-204"; exon_number 5; exon_id "ENSE00003879199.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354624.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291603,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2266854 2266947 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000441131.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-204"; exon_number 6; exon_id "ENSE00001840771.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354624.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2266854,2266947,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2500311 2500589 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000478825.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-207"; exon_number 1; exon_id "ENSE00001956040.1"; level 2; protein_id "ENSP00000420788.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354625.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2500311,2500589,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2425197 2425304 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000478825.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-207"; exon_number 2; exon_id "ENSE00003524028.1"; level 2; protein_id "ENSP00000420788.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354625.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425304,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2408745 2408813 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000478825.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-207"; exon_number 3; exon_id "ENSE00003683335.1"; level 2; protein_id "ENSP00000420788.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354625.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2408745,2408813,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2392354 2392474 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000478825.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-207"; exon_number 4; exon_id "ENSE00001866858.1"; level 2; protein_id "ENSP00000420788.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354625.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2392354,2392474,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2291502 2291603 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000478825.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-207"; exon_number 5; exon_id "ENSE00003851665.1"; level 2; protein_id "ENSP00000420788.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354625.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291603,-";
Error, chr discrepancy in gtf info for chrY HAVANA CDS 2291502 2291574 . - 0 gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000478825.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "protein_coding"; transcript_name "DHRSX-207"; exon_number 5; exon_id "ENSE00003851665.1"; level 2; protein_id "ENSP00000420788.2"; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "mRNA_end_NF"; tag "cds_end_NF"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354625.2"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2291502,2291574,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2500817 2500960 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000430536.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-203"; exon_number 1; exon_id "ENSE00001401837.4"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354626.1"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2500817,2500960,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2425197 2425304 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000430536.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-203"; exon_number 2; exon_id "ENSE00003524028.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354626.1"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2425197,2425304,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2408745 2408813 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000430536.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-203"; exon_number 3; exon_id "ENSE00003683335.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354626.1"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2408745,2408813,-";
Error, chr discrepancy in gtf info for chrY HAVANA exon 2337831 2337999 . - . gene_id "DHRSX^ENSG00000169084.15_PAR_Y"; transcript_id "ENST00000430536.7_PAR_Y"; gene_type "protein_coding"; gene_name "DHRSX"; transcript_type "processed_transcript"; transcript_name "DHRSX-203"; exon_number 4; exon_id "ENSE00001949530.1"; level 2; transcript_support_level "2"; hgnc_id "HGNC:18399"; tag "PAR"; havana_gene "OTTHUMG00000021068.6"; havana_transcript "OTTHUMT00000354626.1"; FI_gene_label "DHRSX^ENSG00000169084.15_PAR_Y"; orig_coord_info "chrY,2337831,2337999,-";
Done.
Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_zO-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.6yEE1rtDOQ/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.6yEE1rtDOQ/cytoBand.txt
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed
-parsing GTF file: /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_zO-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.6yEE1rtDOQ/fi_workdir --reads "/tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 09:57:34 ..... started STAR run
Jun 08 09:57:34 ..... loading genome
Jun 08 09:59:20 ... generating Suffix Array index
Jun 08 10:03:02 ... completed Suffix Array index
Jun 08 10:03:02 ..... processing annotations GTF
Jun 08 10:03:02 ..... inserting junctions into the genome indices
Jun 08 10:04:03 ..... started mapping
Jun 08 11:13:31 ..... finished mapping
Jun 08 11:13:33 ..... started sorting BAM
Jun 08 11:13:36 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_zO-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_zO-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
Execution Time = 76.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_zO-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.6yEE1rtDOQ/fi_workdir --reads "/tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:14:14 : INFO : Done.
Execution Time = 0.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.07 minutes. CMD: samtools index /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[6220000] -done parsing /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 40,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 273,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 36,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 15,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 64,
'per_id < 96' => 20366,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 24,
'exons hit < 2' => 12,
'excessive soft clipping' => 38117,
'seq-similar region overlap' => 1037,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 206,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 120,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 136,
'small anchor length' => 483,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 54,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 24,
' ** passed ** ' => 62824,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 27,
'num genes matched < 2' => 69,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 840,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 770,
'low complexity anchor region' => 131
};
-writing fusion junction support info.
Execution Time = 3.46 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[9000] -fusion SPANNING read extraction for scaff: AC006008.1--ACTR3B
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[194000] -fusion SPANNING read extraction for scaff: ANK3--USP9Y
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[46000] -fusion SPANNING read extraction for scaff: AP3B1--TNFAIP8
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[472000] -fusion SPANNING read extraction for scaff: KIAA1217--CHD8
[1000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[34000] -fusion SPANNING read extraction for scaff: LARGE1--CARD8
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[431000] -fusion SPANNING read extraction for scaff: MAPK10--FAHD1
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[233000] -fusion SPANNING read extraction for scaff: MX1--OR13J1
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[9000] -fusion SPANNING read extraction for scaff: NLN--TMEM232
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[69000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[65000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[70000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[54000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[50000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[54000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[57000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC1
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[53000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC2
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[58000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHA13
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[64000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
[1000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
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[45000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
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[37000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
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[47000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
[1000]
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[43000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
[1000]
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[35000]
[36000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
[1000]
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[33000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
[1000]
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[31000]
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[33000]
[34000]
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[38000]
[39000]
[40000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
[1000]
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[57000]
[58000]
[59000]
[60000]
[61000]
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[63000]
[64000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
[1000]
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[4000]
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[9000]
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[11000]
[12000]
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[14000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
[1000]
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[6000]
[7000]
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[9000]
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[11000]
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
[1000]
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[35000]
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[37000]
[38000]
[39000]
[40000]
[41000]
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[44000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
[1000]
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[30000]
[31000]
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[37000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
[1000]
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[39000]
[40000]
[41000]
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[46000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
[1000]
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[33000]
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[41000]
[42000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
[1000]
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[30000]
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[36000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
[1000]
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[33000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
[1000]
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[31000]
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[33000]
[34000]
[35000]
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[39000]
[40000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
[1000]
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[64000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
[1000]
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[9000]
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[11000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
[1000]
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[6000]
[7000]
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[9000]
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[11000]
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
[1000]
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[39000]
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[45000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
[1000]
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[37000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[41000]
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[47000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
[1000]
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[34000]
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[36000]
[37000]
[38000]
[39000]
[40000]
[41000]
[42000]
[43000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
[1000]
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[11000]
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[27000]
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[30000]
[31000]
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[33000]
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[35000]
[36000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
[1000]
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[24000]
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[26000]
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[32000]
[33000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
[1000]
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[30000]
[31000]
[32000]
[33000]
[34000]
[35000]
[36000]
[37000]
[38000]
[39000]
[40000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
[1000]
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[31000]
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[40000]
[41000]
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[55000]
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[58000]
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[64000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
[1000]
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[9000]
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[11000]
[12000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000]
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[6000]
[7000]
[8000]
[9000]
[10000]
[11000]
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[1000]
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[36000]
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[38000]
[39000]
[40000]
[41000]
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[44000]
[45000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
[1000]
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[28000]
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[30000]
[31000]
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[37000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
[1000]
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[43000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[36000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[33000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[40000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[57000] -fusion SPANNING read extraction for scaff: SAMHD1--RTCB
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[32000] -fusion SPANNING read extraction for scaff: SAMHD1--RFPL3S
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[31000] -fusion SPANNING read extraction for scaff: SAMHD1--AL021937.4
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[36000] -fusion SPANNING read extraction for scaff: SEC24D--METTL14-DT
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[641000] -fusion SPANNING read extraction for scaff: SLC45A3--ERG
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[34000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[28000] -fusion SPANNING read extraction for scaff: TNFAIP8--SLC25A46
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[10000] -fusion SPANNING read extraction for scaff: TNFAIP8--AC008782.1
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[57000] -fusion SPANNING read extraction for scaff: TRPC4AP--BPIFC
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[86000] -fusion SPANNING read extraction for scaff: TSBP1--NOTCH4
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[56000] -fusion SPANNING read extraction for scaff: TSBP1--TSBP1-AS1
[1000]
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[18000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[7000] -fusion SPANNING read extraction for scaff: UPK3B--AC211486.3
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[40000] -fusion SPANNING read extraction for scaff: USP9Y--AC063965.2
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[111000] -fusion SPANNING read extraction for scaff: USP9Y--PTEN
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[59000] -fusion SPANNING read extraction for scaff: USP9Y--XPNPEP1
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[41000] -fusion SPANNING read extraction for scaff: UTY--AC099753.1
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[48000] -fusion SPANNING read extraction for scaff: UTY--VENTXP7
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[59000] -fusion SPANNING read extraction for scaff: VWA2--TDRD1
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[18000] -fusion SPANNING read extraction for scaff: XPNPEP1--CTNNA3
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[80000] -fusion SPANNING read extraction for scaff: ZNF341--SPHK2
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 247461,
'lacks exon overlap' => 223287
};
Execution Time = 9.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -33680.311701
EM: Round [1] log likelihood: -33673.821439
EM: Round [2] log likelihood: -33670.114234
EM: Round [3] log likelihood: -33667.007640
EM: Round [4] log likelihood: -33664.339441
EM: Round [5] log likelihood: -33662.007248
EM: Round [6] log likelihood: -33659.940328
EM: Round [7] log likelihood: -33658.087440
EM: Round [8] log likelihood: -33656.410348
EM: Round [9] log likelihood: -33654.879946
EM: Round [10] log likelihood: -33653.473731
EM: Round [11] log likelihood: -33652.174076
EM: Round [12] log likelihood: -33650.967007
EM: Round [13] log likelihood: -33649.841305
EM: Round [14] log likelihood: -33648.787855
EM: Round [15] log likelihood: -33647.799154
EM: Round [16] log likelihood: -33646.868942
EM: Round [17] log likelihood: -33645.991925
EM: Round [18] log likelihood: -33645.163565
EM: Round [19] log likelihood: -33644.379925
EM: Round [20] log likelihood: -33643.637546
EM: Round [21] log likelihood: -33642.933358
EM: Round [22] log likelihood: -33642.264609
EM: Round [23] log likelihood: -33641.628814
EM: Round [24] log likelihood: -33641.023714
EM: Round [25] log likelihood: -33640.447242
EM: Round [26] log likelihood: -33639.897505
EM: Round [27] log likelihood: -33639.372756
EM: Round [28] log likelihood: -33638.871384
EM: Round [29] log likelihood: -33638.391901
EM: Round [30] log likelihood: -33637.932925
EM: Round [31] log likelihood: -33637.493179
EM: Round [32] log likelihood: -33637.071477
EM: Round [33] log likelihood: -33636.666720
EM: Round [34] log likelihood: -33636.277886
EM: Round [35] log likelihood: -33635.904028
EM: Round [36] log likelihood: -33635.544267
EM: Round [37] log likelihood: -33635.197785
EM: Round [38] log likelihood: -33634.863826
EM: Round [39] log likelihood: -33634.541683
EM: Round [40] log likelihood: -33634.230704
EM: Round [41] log likelihood: -33633.930279
EM: Round [42] log likelihood: -33633.639844
EM: Round [43] log likelihood: -33633.358873
EM: Round [44] log likelihood: -33633.086876
EM: Round [45] log likelihood: -33632.823398
EM: Round [46] log likelihood: -33632.568015
EM: Round [47] log likelihood: -33632.320331
EM: Round [48] log likelihood: -33632.079977
EM: Round [49] log likelihood: -33631.846609
EM: Round [50] log likelihood: -33631.619906
EM: Round [51] log likelihood: -33631.399564
EM: Round [52] log likelihood: -33631.185304
EM: Round [53] log likelihood: -33630.976861
EM: Round [54] log likelihood: -33630.773987
EM: Round [55] log likelihood: -33630.576449
EM: Round [56] log likelihood: -33630.384029
EM: Round [57] log likelihood: -33630.196522
EM: Round [58] log likelihood: -33630.013733
EM: Round [59] log likelihood: -33629.835480
EM: Round [60] log likelihood: -33629.661591
EM: Round [61] log likelihood: -33629.491902
EM: Round [62] log likelihood: -33629.326260
EM: Round [63] log likelihood: -33629.164519
EM: Round [64] log likelihood: -33629.006541
EM: Round [65] log likelihood: -33628.852194
EM: Round [66] log likelihood: -33628.701354
EM: Round [67] log likelihood: -33628.553902
EM: Round [68] log likelihood: -33628.409727
EM: Round [69] log likelihood: -33628.268720
EM: Round [70] log likelihood: -33628.130780
EM: Round [71] log likelihood: -33627.995809
EM: Round [72] log likelihood: -33627.863714
EM: Round [73] log likelihood: -33627.734406
EM: Round [74] log likelihood: -33627.607800
EM: Round [75] log likelihood: -33627.483815
EM: Round [76] log likelihood: -33627.362372
EM: Round [77] log likelihood: -33627.243398
EM: Round [78] log likelihood: -33627.126820
EM: Round [79] log likelihood: -33627.012570
EM: Round [80] log likelihood: -33626.900582
EM: Round [81] log likelihood: -33626.790792
EM: Round [82] log likelihood: -33626.683140
EM: Round [83] log likelihood: -33626.577566
EM: Round [84] log likelihood: -33626.474016
EM: Round [85] log likelihood: -33626.372433
EM: Round [86] log likelihood: -33626.272767
EM: Round [87] log likelihood: -33626.174966
EM: Round [88] log likelihood: -33626.078983
EM: Round [89] log likelihood: -33625.984769
EM: Round [90] log likelihood: -33625.892280
EM: Round [91] log likelihood: -33625.801473
EM: Round [92] log likelihood: -33625.712305
EM: Round [93] log likelihood: -33625.624735
EM: Round [94] log likelihood: -33625.538724
EM: Round [95] log likelihood: -33625.454234
EM: Round [96] log likelihood: -33625.371227
EM: Round [97] log likelihood: -33625.289670
EM: Round [98] log likelihood: -33625.209526
EM: Round [99] log likelihood: -33625.130762
EM: Round [100] log likelihood: -33625.053347
EM: Round [101] log likelihood: -33624.977248
EM: Round [102] log likelihood: -33624.902436
EM: Round [103] log likelihood: -33624.828880
EM: Round [104] log likelihood: -33624.756553
EM: Round [105] log likelihood: -33624.685426
EM: Round [106] log likelihood: -33624.615473
EM: Round [107] log likelihood: -33624.546668
EM: Round [108] log likelihood: -33624.478985
EM: Round [109] log likelihood: -33624.412400
EM: Round [110] log likelihood: -33624.346889
EM: Round [111] log likelihood: -33624.282428
EM: Round [112] log likelihood: -33624.218996
EM: Round [113] log likelihood: -33624.156570
EM: Round [114] log likelihood: -33624.095128
EM: Round [115] log likelihood: -33624.034651
EM: Round [116] log likelihood: -33623.975118
EM: Round [117] log likelihood: -33623.916509
EM: Round [118] log likelihood: -33623.858806
EM: Round [119] log likelihood: -33623.801989
EM: Round [120] log likelihood: -33623.746041
EM: Round [121] log likelihood: -33623.690945
EM: Round [122] log likelihood: -33623.636682
EM: Round [123] log likelihood: -33623.583237
EM: Round [124] log likelihood: -33623.530593
EM: Round [125] log likelihood: -33623.478734
EM: Round [126] log likelihood: -33623.427645
EM: Round [127] log likelihood: -33623.377311
EM: Round [128] log likelihood: -33623.327717
EM: Round [129] log likelihood: -33623.278849
EM: Round [130] log likelihood: -33623.230693
EM: Round [131] log likelihood: -33623.183236
EM: Round [132] log likelihood: -33623.136463
EM: Round [133] log likelihood: -33623.090363
EM: Round [134] log likelihood: -33623.044922
EM: Round [135] log likelihood: -33623.000128
EM: Round [136] log likelihood: -33622.955969
EM: Round [137] log likelihood: -33622.912434
EM: Round [138] log likelihood: -33622.869511
EM: Round [139] log likelihood: -33622.827189
EM: Round [140] log likelihood: -33622.785456
EM: Round [141] log likelihood: -33622.744303
EM: Round [142] log likelihood: -33622.703718
EM: Round [143] log likelihood: -33622.663692
EM: Round [144] log likelihood: -33622.624214
EM: Round [145] log likelihood: -33622.585275
EM: Round [146] log likelihood: -33622.546866
EM: Round [147] log likelihood: -33622.508976
EM: Round [148] log likelihood: -33622.471597
EM: Round [149] log likelihood: -33622.434720
EM: Round [150] log likelihood: -33622.398337
EM: Round [151] log likelihood: -33622.362438
EM: Round [152] log likelihood: -33622.327015
EM: Round [153] log likelihood: -33622.292061
EM: Round [154] log likelihood: -33622.257567
EM: Round [155] log likelihood: -33622.223525
EM: Round [156] log likelihood: -33622.189929
EM: Round [157] log likelihood: -33622.156769
EM: Round [158] log likelihood: -33622.124040
EM: Round [159] log likelihood: -33622.091733
EM: Round [160] log likelihood: -33622.059842
EM: Round [161] log likelihood: -33622.028360
EM: Round [162] log likelihood: -33621.997281
EM: Round [163] log likelihood: -33621.966597
EM: Round [164] log likelihood: -33621.936302
EM: Round [165] log likelihood: -33621.906390
EM: Round [166] log likelihood: -33621.876854
EM: Round [167] log likelihood: -33621.847689
EM: Round [168] log likelihood: -33621.818889
EM: Round [169] log likelihood: -33621.790447
EM: Round [170] log likelihood: -33621.762359
EM: Round [171] log likelihood: -33621.734618
EM: Round [172] log likelihood: -33621.707218
EM: Round [173] log likelihood: -33621.680156
EM: Round [174] log likelihood: -33621.653425
EM: Round [175] log likelihood: -33621.627019
EM: Round [176] log likelihood: -33621.600935
EM: Round [177] log likelihood: -33621.575167
EM: Round [178] log likelihood: -33621.549710
EM: Round [179] log likelihood: -33621.524559
EM: Round [180] log likelihood: -33621.499710
EM: Round [181] log likelihood: -33621.475158
EM: Round [182] log likelihood: -33621.450898
EM: Round [183] log likelihood: -33621.426927
EM: Round [184] log likelihood: -33621.403239
EM: Round [185] log likelihood: -33621.379831
EM: Round [186] log likelihood: -33621.356697
EM: Round [187] log likelihood: -33621.333835
EM: Round [188] log likelihood: -33621.311240
EM: Round [189] log likelihood: -33621.288908
EM: Round [190] log likelihood: -33621.266836
EM: Round [191] log likelihood: -33621.245018
EM: Round [192] log likelihood: -33621.223453
EM: Round [193] log likelihood: -33621.202135
EM: Round [194] log likelihood: -33621.181061
EM: Round [195] log likelihood: -33621.160229
EM: Round [196] log likelihood: -33621.139633
EM: Round [197] log likelihood: -33621.119272
EM: Round [198] log likelihood: -33621.099140
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EM: Round [659] log likelihood: -33618.955084
EM: Round [660] log likelihood: -33618.954511
EM: Round [661] log likelihood: -33618.953942
EM: Round [662] log likelihood: -33618.953376
EM: Round [663] log likelihood: -33618.952814
EM: Round [664] log likelihood: -33618.952256
EM: Round [665] log likelihood: -33618.951700
EM: Round [666] log likelihood: -33618.951148
EM: Round [667] log likelihood: -33618.950600
EM: Round [668] log likelihood: -33618.950055
EM: Round [669] log likelihood: -33618.949513
EM: Round [670] log likelihood: -33618.948975
EM: Round [671] log likelihood: -33618.948440
EM: Round [672] log likelihood: -33618.947908
EM: Round [673] log likelihood: -33618.947380
EM: Round [674] log likelihood: -33618.946854
EM: Round [675] log likelihood: -33618.946332
EM: Round [676] log likelihood: -33618.945813
EM: Round [677] log likelihood: -33618.945298
EM: Round [678] log likelihood: -33618.944785
EM: Round [679] log likelihood: -33618.944276
EM: Round [680] log likelihood: -33618.943770
EM: Round [681] log likelihood: -33618.943267
EM: Round [682] log likelihood: -33618.942767
EM: Round [683] log likelihood: -33618.942270
EM: Round [684] log likelihood: -33618.941776
EM: Round [685] log likelihood: -33618.941285
EM: Round [686] log likelihood: -33618.940797
EM: Round [687] log likelihood: -33618.940312
EM: Round [688] log likelihood: -33618.939830
EM: Round [689] log likelihood: -33618.939351
EM: Round [690] log likelihood: -33618.938875
EM: Round [691] log likelihood: -33618.938402
EM: Round [692] log likelihood: -33618.937931
EM: Round [693] log likelihood: -33618.937464
EM: Round [694] log likelihood: -33618.936999
EM: Round [695] log likelihood: -33618.936537
EM: Round [696] log likelihood: -33618.936078
EM: Round [697] log likelihood: -33618.935622
EM: Round [698] log likelihood: -33618.935169
EM: Round [699] log likelihood: -33618.934718
EM: Round [700] log likelihood: -33618.934270
EM: Round [701] log likelihood: -33618.933825
EM: Round [702] log likelihood: -33618.933382
EM: Round [703] log likelihood: -33618.932943
EM: Round [704] log likelihood: -33618.932505
EM: Round [705] log likelihood: -33618.932071
EM: Round [706] log likelihood: -33618.931639
EM: Round [707] log likelihood: -33618.931210
EM: Round [708] log likelihood: -33618.930783
EM: Round [709] log likelihood: -33618.930359
EM: Round [710] log likelihood: -33618.929937
EM: Round [711] log likelihood: -33618.929518
EM: Round [712] log likelihood: -33618.929102
EM: Round [713] log likelihood: -33618.928688
EM: Round [714] log likelihood: -33618.928277
EM: Round [715] log likelihood: -33618.927868
EM: Round [716] log likelihood: -33618.927461
EM: Round [717] log likelihood: -33618.927057
EM: Round [718] log likelihood: -33618.926656
EM: Round [719] log likelihood: -33618.926257
EM: Round [720] log likelihood: -33618.925860
EM: Round [721] log likelihood: -33618.925465
EM: Round [722] log likelihood: -33618.925073
EM: Round [723] log likelihood: -33618.924684
EM: Round [724] log likelihood: -33618.924296
EM: Round [725] log likelihood: -33618.923912
EM: Round [726] log likelihood: -33618.923529
EM: Round [727] log likelihood: -33618.923149
EM: Round [728] log likelihood: -33618.922770
EM: Round [729] log likelihood: -33618.922395
EM: Round [730] log likelihood: -33618.922021
EM: Round [731] log likelihood: -33618.921650
EM: Round [732] log likelihood: -33618.921281
EM: Round [733] log likelihood: -33618.920914
EM: Round [734] log likelihood: -33618.920549
EM: Round [735] log likelihood: -33618.920187
EM: Round [736] log likelihood: -33618.919826
EM: Round [737] log likelihood: -33618.919468
EM: Round [738] log likelihood: -33618.919112
EM: Round [739] log likelihood: -33618.918758
EM: Round [740] log likelihood: -33618.918407
EM: Round [741] log likelihood: -33618.918057
EM: Round [742] log likelihood: -33618.917709
EM: Round [743] log likelihood: -33618.917364
EM: Round [744] log likelihood: -33618.917020
EM: Round [745] log likelihood: -33618.916679
EM: Round [746] log likelihood: -33618.916340
EM: Round [747] log likelihood: -33618.916002
EM: Round [748] log likelihood: -33618.915667
EM: Round [749] log likelihood: -33618.915334
EM: Round [750] log likelihood: -33618.915002
EM: Round [751] log likelihood: -33618.914673
EM: Round [752] log likelihood: -33618.914346
EM: Round [753] log likelihood: -33618.914020
EM: Round [754] log likelihood: -33618.913697
EM: Round [755] log likelihood: -33618.913375
EM: Round [756] log likelihood: -33618.913055
EM: Round [757] log likelihood: -33618.912737
EM: Round [758] log likelihood: -33618.912422
EM: Round [759] log likelihood: -33618.912107
EM: Round [760] log likelihood: -33618.911795
EM: Round [761] log likelihood: -33618.911485
EM: Round [762] log likelihood: -33618.911176
EM: Round [763] log likelihood: -33618.910870
EM: Round [764] log likelihood: -33618.910565
EM: Round [765] log likelihood: -33618.910262
EM: Round [766] log likelihood: -33618.909961
EM: Round [767] log likelihood: -33618.909661
EM: Round [768] log likelihood: -33618.909364
EM: Round [769] log likelihood: -33618.909068
EM: Round [770] log likelihood: -33618.908773
EM: Round [771] log likelihood: -33618.908481
EM: Round [772] log likelihood: -33618.908190
EM: Round [773] log likelihood: -33618.907901
EM: Round [774] log likelihood: -33618.907614
EM: Round [775] log likelihood: -33618.907328
EM: Round [776] log likelihood: -33618.907044
EM: Round [777] log likelihood: -33618.906762
EM: Round [778] log likelihood: -33618.906482
EM: Round [779] log likelihood: -33618.906203
EM: Round [780] log likelihood: -33618.905925
EM: Round [781] log likelihood: -33618.905650
EM: Round [782] log likelihood: -33618.905376
EM: Round [783] log likelihood: -33618.905103
EM: Round [784] log likelihood: -33618.904833
EM: Round [785] log likelihood: -33618.904563
EM: Round [786] log likelihood: -33618.904296
EM: Round [787] log likelihood: -33618.904030
EM: Round [788] log likelihood: -33618.903765
EM: Round [789] log likelihood: -33618.903502
EM: Round [790] log likelihood: -33618.903241
EM: Round [791] log likelihood: -33618.902981
EM: Round [792] log likelihood: -33618.902723
EM: Round [793] log likelihood: -33618.902466
EM: Round [794] log likelihood: -33618.902210
EM: Round [795] log likelihood: -33618.901956
EM: Round [796] log likelihood: -33618.901704
EM: Round [797] log likelihood: -33618.901453
EM: Round [798] log likelihood: -33618.901204
EM: Round [799] log likelihood: -33618.900956
EM: Round [800] log likelihood: -33618.900709
EM: Round [801] log likelihood: -33618.900464
EM: Round [802] log likelihood: -33618.900221
EM: Round [803] log likelihood: -33618.899979
EM: Round [804] log likelihood: -33618.899738
EM: Round [805] log likelihood: -33618.899498
EM: Round [806] log likelihood: -33618.899260
EM: Round [807] log likelihood: -33618.899024
EM: Round [808] log likelihood: -33618.898789
EM: Round [809] log likelihood: -33618.898555
EM: Round [810] log likelihood: -33618.898322
EM: Round [811] log likelihood: -33618.898091
EM: Round [812] log likelihood: -33618.897861
EM: Round [813] log likelihood: -33618.897633
EM: Round [814] log likelihood: -33618.897406
EM: Round [815] log likelihood: -33618.897180
EM: Round [816] log likelihood: -33618.896955
EM: Round [817] log likelihood: -33618.896732
EM: Round [818] log likelihood: -33618.896510
EM: Round [819] log likelihood: -33618.896290
EM: Round [820] log likelihood: -33618.896070
EM: Round [821] log likelihood: -33618.895852
EM: Round [822] log likelihood: -33618.895636
EM: Round [823] log likelihood: -33618.895420
EM: Round [824] log likelihood: -33618.895206
EM: Round [825] log likelihood: -33618.894993
EM: Round [826] log likelihood: -33618.894781
EM: Round [827] log likelihood: -33618.894570
EM: Round [828] log likelihood: -33618.894361
EM: Round [829] log likelihood: -33618.894153
EM: Round [830] log likelihood: -33618.893946
EM: Round [831] log likelihood: -33618.893740
EM: Round [832] log likelihood: -33618.893536
EM: Round [833] log likelihood: -33618.893332
EM: Round [834] log likelihood: -33618.893130
EM: Round [835] log likelihood: -33618.892929
EM: Round [836] log likelihood: -33618.892729
EM: Round [837] log likelihood: -33618.892531
EM: Round [838] log likelihood: -33618.892333
EM: Round [839] log likelihood: -33618.892137
EM: Round [840] log likelihood: -33618.891941
EM: Round [841] log likelihood: -33618.891747
EM: Round [842] log likelihood: -33618.891554
EM: Round [843] log likelihood: -33618.891362
EM: Round [844] log likelihood: -33618.891171
EM: Round [845] log likelihood: -33618.890982
EM: Round [846] log likelihood: -33618.890793
EM: Round [847] log likelihood: -33618.890605
EM: Round [848] log likelihood: -33618.890419
EM: Round [849] log likelihood: -33618.890234
EM: Round [850] log likelihood: -33618.890049
EM: Round [851] log likelihood: -33618.889866
EM: Round [852] log likelihood: -33618.889684
EM: Round [853] log likelihood: -33618.889503
EM: Round [854] log likelihood: -33618.889322
EM: Round [855] log likelihood: -33618.889143
EM: Round [856] log likelihood: -33618.888965
EM: Round [857] log likelihood: -33618.888788
EM: Round [858] log likelihood: -33618.888612
EM: Round [859] log likelihood: -33618.888437
EM: Round [860] log likelihood: -33618.888263
EM: Round [861] log likelihood: -33618.888090
EM: Round [862] log likelihood: -33618.887918
EM: Round [863] log likelihood: -33618.887747
EM: Round [864] log likelihood: -33618.887577
EM: Round [865] log likelihood: -33618.887408
EM: Round [866] log likelihood: -33618.887240
EM: Round [867] log likelihood: -33618.887072
EM: Round [868] log likelihood: -33618.886906
EM: Round [869] log likelihood: -33618.886741
EM: Round [870] log likelihood: -33618.886577
EM: Round [871] log likelihood: -33618.886413
EM: Round [872] log likelihood: -33618.886251
EM: Round [873] log likelihood: -33618.886089
EM: Round [874] log likelihood: -33618.885929
EM: Round [875] log likelihood: -33618.885769
EM: Round [876] log likelihood: -33618.885610
EM: Round [877] log likelihood: -33618.885452
EM: Round [878] log likelihood: -33618.885295
EM: Round [879] log likelihood: -33618.885139
EM: Round [880] log likelihood: -33618.884984
EM: Round [881] log likelihood: -33618.884830
EM: Round [882] log likelihood: -33618.884676
EM: Round [883] log likelihood: -33618.884524
EM: Round [884] log likelihood: -33618.884372
EM: Round [885] log likelihood: -33618.884221
EM: Round [886] log likelihood: -33618.884071
EM: Round [887] log likelihood: -33618.883922
EM: Round [888] log likelihood: -33618.883774
EM: Round [889] log likelihood: -33618.883627
EM: Round [890] log likelihood: -33618.883480
EM: Round [891] log likelihood: -33618.883334
EM: Round [892] log likelihood: -33618.883189
EM: Round [893] log likelihood: -33618.883045
EM: Round [894] log likelihood: -33618.882902
EM: Round [895] log likelihood: -33618.882759
EM: Round [896] log likelihood: -33618.882618
EM: Round [897] log likelihood: -33618.882477
EM: Round [898] log likelihood: -33618.882337
EM: Round [899] log likelihood: -33618.882198
EM: Round [900] log likelihood: -33618.882059
EM: Round [901] log likelihood: -33618.881921
EM: Round [902] log likelihood: -33618.881784
EM: Round [903] log likelihood: -33618.881648
EM: Round [904] log likelihood: -33618.881513
EM: Round [905] log likelihood: -33618.881378
EM: Round [906] log likelihood: -33618.881244
EM: Round [907] log likelihood: -33618.881111
EM: Round [908] log likelihood: -33618.880979
EM: Round [909] log likelihood: -33618.880847
EM: Round [910] log likelihood: -33618.880716
EM: Round [911] log likelihood: -33618.880586
EM: Round [912] log likelihood: -33618.880457
EM: Round [913] log likelihood: -33618.880328
EM: Round [914] log likelihood: -33618.880200
EM: Round [915] log likelihood: -33618.880073
EM: Round [916] log likelihood: -33618.879947
EM: Round [917] log likelihood: -33618.879821
EM: Round [918] log likelihood: -33618.879696
EM: Round [919] log likelihood: -33618.879571
EM: Round [920] log likelihood: -33618.879448
EM: Round [921] log likelihood: -33618.879325
EM: Round [922] log likelihood: -33618.879202
EM: Round [923] log likelihood: -33618.879081
EM: Round [924] log likelihood: -33618.878960
EM: Round [925] log likelihood: -33618.878840
EM: Round [926] log likelihood: -33618.878720
EM: Round [927] log likelihood: -33618.878601
EM: Round [928] log likelihood: -33618.878483
EM: Round [929] log likelihood: -33618.878365
EM: Round [930] log likelihood: -33618.878249
EM: Round [931] log likelihood: -33618.878132
EM: Round [932] log likelihood: -33618.878017
EM: Round [933] log likelihood: -33618.877902
EM: Round [934] log likelihood: -33618.877787
EM: Round [935] log likelihood: -33618.877674
EM: Round [936] log likelihood: -33618.877561
EM: Round [937] log likelihood: -33618.877448
EM: Round [938] log likelihood: -33618.877337
EM: Round [939] log likelihood: -33618.877225
EM: Round [940] log likelihood: -33618.877115
EM: Round [941] log likelihood: -33618.877005
EM: Round [942] log likelihood: -33618.876896
EM: Round [943] log likelihood: -33618.876787
EM: Round [944] log likelihood: -33618.876679
EM: Round [945] log likelihood: -33618.876572
EM: Round [946] log likelihood: -33618.876465
EM: Round [947] log likelihood: -33618.876358
EM: Round [948] log likelihood: -33618.876253
EM: Round [949] log likelihood: -33618.876148
EM: Round [950] log likelihood: -33618.876043
EM: Round [951] log likelihood: -33618.875939
EM: Round [952] log likelihood: -33618.875836
EM: Round [953] log likelihood: -33618.875733
EM: Round [954] log likelihood: -33618.875631
EM: Round [955] log likelihood: -33618.875529
EM: Round [956] log likelihood: -33618.875428
EM: Round [957] log likelihood: -33618.875328
EM: Round [958] log likelihood: -33618.875228
EM: Stopping iterations at round 958 due to insufficient improvement in likelihood.
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/659_zO-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 1.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir
-done, see /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -23654.364574
EM: Round [1] log likelihood: -23653.406669
EM: Round [2] log likelihood: -23653.405700
EM: Round [3] log likelihood: -23653.405691
EM: Stopping iterations at round 3 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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 296392849
Execution Time = 5.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.6yEE1rtDOQ/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.6yEE1rtDOQ/fi_workdir/microH.dat
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.6yEE1rtDOQ/fi_workdir/microH.dat /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_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.6yEE1rtDOQ/fi_workdir/microH.dat /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.6yEE1rtDOQ --json_outfile /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_zO-T1-TRNA-1_B23MHV2LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.6yEE1rtDOQ --json_outfile /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_zO-T1-TRNA-1_B23MHV2LT4_1
Running: touch /tmp/nxf.6yEE1rtDOQ/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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_zO-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.05 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.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_zO-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000239268.3]
WARNING, no entry stored in dbm for [ENSG00000239268.3]
WARNING, no entry stored in dbm for [ENSG00000224745.1]
WARNING, no entry stored in dbm for [ENSG00000224745.1]
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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000275389.1]
WARNING, no entry stored in dbm for [ENSG00000281731.3]
WARNING, no entry stored in dbm for [ENSG00000281731.3]
WARNING, no entry stored in dbm for [ENSG00000281731.3]
WARNING, no entry stored in dbm for [ENSG00000281731.3]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.6yEE1rtDOQ/ctat_genome_lib_build_dir > /tmp/nxf.6yEE1rtDOQ/659_zO-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.6yEE1rtDOQ/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory