Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/99b60627a3e434facb4168dc344448/aih-tih-sc-01c779-R1_A23YTGFLT4_1_1.fastp.fastq.gz 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/7b/bff650c8fb347c73b330049969f2d0/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/bff650c8fb347c73b330049969f2d0/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/99b60627a3e434facb4168dc344448/aih-tih-sc-01c779-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/f14099cfa6393f7a0e613ed7ebfb14/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Error, strand conflict in gtf info for chr1 ENSEMBL exon 218541690 218541899 . - . gene_id "U3^ENSG00000212610.2"; transcript_id "ENST00000391308.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.29-201"; exon_number 1; exon_id "ENSE00001509092.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212610.2"; orig_coord_info "chr1,218541690,218541899,-"; Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 75627950 75628168 . + . gene_id "U3^ENSG00000221638.2"; transcript_id "ENST00000408711.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.40-201"; exon_number 1; exon_id "ENSE00001565346.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221638.2"; orig_coord_info "chr2,75627950,75628168,+"; Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 114005440 114005655 . - . gene_id "U3^ENSG00000212182.2"; transcript_id "ENST00000390880.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.17-201"; exon_number 1; exon_id "ENSE00001508664.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212182.2"; orig_coord_info "chr2,114005440,114005655,-"; Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 240289216 240289443 . + . gene_id "U3^ENSG00000276366.1"; transcript_id "ENST00000611947.1"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.49-201"; exon_number 1; exon_id "ENSE00003712639.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000276366.1"; orig_coord_info "chr2,240289216,240289443,+"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 30304321 30304536 . - . gene_id "U3^ENSG00000281710.1"; transcript_id "ENST00000628922.1"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.52-201"; exon_number 1; exon_id "ENSE00003765285.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000281710.1"; orig_coord_info "chr3,30304321,30304536,-"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 45255409 45255620 . - . gene_id "U3^ENSG00000202268.2"; transcript_id "ENST00000365398.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.14-201"; exon_number 1; exon_id "ENSE00001440161.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000202268.2"; orig_coord_info "chr3,45255409,45255620,-"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 60856389 60856605 . - . gene_id "U3^ENSG00000212211.2"; transcript_id "ENST00000390909.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.19-201"; exon_number 1; exon_id "ENSE00001508693.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212211.2"; orig_coord_info "chr3,60856389,60856605,-"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 64071807 64072019 . - . gene_id "U3^ENSG00000200222.2"; transcript_id "ENST00000363352.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.4-201"; exon_number 1; exon_id "ENSE00001438115.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200222.2"; orig_coord_info "chr3,64071807,64072019,-"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 90030284 90030495 . + . gene_id "U3^ENSG00000212598.2"; transcript_id "ENST00000391296.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.28-201"; exon_number 1; exon_id "ENSE00001509080.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212598.2"; orig_coord_info "chr3,90030284,90030495,+"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 109018909 109019116 . - . gene_id "U3^ENSG00000221633.2"; transcript_id "ENST00000408706.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.39-201"; exon_number 1; exon_id "ENSE00001565341.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221633.2"; orig_coord_info "chr3,109018909,109019116,-"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 158700691 158700909 . + . gene_id "U3^ENSG00000271817.2"; transcript_id "ENST00000607547.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.44-201"; exon_number 1; exon_id "ENSE00003695581.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000271817.2"; orig_coord_info "chr4,158700691,158700909,+"; Error, chr discrepancy in gtf info for chr5 ENSEMBL exon 35429064 35429277 . + . gene_id "U3^ENSG00000201368.2"; transcript_id "ENST00000364498.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.11-201"; exon_number 1; exon_id "ENSE00001439261.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000201368.2"; orig_coord_info "chr5,35429064,35429277,+"; Error, chr discrepancy in gtf info for chr5 ENSEMBL exon 149695748 149695959 . - . gene_id "U3^ENSG00000221043.2"; transcript_id "ENST00000408116.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.31-201"; exon_number 1; exon_id "ENSE00001564751.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221043.2"; orig_coord_info "chr5,149695748,149695959,-"; Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 28015568 28015777 . + . gene_id "U3^ENSG00000199851.2"; transcript_id "ENST00000362981.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.2-201"; exon_number 1; exon_id "ENSE00001437744.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000199851.2"; orig_coord_info "chr6,28015568,28015777,+"; Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 71126893 71127105 . - . gene_id "U3^ENSG00000221345.2"; transcript_id "ENST00000408418.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.35-201"; exon_number 1; exon_id "ENSE00001565053.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221345.2"; orig_coord_info "chr6,71126893,71127105,-"; Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 75398860 75399067 . - . gene_id "U3^ENSG00000221332.2"; transcript_id "ENST00000408405.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.34-201"; exon_number 1; exon_id "ENSE00001565040.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221332.2"; orig_coord_info "chr6,75398860,75399067,-"; Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 92119423 92119633 . + . gene_id "U3^ENSG00000200492.2"; transcript_id "ENST00000363622.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.5-201"; exon_number 1; exon_id "ENSE00001438385.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200492.2"; orig_coord_info "chr6,92119423,92119633,+"; Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 92790453 92790665 . + . gene_id "U3^ENSG00000221455.2"; transcript_id "ENST00000408528.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.36-201"; exon_number 1; exon_id "ENSE00001565163.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221455.2"; orig_coord_info "chr6,92790453,92790665,+"; Error, chr discrepancy in gtf info for chr7 ENSEMBL exon 10222797 10223011 . + . gene_id "U3^ENSG00000212422.2"; transcript_id "ENST00000391120.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.21-201"; exon_number 1; exon_id "ENSE00001508904.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212422.2"; orig_coord_info "chr7,10222797,10223011,+"; Error, chr discrepancy in gtf info for chr7 ENSEMBL exon 25264656 25264882 . + . gene_id "U3^ENSG00000202233.2"; transcript_id "ENST00000365363.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.13-201"; exon_number 1; exon_id "ENSE00001440126.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000202233.2"; orig_coord_info "chr7,25264656,25264882,+"; Error, chr discrepancy in gtf info for chr7 ENSEMBL exon 107999791 107999982 . - . gene_id "U3^ENSG00000238297.2"; transcript_id "ENST00000458938.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.43-201"; exon_number 1; exon_id "ENSE00001809260.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000238297.2"; orig_coord_info "chr7,107999791,107999982,-"; Error, chr discrepancy in gtf info for chr7 ENSEMBL exon 148389645 148389859 . + . gene_id "U3^ENSG00000199370.2"; transcript_id "ENST00000362500.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.1-201"; exon_number 1; exon_id "ENSE00001437263.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000199370.2"; orig_coord_info "chr7,148389645,148389859,+"; Error, chr discrepancy in gtf info for chr8 ENSEMBL exon 43378297 43378510 . + . gene_id "U3^ENSG00000201329.2"; transcript_id "ENST00000364459.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.9-201"; exon_number 1; exon_id "ENSE00001439222.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000201329.2"; orig_coord_info "chr8,43378297,43378510,+"; Error, chr discrepancy in gtf info for chr8 ENSEMBL exon 123180310 123180525 . - . gene_id "U3^ENSG00000221461.2"; transcript_id "ENST00000408534.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.37-201"; exon_number 1; exon_id "ENSE00001565169.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221461.2"; orig_coord_info "chr8,123180310,123180525,-"; Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 19598247 19598463 . + . gene_id "U3^ENSG00000200545.2"; transcript_id "ENST00000363675.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.7-201"; exon_number 1; exon_id "ENSE00001438438.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200545.2"; orig_coord_info "chr10,19598247,19598463,+"; Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 28408039 28408251 . - . gene_id "U3^ENSG00000222666.2"; transcript_id "ENST00000410734.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.42-201"; exon_number 1; exon_id "ENSE00001590552.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000222666.2"; orig_coord_info "chr10,28408039,28408251,-"; Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 32081764 32081973 . + . gene_id "U3^ENSG00000212551.2"; transcript_id "ENST00000391249.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.27-201"; exon_number 1; exon_id "ENSE00001509033.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212551.2"; orig_coord_info "chr11,32081764,32081973,+"; Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 63651296 63651499 . - . gene_id "U3^ENSG00000200693.2"; transcript_id "ENST00000363823.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.8-201"; exon_number 1; exon_id "ENSE00001438586.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200693.2"; orig_coord_info "chr14,63651296,63651499,-"; Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 91714915 91715130 . - . gene_id "U3^ENSG00000275154.1"; transcript_id "ENST00000363172.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.47-201"; exon_number 1; exon_id "ENSE00001807572.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000275154.1"; orig_coord_info "chr14,91714915,91715130,-"; Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 101145480 101145695 . - . gene_id "U3^ENSG00000277754.1"; transcript_id "ENST00000384034.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.51-201"; exon_number 1; exon_id "ENSE00001808913.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000277754.1"; orig_coord_info "chr14,101145480,101145695,-"; Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 36852640 36852859 . + . gene_id "U3^ENSG00000212511.2"; transcript_id "ENST00000391209.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.24-201"; exon_number 1; exon_id "ENSE00001508993.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212511.2"; orig_coord_info "chr15,36852640,36852859,+"; Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 69457941 69458149 . - . gene_id "U3^ENSG00000207119.2"; transcript_id "ENST00000384391.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.15-201"; exon_number 1; exon_id "ENSE00001499400.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000207119.2"; orig_coord_info "chr15,69457941,69458149,-"; Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 44025020 44025223 . - . gene_id "U3^ENSG00000221044.2"; transcript_id "ENST00000408117.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.32-201"; exon_number 1; exon_id "ENSE00001977749.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221044.2"; orig_coord_info "chr17,44025020,44025223,-"; Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 44303965 44304203 . + . gene_id "U3^ENSG00000221496.2"; transcript_id "ENST00000408569.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.38-201"; exon_number 1; exon_id "ENSE00001565204.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221496.2"; orig_coord_info "chr17,44303965,44304203,+"; Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 48382371 48382586 . - . gene_id "U3^ENSG00000200538.2"; transcript_id "ENST00000363668.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.6-201"; exon_number 1; exon_id "ENSE00001807711.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000200538.2"; orig_coord_info "chr17,48382371,48382586,-"; Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 58631641 58631836 . - . gene_id "U3^ENSG00000212195.2"; transcript_id "ENST00000390893.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.18-201"; exon_number 1; exon_id "ENSE00001508677.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212195.2"; orig_coord_info "chr17,58631641,58631836,-"; Error, chr discrepancy in gtf info for chr18 ENSEMBL exon 7995570 7995785 . + . gene_id "U3^ENSG00000199856.2"; transcript_id "ENST00000362986.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.3-201"; exon_number 1; exon_id "ENSE00001437749.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000199856.2"; orig_coord_info "chr18,7995570,7995785,+"; Error, chr discrepancy in gtf info for chr18 ENSEMBL exon 26689316 26689529 . - . gene_id "U3^ENSG00000275900.1"; transcript_id "ENST00000391065.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.48-201"; exon_number 1; exon_id "ENSE00001508849.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000275900.1"; orig_coord_info "chr18,26689316,26689529,-"; Error, chr discrepancy in gtf info for chr18 ENSEMBL exon 56957270 56957469 . + . gene_id "U3^ENSG00000212539.2"; transcript_id "ENST00000391237.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.26-201"; exon_number 1; exon_id "ENSE00001509021.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212539.2"; orig_coord_info "chr18,56957270,56957469,+"; Error, chr discrepancy in gtf info for chr19 ENSEMBL exon 49949316 49949527 . - . gene_id "U3^ENSG00000221125.2"; transcript_id "ENST00000408198.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.33-201"; exon_number 1; exon_id "ENSE00001564833.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000221125.2"; orig_coord_info "chr19,49949316,49949527,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 3384229 3384440 . + . gene_id "U3^ENSG00000201346.2"; transcript_id "ENST00000364476.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.10-201"; exon_number 1; exon_id "ENSE00001439239.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000201346.2"; orig_coord_info "chr20,3384229,3384440,+"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 16982831 16983033 . - . gene_id "U3^ENSG00000212165.2"; transcript_id "ENST00000390863.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.16-201"; exon_number 1; exon_id "ENSE00001508647.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212165.2"; orig_coord_info "chr20,16982831,16983033,-"; Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 29180425 29180639 . - . gene_id "U3^ENSG00000212479.2"; transcript_id "ENST00000391177.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.23-201"; exon_number 1; exon_id "ENSE00001508961.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212479.2"; orig_coord_info "chr21,29180425,29180639,-"; Error, chr discrepancy in gtf info for chrX ENSEMBL exon 69692956 69693155 . + . gene_id "U3^ENSG00000212434.2"; transcript_id "ENST00000391132.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.22-201"; exon_number 1; exon_id "ENSE00001508916.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212434.2"; orig_coord_info "chrX,69692956,69693155,+"; Error, chr discrepancy in gtf info for chrX ENSEMBL exon 72726122 72726337 . - . gene_id "U3^ENSG00000273788.1"; transcript_id "ENST00000365612.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.45-201"; exon_number 1; exon_id "ENSE00001806856.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000273788.1"; orig_coord_info "chrX,72726122,72726337,-"; Error, chr discrepancy in gtf info for chrX ENSEMBL exon 113944186 113944399 . - . gene_id "U3^ENSG00000201674.2"; transcript_id "ENST00000364804.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.12-201"; exon_number 1; exon_id "ENSE00001439567.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000201674.2"; orig_coord_info "chrX,113944186,113944399,-"; Error, chr discrepancy in gtf info for chrX ENSEMBL exon 122840426 122840645 . + . gene_id "U3^ENSG00000212321.2"; transcript_id "ENST00000391019.2"; gene_type "snoRNA"; gene_name "U3"; transcript_type "snoRNA"; transcript_name "U3.20-201"; exon_number 1; exon_id "ENSE00001508803.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U3^ENSG00000212321.2"; orig_coord_info "chrX,122840426,122840645,+"; Error - no gene spans 100M bases in length.... likely problem at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 589. main::get_gene_span_info("chr1\x{9}ENSEMBL\x{9}exon\x{9}116278606\x{9}116278821\x{9}.\x{9}+\x{9}.\x{9}gene_id \"U3^ENSG0"...) called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 417 main::get_gene_contig_gtf("chr1\x{9}ENSEMBL\x{9}exon\x{9}116278606\x{9}116278821\x{9}.\x{9}+\x{9}.\x{9}gene_id \"U3^ENSG0"..., "/tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir/ref_genome.fa") called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 214 eval {...} called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 210 Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf > /tmp/nxf.La7UuypYL0/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf > /tmp/nxf.La7UuypYL0/cytoBand.txt Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.La7UuypYL0/fi_workdir --reads "/tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.La7UuypYL0/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.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 03 21:00:30 ..... started STAR run Jun 03 21:00:30 ..... loading genome Jun 03 21:02:15 ... generating Suffix Array index Jun 03 21:06:19 ... completed Suffix Array index Jun 03 21:06:19 ..... processing annotations GTF Jun 03 21:06:19 ..... inserting junctions into the genome indices Jun 03 21:07:21 ..... started mapping Jun 03 22:08:57 ..... finished mapping Jun 03 22:08:58 ..... started sorting BAM Jun 03 22:09:01 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 68.60 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.La7UuypYL0/fi_workdir --reads "/tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 22:09:31 : INFO : Done. Execution Time = 0.44 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] 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[5270000] [5280000] [5290000] -done parsing /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'low complexity anchor region' => 31, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 4737, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 132, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 126, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 460, 'excessive soft clipping' => 31379, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4, 'seq-similar region overlap' => 15, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 26323, 'num genes matched < 2' => 61, ' ** passed ** ' => 18266, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 240, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 11, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 11796, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 93, 'exons hit < 2' => 22, 'per_id < 96' => 24648, 'small anchor length' => 47, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1 }; -writing fusion junction support info. Execution Time = 3.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: ABL2--CYCSP53 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] 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[316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] -fusion SPANNING read extraction for scaff: ABL2--PRRC2C [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: BAD--AC024405.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: BAD--OR4C50P [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] -fusion SPANNING read extraction for scaff: CARS1--OSBPL5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: CEP89--RPS3AP50 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: CEP89--AKR1B1P7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] -fusion SPANNING read extraction for scaff: CIZ1--GOLGA2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] -fusion SPANNING read extraction for scaff: COG8--LSM12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: COQ6--SCG2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: COQ6--MLXP1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] -fusion SPANNING read extraction for scaff: CYB5B--MPP2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] -fusion SPANNING read extraction for scaff: CYLD--NKD1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] -fusion SPANNING read extraction for scaff: DHX9--LINC01720 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] -fusion SPANNING read extraction for scaff: EXPH5--TSPAN18 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] -fusion SPANNING read extraction for scaff: EXT2--EXPH5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] -fusion SPANNING read extraction for scaff: ITPR2--TM7SF3 [1000] [2000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] -fusion SPANNING read extraction for scaff: LAMTOR2--HDGF [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] -fusion SPANNING read extraction for scaff: MARK2--CCDC82 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: MED21--AC023051.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: MRPS14--LINC01724 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] -fusion SPANNING read extraction for scaff: PAPOLA--AK7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] -fusion SPANNING read extraction for scaff: PCCA--CLYBL [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PGAP1--ANKRD44 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: PTPRK--GRID2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] 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[708000] [709000] [710000] [711000] [712000] [713000] [714000] [715000] [716000] [717000] [718000] [719000] [720000] [721000] [722000] [723000] [724000] [725000] [726000] [727000] [728000] [729000] [730000] [731000] [732000] [733000] [734000] [735000] [736000] [737000] [738000] [739000] [740000] [741000] [742000] [743000] [744000] [745000] [746000] [747000] [748000] [749000] [750000] [751000] [752000] [753000] [754000] [755000] [756000] [757000] [758000] [759000] [760000] [761000] [762000] [763000] [764000] [765000] [766000] [767000] [768000] [769000] [770000] [771000] [772000] [773000] [774000] [775000] [776000] [777000] [778000] [779000] [780000] [781000] [782000] [783000] [784000] [785000] [786000] [787000] [788000] [789000] [790000] [791000] [792000] [793000] [794000] [795000] [796000] [797000] [798000] [799000] [800000] [801000] [802000] [803000] [804000] [805000] [806000] [807000] [808000] [809000] [810000] [811000] [812000] [813000] [814000] [815000] [816000] [817000] [818000] [819000] [820000] [821000] [822000] [823000] [824000] [825000] [826000] [827000] [828000] [829000] [830000] [831000] [832000] [833000] [834000] [835000] [836000] [837000] [838000] [839000] [840000] [841000] [842000] [843000] [844000] [845000] [846000] [847000] [848000] [849000] [850000] [851000] [852000] [853000] [854000] [855000] [856000] [857000] [858000] [859000] [860000] [861000] [862000] [863000] [864000] [865000] [866000] [867000] [868000] [869000] [870000] [871000] [872000] [873000] [874000] [875000] [876000] [877000] [878000] [879000] [880000] [881000] [882000] [883000] [884000] [885000] [886000] [887000] [888000] [889000] [890000] [891000] [892000] [893000] [894000] [895000] [896000] [897000] [898000] [899000] [900000] [901000] [902000] [903000] [904000] [905000] [906000] [907000] [908000] [909000] [910000] [911000] [912000] [913000] [914000] [915000] [916000] [917000] [918000] [919000] [920000] [921000] [922000] [923000] [924000] [925000] [926000] [927000] [928000] [929000] [930000] [931000] [932000] [933000] [934000] [935000] [936000] [937000] [938000] [939000] [940000] [941000] [942000] [943000] [944000] [945000] [946000] [947000] [948000] [949000] [950000] [951000] [952000] [953000] [954000] [955000] [956000] [957000] [958000] [959000] [960000] [961000] [962000] [963000] [964000] [965000] [966000] [967000] [968000] [969000] [970000] [971000] [972000] [973000] [974000] [975000] [976000] [977000] [978000] [979000] [980000] [981000] [982000] [983000] [984000] [985000] [986000] [987000] [988000] [989000] [990000] [991000] [992000] [993000] [994000] [995000] [996000] [997000] [998000] [999000] [1000000] [1001000] [1002000] [1003000] [1004000] [1005000] [1006000] [1007000] [1008000] [1009000] [1010000] [1011000] [1012000] [1013000] [1014000] [1015000] [1016000] [1017000] [1018000] [1019000] [1020000] [1021000] [1022000] [1023000] [1024000] [1025000] [1026000] [1027000] [1028000] [1029000] [1030000] [1031000] [1032000] [1033000] [1034000] [1035000] [1036000] [1037000] [1038000] [1039000] [1040000] [1041000] [1042000] [1043000] [1044000] [1045000] [1046000] [1047000] [1048000] [1049000] [1050000] [1051000] [1052000] [1053000] [1054000] [1055000] [1056000] [1057000] [1058000] [1059000] [1060000] [1061000] [1062000] [1063000] [1064000] [1065000] [1066000] [1067000] [1068000] [1069000] [1070000] [1071000] [1072000] [1073000] [1074000] [1075000] [1076000] [1077000] [1078000] [1079000] [1080000] [1081000] [1082000] [1083000] [1084000] [1085000] [1086000] [1087000] [1088000] [1089000] [1090000] [1091000] [1092000] [1093000] [1094000] [1095000] [1096000] [1097000] [1098000] [1099000] [1100000] [1101000] [1102000] [1103000] [1104000] [1105000] [1106000] [1107000] [1108000] [1109000] [1110000] [1111000] [1112000] [1113000] [1114000] [1115000] [1116000] [1117000] [1118000] [1119000] [1120000] [1121000] [1122000] [1123000] [1124000] [1125000] [1126000] [1127000] [1128000] [1129000] [1130000] [1131000] [1132000] [1133000] [1134000] [1135000] [1136000] [1137000] [1138000] [1139000] [1140000] [1141000] [1142000] [1143000] [1144000] [1145000] [1146000] [1147000] [1148000] [1149000] [1150000] [1151000] [1152000] [1153000] [1154000] [1155000] [1156000] [1157000] [1158000] [1159000] [1160000] [1161000] [1162000] [1163000] [1164000] [1165000] [1166000] [1167000] [1168000] [1169000] [1170000] [1171000] [1172000] [1173000] [1174000] [1175000] [1176000] [1177000] [1178000] [1179000] [1180000] [1181000] [1182000] [1183000] [1184000] [1185000] [1186000] [1187000] [1188000] [1189000] [1190000] [1191000] [1192000] [1193000] [1194000] [1195000] [1196000] [1197000] [1198000] [1199000] [1200000] [1201000] [1202000] [1203000] [1204000] [1205000] [1206000] [1207000] [1208000] [1209000] [1210000] [1211000] [1212000] [1213000] [1214000] [1215000] [1216000] [1217000] [1218000] [1219000] [1220000] [1221000] [1222000] [1223000] [1224000] [1225000] [1226000] [1227000] [1228000] [1229000] [1230000] [1231000] [1232000] [1233000] [1234000] [1235000] [1236000] [1237000] [1238000] [1239000] [1240000] [1241000] [1242000] [1243000] [1244000] [1245000] [1246000] [1247000] [1248000] [1249000] [1250000] [1251000] [1252000] [1253000] [1254000] [1255000] [1256000] [1257000] [1258000] [1259000] [1260000] [1261000] [1262000] [1263000] [1264000] [1265000] [1266000] [1267000] [1268000] [1269000] [1270000] [1271000] [1272000] [1273000] [1274000] [1275000] [1276000] [1277000] [1278000] [1279000] [1280000] [1281000] [1282000] [1283000] [1284000] [1285000] [1286000] [1287000] [1288000] [1289000] [1290000] [1291000] [1292000] [1293000] [1294000] [1295000] [1296000] [1297000] [1298000] [1299000] [1300000] [1301000] [1302000] -fusion SPANNING read extraction for scaff: RANBP2--LIMS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] -fusion SPANNING read extraction for scaff: RBM39--LINC01393 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] -fusion SPANNING read extraction for scaff: SFMBT1--TKT [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] -fusion SPANNING read extraction for scaff: SIPA1L2--ANKRD29 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] -fusion SPANNING read extraction for scaff: SNX14--SYNCRIP [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] -fusion SPANNING read extraction for scaff: STARD13--AL139383.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] -fusion SPANNING read extraction for scaff: TECPR1--BAIAP2L1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] -fusion SPANNING read extraction for scaff: TECPR1--PPIAP82 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] -fusion SPANNING read extraction for scaff: TMEM241--NPC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: TMEM241--ANKRD29 [1000] [2000] -fusion SPANNING read extraction for scaff: TSPAN18--MED28P5 [1000] [2000] -fusion SPANNING read extraction for scaff: TSPAN18--AP001836.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] -fusion SPANNING read extraction for scaff: USP50--TRPM7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] -fusion SPANNING read extraction for scaff: UTRN--STX11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] -fusion SPANNING read extraction for scaff: VOPP1--FKBP9P1 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 52958, 'lacks exon overlap' => 49359 }; Execution Time = 7.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -11379.378474 EM: Round [1] log likelihood: -11379.338033 EM: Round [2] log likelihood: -11379.331829 EM: Round [3] log likelihood: -11379.325675 EM: Round [4] log likelihood: -11379.319569 EM: Round [5] log likelihood: -11379.313510 EM: Round [6] log likelihood: -11379.307496 EM: Round [7] log likelihood: -11379.301528 EM: Round [8] log likelihood: -11379.295604 EM: Round [9] log likelihood: -11379.289725 EM: Round [10] log likelihood: -11379.283889 EM: Round [11] log likelihood: -11379.278097 EM: Round [12] log likelihood: -11379.272346 EM: Round [13] log likelihood: -11379.266638 EM: Round [14] log likelihood: -11379.260971 EM: Round [15] log likelihood: -11379.255345 EM: Round [16] log likelihood: -11379.249759 EM: Round [17] log likelihood: -11379.244213 EM: Round [18] log likelihood: -11379.238706 EM: Round [19] log likelihood: -11379.233238 EM: Round [20] log likelihood: -11379.227808 EM: Round [21] log likelihood: -11379.222416 EM: Round [22] log likelihood: -11379.217061 EM: Round [23] log likelihood: -11379.211744 EM: Round [24] log likelihood: -11379.206462 EM: Round [25] log likelihood: -11379.201217 EM: Round [26] log likelihood: -11379.196008 EM: Round [27] log likelihood: -11379.190833 EM: Round [28] log likelihood: -11379.185693 EM: Round [29] log likelihood: -11379.180588 EM: Round [30] log likelihood: -11379.175517 EM: Round [31] log likelihood: -11379.170479 EM: Round [32] log likelihood: -11379.165474 EM: Round [33] log likelihood: -11379.160502 EM: Round [34] log likelihood: -11379.155563 EM: Round [35] log likelihood: -11379.150655 EM: Round [36] log likelihood: -11379.145779 EM: Round [37] log likelihood: -11379.140935 EM: Round [38] log likelihood: -11379.136121 EM: Round [39] log likelihood: -11379.131338 EM: Round [40] log likelihood: -11379.126585 EM: Round [41] log likelihood: -11379.121862 EM: Round [42] log likelihood: -11379.117169 EM: Round [43] log likelihood: -11379.112505 EM: Round [44] log likelihood: -11379.107870 EM: Round [45] log likelihood: -11379.103264 EM: Round [46] log likelihood: -11379.098686 EM: Round [47] log likelihood: -11379.094136 EM: Round [48] log likelihood: -11379.089614 EM: Round [49] log likelihood: -11379.085120 EM: Round [50] log likelihood: -11379.080652 EM: Round [51] log likelihood: -11379.076211 EM: Round [52] log likelihood: -11379.071797 EM: Round [53] log likelihood: -11379.067410 EM: Round [54] log likelihood: -11379.063048 EM: Round [55] log likelihood: -11379.058712 EM: Round [56] log likelihood: -11379.054402 EM: Round [57] log likelihood: -11379.050117 EM: Round [58] log likelihood: -11379.045857 EM: Round [59] log likelihood: -11379.041621 EM: Round [60] log likelihood: -11379.037410 EM: Round [61] log likelihood: -11379.033224 EM: Round [62] log likelihood: -11379.029061 EM: Round [63] log likelihood: -11379.024923 EM: Round [64] log likelihood: -11379.020808 EM: Round [65] log likelihood: -11379.016716 EM: Round [66] log likelihood: -11379.012647 EM: Round [67] log likelihood: -11379.008601 EM: Round [68] log likelihood: -11379.004578 EM: Round [69] log likelihood: -11379.000577 EM: Round [70] log likelihood: -11378.996599 EM: Round [71] log likelihood: -11378.992642 EM: Round [72] log likelihood: -11378.988707 EM: Round [73] log likelihood: -11378.984794 EM: Round [74] log likelihood: -11378.980902 EM: Round [75] log likelihood: -11378.977032 EM: Round [76] log likelihood: -11378.973182 EM: Round [77] log likelihood: -11378.969354 EM: Round [78] log likelihood: -11378.965546 EM: Round [79] log likelihood: -11378.961758 EM: Round [80] log likelihood: -11378.957991 EM: Round [81] log likelihood: -11378.954243 EM: Round [82] log likelihood: -11378.950516 EM: Round [83] log likelihood: -11378.946808 EM: Round [84] log likelihood: -11378.943120 EM: Round [85] log likelihood: -11378.939451 EM: Round [86] log likelihood: -11378.935801 EM: Round [87] log likelihood: -11378.932170 EM: Round [88] log likelihood: -11378.928558 EM: Round [89] log likelihood: -11378.924965 EM: Round [90] log likelihood: -11378.921390 EM: Round [91] log likelihood: -11378.917834 EM: Round [92] log likelihood: -11378.914296 EM: Round [93] log likelihood: -11378.910776 EM: Round [94] log likelihood: -11378.907273 EM: Round [95] log likelihood: -11378.903789 EM: Round [96] log likelihood: -11378.900322 EM: Round [97] log likelihood: -11378.896872 EM: Round [98] log likelihood: -11378.893440 EM: Round [99] log likelihood: -11378.890025 EM: Round [100] log likelihood: -11378.886627 EM: Round [101] log likelihood: -11378.883246 EM: Round [102] log likelihood: -11378.879881 EM: Round [103] log likelihood: -11378.876533 EM: Round [104] log likelihood: -11378.873202 EM: Round [105] log likelihood: -11378.869886 EM: Round [106] log likelihood: -11378.866587 EM: Round [107] log likelihood: -11378.863304 EM: Round [108] log likelihood: -11378.860037 EM: Round [109] log likelihood: -11378.856786 EM: Round [110] log likelihood: -11378.853550 EM: Round [111] log likelihood: -11378.850330 EM: Round [112] log likelihood: -11378.847125 EM: Round [113] log likelihood: -11378.843935 EM: Round [114] log likelihood: -11378.840761 EM: Round [115] log likelihood: -11378.837602 EM: Round [116] log likelihood: -11378.834457 EM: Round [117] log likelihood: -11378.831328 EM: Round [118] log likelihood: -11378.828213 EM: Round [119] log likelihood: -11378.825112 EM: Round [120] log likelihood: -11378.822026 EM: Round [121] log likelihood: -11378.818955 EM: Round [122] log likelihood: -11378.815898 EM: Round [123] log likelihood: -11378.812854 EM: Round [124] log likelihood: -11378.809825 EM: Round [125] log likelihood: -11378.806810 EM: Round [126] log likelihood: -11378.803808 EM: Round [127] log likelihood: -11378.800821 EM: Round [128] log likelihood: -11378.797847 EM: Round [129] log likelihood: -11378.794886 EM: Round [130] log likelihood: -11378.791939 EM: Round [131] log likelihood: -11378.789005 EM: Round [132] log likelihood: -11378.786084 EM: Round [133] log likelihood: -11378.783176 EM: Round [134] log likelihood: -11378.780281 EM: Round [135] log likelihood: -11378.777400 EM: Round [136] log likelihood: -11378.774531 EM: Round [137] log likelihood: -11378.771675 EM: Round [138] log likelihood: -11378.768831 EM: Round [139] log likelihood: -11378.766000 EM: Round [140] log likelihood: -11378.763181 EM: Round [141] log likelihood: -11378.760375 EM: Round [142] log likelihood: -11378.757581 EM: Round [143] log likelihood: -11378.754799 EM: Round [144] log likelihood: -11378.752029 EM: Round [145] log likelihood: -11378.749272 EM: Round [146] log likelihood: -11378.746526 EM: Round [147] log likelihood: -11378.743792 EM: Round [148] log likelihood: -11378.741070 EM: Round [149] log likelihood: -11378.738359 EM: Round [150] log likelihood: -11378.735660 EM: Round [151] log likelihood: -11378.732973 EM: Round [152] log likelihood: -11378.730297 EM: Round [153] log likelihood: -11378.727632 EM: Round [154] log likelihood: -11378.724979 EM: Round [155] log likelihood: -11378.722337 EM: Round [156] log likelihood: -11378.719706 EM: Round [157] log likelihood: -11378.717086 EM: Round [158] log likelihood: -11378.714477 EM: Round [159] log likelihood: -11378.711879 EM: Round [160] log likelihood: -11378.709291 EM: Round [161] log likelihood: -11378.706715 EM: Round [162] log likelihood: -11378.704149 EM: Round [163] log likelihood: -11378.701594 EM: Round [164] log likelihood: -11378.699049 EM: Round [165] log likelihood: -11378.696515 EM: Round [166] log likelihood: -11378.693991 EM: Round [167] log likelihood: -11378.691477 EM: Round [168] log likelihood: -11378.688974 EM: Round [169] log likelihood: -11378.686481 EM: Round [170] log likelihood: -11378.683998 EM: Round [171] log likelihood: -11378.681525 EM: Round [172] log likelihood: -11378.679062 EM: Round [173] log likelihood: -11378.676609 EM: Round [174] log likelihood: -11378.674166 EM: Round [175] log likelihood: -11378.671732 EM: Round [176] log likelihood: -11378.669309 EM: Round [177] log likelihood: -11378.666895 EM: Round [178] log likelihood: -11378.664490 EM: Round [179] log likelihood: -11378.662096 EM: Round [180] log likelihood: -11378.659710 EM: Round [181] log likelihood: -11378.657334 EM: Round [182] log likelihood: -11378.654968 EM: Round [183] log likelihood: -11378.652611 EM: Round [184] log likelihood: -11378.650263 EM: Round [185] log likelihood: -11378.647924 EM: Round [186] log likelihood: -11378.645595 EM: Round [187] log likelihood: -11378.643274 EM: Round [188] log likelihood: -11378.640963 EM: Round [189] log likelihood: -11378.638660 EM: Round [190] log likelihood: -11378.636367 EM: Round [191] log likelihood: -11378.634082 EM: Round [192] log likelihood: -11378.631806 EM: Round [193] log likelihood: -11378.629539 EM: Round [194] log likelihood: -11378.627280 EM: Round [195] log likelihood: -11378.625030 EM: Round [196] log likelihood: -11378.622789 EM: Round [197] log likelihood: -11378.620556 EM: Round [198] log likelihood: -11378.618332 EM: Round [199] log likelihood: -11378.616117 EM: Round [200] log likelihood: -11378.613909 EM: Round [201] log likelihood: -11378.611710 EM: Round [202] log likelihood: -11378.609519 EM: Round [203] log likelihood: -11378.607337 EM: Round [204] log likelihood: -11378.605162 EM: Round [205] log likelihood: -11378.602996 EM: Round [206] log likelihood: -11378.600838 EM: Round [207] log likelihood: -11378.598688 EM: Round [208] log likelihood: -11378.596546 EM: Round [209] log likelihood: -11378.594412 EM: Round [210] log likelihood: -11378.592286 EM: Round [211] log likelihood: -11378.590167 EM: Round [212] log likelihood: -11378.588057 EM: Round [213] log likelihood: -11378.585954 EM: Round [214] log likelihood: -11378.583859 EM: Round [215] log likelihood: -11378.581772 EM: Round [216] log likelihood: -11378.579692 EM: Round [217] log likelihood: -11378.577620 EM: Round [218] log likelihood: -11378.575555 EM: Round [219] log likelihood: -11378.573498 EM: Round [220] log likelihood: -11378.571449 EM: Round [221] log likelihood: -11378.569407 EM: Round [222] log likelihood: -11378.567372 EM: Round [223] log likelihood: -11378.565344 EM: Round [224] log likelihood: -11378.563324 EM: Round [225] log likelihood: -11378.561311 EM: Round [226] log likelihood: -11378.559306 EM: Round [227] log likelihood: -11378.557307 EM: Round [228] log likelihood: -11378.555316 EM: Round [229] log likelihood: -11378.553331 EM: Round [230] log likelihood: -11378.551354 EM: Round [231] log likelihood: -11378.549384 EM: Round [232] log likelihood: -11378.547421 EM: Round [233] log likelihood: -11378.545464 EM: Round [234] log likelihood: -11378.543515 EM: Round [235] log likelihood: -11378.541572 EM: Round [236] log likelihood: -11378.539637 EM: Round [237] log likelihood: -11378.537708 EM: Round [238] log likelihood: -11378.535785 EM: Round [239] log likelihood: -11378.533870 EM: Round [240] log likelihood: -11378.531961 EM: Round [241] log likelihood: -11378.530059 EM: Round [242] log likelihood: -11378.528163 EM: Round [243] log likelihood: -11378.526275 EM: Round [244] log likelihood: -11378.524392 EM: Round [245] log likelihood: -11378.522516 EM: Round [246] log likelihood: -11378.520647 EM: Round [247] log likelihood: -11378.518784 EM: Round [248] log likelihood: -11378.516927 EM: Round [249] log likelihood: -11378.515077 EM: Round [250] log likelihood: -11378.513233 EM: Round [251] log likelihood: -11378.511395 EM: Round [252] log likelihood: -11378.509564 EM: Round [253] log likelihood: -11378.507739 EM: Round [254] log likelihood: -11378.505920 EM: Round [255] log likelihood: -11378.504107 EM: Round [256] log likelihood: -11378.502300 EM: Round [257] log likelihood: -11378.500500 EM: Round [258] log likelihood: -11378.498705 EM: Round [259] log likelihood: -11378.496917 EM: Round [260] log likelihood: -11378.495135 EM: Round [261] log likelihood: -11378.493358 EM: Round [262] log likelihood: -11378.491588 EM: Round [263] log likelihood: -11378.489823 EM: Round [264] log likelihood: -11378.488065 EM: Round [265] log likelihood: -11378.486312 EM: Round [266] log likelihood: -11378.484565 EM: Round [267] log likelihood: -11378.482824 EM: Round [268] log likelihood: -11378.481088 EM: Round [269] log likelihood: -11378.479359 EM: Round [270] log likelihood: -11378.477635 EM: Round [271] log likelihood: -11378.475916 EM: Round [272] log likelihood: -11378.474204 EM: Round [273] log likelihood: -11378.472497 EM: Round [274] log likelihood: -11378.470795 EM: Round [275] log likelihood: -11378.469100 EM: Round [276] log likelihood: -11378.467409 EM: Round [277] log likelihood: -11378.465724 EM: Round [278] log likelihood: -11378.464045 EM: Round [279] log likelihood: -11378.462371 EM: Round [280] log likelihood: -11378.460703 EM: Round [281] log likelihood: -11378.459040 EM: Round [282] log likelihood: -11378.457382 EM: Round [283] log likelihood: -11378.455730 EM: Round [284] log likelihood: -11378.454083 EM: Round [285] log likelihood: -11378.452442 EM: Round [286] log likelihood: -11378.450805 EM: Round [287] log likelihood: -11378.449174 EM: Round [288] log likelihood: -11378.447549 EM: Round [289] log likelihood: -11378.445928 EM: Round [290] log likelihood: -11378.444312 EM: Round [291] log likelihood: -11378.442702 EM: Round [292] log likelihood: -11378.441097 EM: Round [293] log likelihood: -11378.439497 EM: Round [294] log likelihood: -11378.437902 EM: Round [295] log likelihood: -11378.436312 EM: Round [296] log likelihood: -11378.434727 EM: Round [297] log likelihood: -11378.433147 EM: Round [298] log likelihood: -11378.431572 EM: Round [299] log likelihood: -11378.430002 EM: Round [300] log likelihood: -11378.428437 EM: Round [301] log likelihood: -11378.426877 EM: Round [302] log likelihood: -11378.425322 EM: Round [303] log likelihood: -11378.423771 EM: Round [304] log likelihood: -11378.422226 EM: Round [305] log likelihood: -11378.420685 EM: Round [306] log likelihood: -11378.419149 EM: Round [307] log likelihood: -11378.417618 EM: Round [308] log likelihood: -11378.416092 EM: Round [309] log likelihood: -11378.414570 EM: 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-11378.117676 EM: Round [592] log likelihood: -11378.116954 EM: Round [593] log likelihood: -11378.116233 EM: Round [594] log likelihood: -11378.115515 EM: Round [595] log likelihood: -11378.114798 EM: Round [596] log likelihood: -11378.114082 EM: Round [597] log likelihood: -11378.113368 EM: Round [598] log likelihood: -11378.112656 EM: Round [599] log likelihood: -11378.111946 EM: Round [600] log likelihood: -11378.111237 EM: Round [601] log likelihood: -11378.110529 EM: Round [602] log likelihood: -11378.109824 EM: Round [603] log likelihood: -11378.109120 EM: Round [604] log likelihood: -11378.108417 EM: Round [605] log likelihood: -11378.107716 EM: Round [606] log likelihood: -11378.107017 EM: Round [607] log likelihood: -11378.106320 EM: Round [608] log likelihood: -11378.105623 EM: Round [609] log likelihood: -11378.104929 EM: Round [610] log likelihood: -11378.104236 EM: Round [611] log likelihood: -11378.103545 EM: Round [612] log likelihood: -11378.102855 EM: Round [613] log 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Round [635] log likelihood: -11378.087413 EM: Round [636] log likelihood: -11378.086759 EM: Round [637] log likelihood: -11378.086107 EM: Round [638] log likelihood: -11378.085457 EM: Round [639] log likelihood: -11378.084807 EM: Round [640] log likelihood: -11378.084160 EM: Round [641] log likelihood: -11378.083514 EM: Round [642] log likelihood: -11378.082869 EM: Round [643] log likelihood: -11378.082225 EM: Round [644] log likelihood: -11378.081583 EM: Round [645] log likelihood: -11378.080943 EM: Round [646] log likelihood: -11378.080304 EM: Round [647] log likelihood: -11378.079666 EM: Round [648] log likelihood: -11378.079030 EM: Round [649] log likelihood: -11378.078395 EM: Round [650] log likelihood: -11378.077762 EM: Round [651] log likelihood: -11378.077130 EM: Round [652] log likelihood: -11378.076499 EM: Round [653] log likelihood: -11378.075870 EM: Round [654] log likelihood: -11378.075242 EM: Round [655] log likelihood: -11378.074615 EM: Round [656] log likelihood: -11378.073990 EM: Round [657] log likelihood: -11378.073367 EM: Round [658] log likelihood: -11378.072744 EM: Round [659] log likelihood: -11378.072123 EM: Round [660] log likelihood: -11378.071504 EM: Round [661] log likelihood: -11378.070885 EM: Round [662] log likelihood: -11378.070268 EM: Round [663] log likelihood: -11378.069653 EM: Round [664] log likelihood: -11378.069039 EM: Round [665] log likelihood: -11378.068426 EM: Round [666] log likelihood: -11378.067814 EM: Round [667] log likelihood: -11378.067204 EM: Round [668] log likelihood: -11378.066595 EM: Round [669] log likelihood: -11378.065988 EM: Round [670] log likelihood: -11378.065382 EM: Round [671] log likelihood: -11378.064777 EM: Round [672] log likelihood: -11378.064173 EM: Round [673] log likelihood: -11378.063571 EM: Round [674] log likelihood: -11378.062970 EM: Round [675] log likelihood: -11378.062371 EM: Round [676] log likelihood: -11378.061772 EM: Round [677] log likelihood: -11378.061175 EM: Round [678] log 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-11378.036145 EM: Round [722] log likelihood: -11378.035603 EM: Round [723] log likelihood: -11378.035062 EM: Round [724] log likelihood: -11378.034523 EM: Round [725] log likelihood: -11378.033984 EM: Round [726] log likelihood: -11378.033447 EM: Round [727] log likelihood: -11378.032911 EM: Round [728] log likelihood: -11378.032376 EM: Round [729] log likelihood: -11378.031842 EM: Round [730] log likelihood: -11378.031309 EM: Round [731] log likelihood: -11378.030777 EM: Round [732] log likelihood: -11378.030246 EM: Round [733] log likelihood: -11378.029717 EM: Round [734] log likelihood: -11378.029189 EM: Round [735] log likelihood: -11378.028661 EM: Round [736] log likelihood: -11378.028135 EM: Round [737] log likelihood: -11378.027610 EM: Round [738] log likelihood: -11378.027086 EM: Round [739] log likelihood: -11378.026564 EM: Round [740] log likelihood: -11378.026042 EM: Round [741] log likelihood: -11378.025521 EM: Round [742] log likelihood: -11378.025002 EM: Round [743] log likelihood: -11378.024483 EM: Round [744] log likelihood: -11378.023966 EM: Round [745] log likelihood: -11378.023450 EM: Round [746] log likelihood: -11378.022935 EM: Round [747] log likelihood: -11378.022421 EM: Round [748] log likelihood: -11378.021908 EM: Round [749] log likelihood: -11378.021396 EM: Round [750] log likelihood: -11378.020885 EM: Round [751] log likelihood: -11378.020375 EM: Round [752] log likelihood: -11378.019866 EM: Round [753] log likelihood: -11378.019358 EM: Round [754] log likelihood: -11378.018852 EM: Round [755] log likelihood: -11378.018346 EM: Round [756] log likelihood: -11378.017842 EM: Round [757] log likelihood: -11378.017338 EM: Round [758] log likelihood: -11378.016836 EM: Round [759] log likelihood: -11378.016335 EM: Round [760] log likelihood: -11378.015834 EM: Round [761] log likelihood: -11378.015335 EM: Round [762] log likelihood: -11378.014837 EM: Round [763] log likelihood: -11378.014339 EM: Round [764] log likelihood: -11378.013843 EM: Round [765] log likelihood: -11378.013348 EM: Round [766] log likelihood: -11378.012854 EM: Round [767] log likelihood: -11378.012361 EM: Round [768] log likelihood: -11378.011869 EM: Round [769] log likelihood: -11378.011378 EM: Round [770] log likelihood: -11378.010888 EM: Round [771] log likelihood: -11378.010399 EM: Round [772] log likelihood: -11378.009911 EM: Round [773] log likelihood: -11378.009424 EM: Round [774] log likelihood: -11378.008938 EM: Round [775] log likelihood: -11378.008453 EM: Round [776] log likelihood: -11378.007969 EM: Round [777] log likelihood: -11378.007486 EM: Round [778] log likelihood: -11378.007004 EM: Round [779] log likelihood: -11378.006523 EM: Round [780] log likelihood: -11378.006043 EM: Round [781] log likelihood: -11378.005564 EM: Round [782] log likelihood: -11378.005086 EM: Round [783] log likelihood: -11378.004608 EM: Round [784] log likelihood: -11378.004132 EM: Round [785] log likelihood: -11378.003657 EM: Round [786] log likelihood: -11378.003183 EM: Round [787] log likelihood: -11378.002710 EM: Round [788] log likelihood: -11378.002238 EM: Round [789] log likelihood: -11378.001767 EM: Round [790] log likelihood: -11378.001296 EM: Round [791] log likelihood: -11378.000827 EM: Round [792] log likelihood: -11378.000359 EM: Round [793] log likelihood: -11377.999891 EM: Round [794] log likelihood: -11377.999425 EM: Round [795] log likelihood: -11377.998959 EM: Round [796] log likelihood: -11377.998495 EM: Round [797] log likelihood: -11377.998031 EM: Round [798] log likelihood: -11377.997569 EM: Round [799] log likelihood: -11377.997107 EM: Round [800] log likelihood: -11377.996646 EM: Round [801] log likelihood: -11377.996187 EM: Round [802] log likelihood: -11377.995728 EM: Round [803] log likelihood: -11377.995270 EM: Round [804] log likelihood: -11377.994813 EM: Round [805] log likelihood: -11377.994357 EM: Round [806] log likelihood: -11377.993902 EM: Round [807] log likelihood: -11377.993447 EM: Round [808] log likelihood: -11377.992994 EM: Round [809] log likelihood: -11377.992542 EM: Round [810] log likelihood: -11377.992090 EM: Round [811] log likelihood: -11377.991640 EM: Round [812] log likelihood: -11377.991190 EM: Round [813] log likelihood: -11377.990742 EM: Round [814] log likelihood: -11377.990294 EM: Round [815] log likelihood: -11377.989847 EM: Round [816] log likelihood: -11377.989401 EM: Round [817] log likelihood: -11377.988956 EM: Round [818] log likelihood: -11377.988512 EM: Round [819] log likelihood: -11377.988068 EM: Round [820] log likelihood: -11377.987626 EM: Round [821] log likelihood: -11377.987185 EM: Round [822] log likelihood: -11377.986744 EM: Round [823] log likelihood: -11377.986304 EM: Round [824] log likelihood: -11377.985865 EM: Round [825] log likelihood: -11377.985427 EM: Round [826] log likelihood: -11377.984990 EM: Round [827] log likelihood: -11377.984554 EM: Round [828] log likelihood: -11377.984119 EM: Round [829] log likelihood: -11377.983685 EM: Round [830] log likelihood: -11377.983251 EM: Round [831] log likelihood: -11377.982818 EM: Round [832] log likelihood: -11377.982387 EM: Round [833] log likelihood: -11377.981956 EM: Round [834] log likelihood: -11377.981526 EM: Round [835] log likelihood: -11377.981096 EM: Round [836] log likelihood: -11377.980668 EM: Round [837] log likelihood: -11377.980241 EM: Round [838] log likelihood: -11377.979814 EM: Round [839] log likelihood: -11377.979388 EM: Round [840] log likelihood: -11377.978963 EM: Round [841] log likelihood: -11377.978539 EM: Round [842] log likelihood: -11377.978116 EM: Round [843] log likelihood: -11377.977694 EM: Round [844] log likelihood: -11377.977272 EM: Round [845] log likelihood: -11377.976852 EM: Round [846] log likelihood: -11377.976432 EM: Round [847] log likelihood: -11377.976013 EM: Round [848] log likelihood: -11377.975595 EM: Round [849] log likelihood: -11377.975177 EM: Round [850] log likelihood: -11377.974761 EM: Round [851] log likelihood: -11377.974345 EM: Round [852] log likelihood: -11377.973930 EM: Round [853] log likelihood: -11377.973516 EM: Round [854] log likelihood: -11377.973103 EM: Round [855] log likelihood: -11377.972691 EM: Round [856] log likelihood: -11377.972279 EM: Round [857] log likelihood: -11377.971869 EM: Round [858] log likelihood: -11377.971459 EM: Round [859] log likelihood: -11377.971050 EM: Round [860] log likelihood: -11377.970641 EM: Round [861] log likelihood: -11377.970234 EM: Round [862] log likelihood: -11377.969827 EM: Round [863] log likelihood: -11377.969421 EM: Round [864] log likelihood: -11377.969016 EM: Round [865] log likelihood: -11377.968612 EM: Round [866] log likelihood: -11377.968209 EM: Round [867] log likelihood: -11377.967806 EM: Round [868] log likelihood: -11377.967404 EM: Round [869] log likelihood: -11377.967003 EM: Round [870] log likelihood: -11377.966603 EM: Round [871] log likelihood: -11377.966203 EM: Round [872] log likelihood: -11377.965805 EM: Round [873] log likelihood: -11377.965407 EM: Round [874] log likelihood: -11377.965010 EM: Round [875] log likelihood: -11377.964614 EM: Round [876] log likelihood: -11377.964218 EM: Round [877] log likelihood: -11377.963823 EM: Round [878] log likelihood: -11377.963429 EM: Round [879] log likelihood: -11377.963036 EM: Round [880] log likelihood: -11377.962644 EM: Round [881] log likelihood: -11377.962252 EM: Round [882] log likelihood: -11377.961861 EM: Round [883] log likelihood: -11377.961471 EM: Round [884] log likelihood: -11377.961082 EM: Round [885] log likelihood: -11377.960693 EM: Round [886] log likelihood: -11377.960306 EM: Round [887] log likelihood: -11377.959919 EM: Round [888] log likelihood: -11377.959532 EM: Round [889] log likelihood: -11377.959147 EM: Round [890] log likelihood: -11377.958762 EM: Round [891] log likelihood: -11377.958378 EM: Round [892] log likelihood: -11377.957995 EM: Round [893] log likelihood: -11377.957612 EM: Round [894] log likelihood: -11377.957231 EM: Round [895] log likelihood: -11377.956850 EM: Round [896] log likelihood: -11377.956469 EM: Round [897] log likelihood: -11377.956090 EM: Round [898] log likelihood: -11377.955711 EM: Round [899] log likelihood: -11377.955333 EM: Round [900] log likelihood: -11377.954956 EM: Round [901] log likelihood: -11377.954579 EM: Round [902] log likelihood: -11377.954203 EM: Round [903] log likelihood: -11377.953828 EM: Round [904] log likelihood: -11377.953454 EM: Round [905] log likelihood: -11377.953080 EM: Round [906] log likelihood: -11377.952708 EM: Round [907] log likelihood: -11377.952335 EM: Round [908] log likelihood: -11377.951964 EM: Round [909] log likelihood: -11377.951593 EM: Round [910] log likelihood: -11377.951223 EM: Round [911] log likelihood: -11377.950854 EM: Round [912] log likelihood: -11377.950486 EM: Round [913] log likelihood: -11377.950118 EM: Round [914] log likelihood: -11377.949751 EM: Round [915] log likelihood: -11377.949384 EM: Round [916] log likelihood: -11377.949019 EM: Round [917] log likelihood: -11377.948654 EM: Round [918] log likelihood: -11377.948289 EM: Round [919] log likelihood: -11377.947926 EM: Round [920] log likelihood: -11377.947563 EM: Round [921] log likelihood: -11377.947201 EM: Round [922] log likelihood: -11377.946839 EM: Round [923] log likelihood: -11377.946479 EM: Round [924] log likelihood: -11377.946119 EM: Round [925] log likelihood: -11377.945759 EM: Round [926] log likelihood: -11377.945401 EM: Round [927] log likelihood: -11377.945043 EM: Round [928] log likelihood: -11377.944685 EM: Round [929] log likelihood: -11377.944329 EM: Round [930] log likelihood: -11377.943973 EM: Round [931] log likelihood: -11377.943618 EM: Round [932] log likelihood: -11377.943263 EM: Round [933] log likelihood: -11377.942910 EM: Round [934] log likelihood: -11377.942556 EM: Round [935] log likelihood: -11377.942204 EM: Round [936] log likelihood: -11377.941852 EM: Round [937] log likelihood: -11377.941501 EM: Round [938] log likelihood: -11377.941151 EM: Round [939] log likelihood: -11377.940801 EM: Round [940] log likelihood: -11377.940452 EM: Round [941] log likelihood: -11377.940104 EM: Round [942] log likelihood: -11377.939756 EM: Round [943] log likelihood: -11377.939409 EM: Round [944] log likelihood: -11377.939063 EM: Round [945] log likelihood: -11377.938717 EM: Round [946] log likelihood: -11377.938372 EM: Round [947] log likelihood: -11377.938027 EM: Round [948] log likelihood: -11377.937684 EM: Round [949] log likelihood: -11377.937341 EM: Round [950] log likelihood: -11377.936998 EM: Round [951] log likelihood: -11377.936657 EM: Round [952] log likelihood: -11377.936315 EM: Round [953] log likelihood: -11377.935975 EM: Round [954] log likelihood: -11377.935635 EM: Round [955] log likelihood: -11377.935296 EM: Round [956] log likelihood: -11377.934958 EM: Round [957] log likelihood: -11377.934620 EM: Round [958] log likelihood: -11377.934283 EM: Round [959] log likelihood: -11377.933946 EM: Round [960] log likelihood: -11377.933610 EM: Round [961] log likelihood: -11377.933275 EM: Round [962] log likelihood: -11377.932940 EM: Round [963] log likelihood: -11377.932607 EM: Round [964] log likelihood: -11377.932273 EM: Round [965] log likelihood: -11377.931941 EM: Round [966] log likelihood: -11377.931609 EM: Round [967] log likelihood: -11377.931277 EM: Round [968] log likelihood: -11377.930946 EM: Round [969] log likelihood: -11377.930616 EM: Round [970] log likelihood: -11377.930287 EM: Round [971] log likelihood: -11377.929958 EM: Round [972] log likelihood: -11377.929630 EM: Round [973] log likelihood: -11377.929302 EM: Round [974] log likelihood: -11377.928975 EM: Round [975] log likelihood: -11377.928649 EM: Round [976] log likelihood: -11377.928323 EM: Round [977] log likelihood: -11377.927998 EM: Round [978] log likelihood: -11377.927673 EM: Round [979] log likelihood: -11377.927349 EM: Round [980] log likelihood: -11377.927026 EM: Round [981] log likelihood: -11377.926703 EM: Round [982] log likelihood: -11377.926381 EM: Round [983] log likelihood: -11377.926060 EM: Round [984] log likelihood: -11377.925739 EM: Round [985] log likelihood: -11377.925419 EM: Round [986] log likelihood: -11377.925099 EM: Round [987] log likelihood: -11377.924780 EM: Round [988] log likelihood: -11377.924462 EM: Round [989] log likelihood: -11377.924144 EM: Round [990] log likelihood: -11377.923827 EM: Round [991] log likelihood: -11377.923510 EM: Round [992] log likelihood: -11377.923194 EM: Round [993] log likelihood: -11377.922879 EM: Round [994] log likelihood: -11377.922564 EM: Round [995] log likelihood: -11377.922250 EM: Round [996] log likelihood: -11377.921936 EM: Round [997] log likelihood: -11377.921623 EM: Round [998] log likelihood: -11377.921311 EM: Round [999] log likelihood: -11377.920999 EM: Round [1000] log likelihood: -11377.920688 EM: Round [1001] log likelihood: -11377.920377 Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa > /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir -done, see /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -10694.909551 EM: Round [1] log likelihood: -10694.864499 EM: Round [2] log likelihood: -10694.853768 EM: Round [3] log likelihood: -10694.843171 EM: Round [4] log likelihood: -10694.832702 EM: Round [5] log likelihood: -10694.822357 EM: Round [6] log likelihood: -10694.812135 EM: Round [7] log likelihood: -10694.802032 EM: Round [8] log likelihood: -10694.792045 EM: Round [9] log likelihood: -10694.782173 EM: Round [10] log likelihood: -10694.772413 EM: Round [11] log likelihood: -10694.762762 EM: Round [12] log likelihood: -10694.753219 EM: Round [13] log likelihood: -10694.743780 EM: Round [14] log likelihood: -10694.734445 EM: Round [15] log likelihood: -10694.725210 EM: Round [16] log likelihood: -10694.716075 EM: Round [17] log likelihood: -10694.707036 EM: Round [18] log likelihood: -10694.698092 EM: Round [19] log likelihood: -10694.689242 EM: Round [20] log likelihood: -10694.680483 EM: Round [21] log likelihood: -10694.671814 EM: Round [22] log likelihood: -10694.663232 EM: Round [23] log likelihood: -10694.654738 EM: Round [24] log likelihood: -10694.646328 EM: Round [25] log likelihood: -10694.638001 EM: Round [26] log likelihood: -10694.629756 EM: Round [27] log likelihood: -10694.621591 EM: Round [28] log likelihood: -10694.613505 EM: Round [29] log likelihood: -10694.605497 EM: Round [30] log likelihood: -10694.597565 EM: Round [31] log likelihood: -10694.589707 EM: Round [32] log likelihood: -10694.581923 EM: Round [33] log likelihood: -10694.574212 EM: Round [34] log likelihood: -10694.566571 EM: Round [35] log likelihood: -10694.559000 EM: Round [36] log likelihood: -10694.551498 EM: Round [37] log likelihood: -10694.544064 EM: Round [38] log likelihood: -10694.536696 EM: Round [39] log likelihood: -10694.529393 EM: Round [40] log likelihood: -10694.522155 EM: Round [41] log likelihood: -10694.514980 EM: Round [42] log likelihood: -10694.507868 EM: Round [43] log likelihood: -10694.500817 EM: Round [44] log likelihood: -10694.493826 EM: Round [45] log likelihood: -10694.486894 EM: Round [46] log likelihood: -10694.480022 EM: Round [47] log likelihood: -10694.473207 EM: Round [48] log likelihood: -10694.466448 EM: Round [49] log likelihood: -10694.459746 EM: Round [50] log likelihood: -10694.453098 EM: Round [51] log likelihood: -10694.446505 EM: Round [52] log likelihood: -10694.439966 EM: Round [53] log likelihood: -10694.433479 EM: Round [54] log likelihood: -10694.427044 EM: Round [55] log likelihood: -10694.420661 EM: Round [56] log likelihood: -10694.414328 EM: Round [57] log likelihood: -10694.408044 EM: Round [58] log likelihood: -10694.401810 EM: Round [59] log likelihood: -10694.395624 EM: Round [60] log likelihood: -10694.389486 EM: Round [61] log likelihood: -10694.383395 EM: Round [62] log likelihood: -10694.377350 EM: Round [63] log likelihood: -10694.371351 EM: Round [64] log likelihood: -10694.365397 EM: Round [65] log likelihood: -10694.359488 EM: Round [66] log likelihood: -10694.353623 EM: Round [67] log likelihood: -10694.347801 EM: Round [68] log likelihood: -10694.342022 EM: Round [69] log likelihood: -10694.336285 EM: Round [70] log likelihood: -10694.330590 EM: Round [71] log likelihood: -10694.324936 EM: Round [72] log likelihood: -10694.319323 EM: Round [73] log likelihood: -10694.313750 EM: Round [74] log likelihood: 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-10693.026729 EM: Round [942] log likelihood: -10693.026341 EM: Round [943] log likelihood: -10693.025953 EM: Round [944] log likelihood: -10693.025566 EM: Round [945] log likelihood: -10693.025180 EM: Round [946] log likelihood: -10693.024795 EM: Round [947] log likelihood: -10693.024411 EM: Round [948] log likelihood: -10693.024027 EM: Round [949] log likelihood: -10693.023644 EM: Round [950] log likelihood: -10693.023262 EM: Round [951] log likelihood: -10693.022880 EM: Round [952] log likelihood: -10693.022499 EM: Round [953] log likelihood: -10693.022119 EM: Round [954] log likelihood: -10693.021740 EM: Round [955] log likelihood: -10693.021361 EM: Round [956] log likelihood: -10693.020984 EM: Round [957] log likelihood: -10693.020607 EM: Round [958] log likelihood: -10693.020230 EM: Round [959] log likelihood: -10693.019855 EM: Round [960] log likelihood: -10693.019480 EM: Round [961] log likelihood: -10693.019106 EM: Round [962] log likelihood: -10693.018732 EM: Round [963] log likelihood: -10693.018360 EM: Round [964] log likelihood: -10693.017988 EM: Round [965] log likelihood: -10693.017617 EM: Round [966] log likelihood: -10693.017246 EM: Round [967] log likelihood: -10693.016877 EM: Round [968] log likelihood: -10693.016508 EM: Round [969] log likelihood: -10693.016139 EM: Round [970] log likelihood: -10693.015772 EM: Round [971] log likelihood: -10693.015405 EM: Round [972] log likelihood: -10693.015039 EM: Round [973] log likelihood: -10693.014673 EM: Round [974] log likelihood: -10693.014308 EM: Round [975] log likelihood: -10693.013944 EM: Round [976] log likelihood: -10693.013581 EM: Round [977] log likelihood: -10693.013218 EM: Round [978] log likelihood: -10693.012857 EM: Round [979] log likelihood: -10693.012495 EM: Round [980] log likelihood: -10693.012135 EM: Round [981] log likelihood: -10693.011775 EM: Round [982] log likelihood: -10693.011416 EM: Round [983] log likelihood: -10693.011058 EM: Round [984] log likelihood: -10693.010700 EM: Round [985] log likelihood: -10693.010343 EM: Round [986] log likelihood: -10693.009986 EM: Round [987] log likelihood: -10693.009631 EM: Round [988] log likelihood: -10693.009276 EM: Round [989] log likelihood: -10693.008922 EM: Round [990] log likelihood: -10693.008568 EM: Round [991] log likelihood: -10693.008215 EM: Round [992] log likelihood: -10693.007863 EM: Round [993] log likelihood: -10693.007511 EM: Round [994] log likelihood: -10693.007160 EM: Round [995] log likelihood: -10693.006810 EM: Round [996] log likelihood: -10693.006461 EM: Round [997] log likelihood: -10693.006112 EM: Round [998] log likelihood: -10693.005764 EM: Round [999] log likelihood: -10693.005416 EM: Round [1000] log likelihood: -10693.005069 EM: Round [1001] log likelihood: -10693.004723 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 270853024 Execution Time = 4.96 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf > /tmp/nxf.La7UuypYL0/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.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gtf > /tmp/nxf.La7UuypYL0/fi_workdir/microH.dat Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.La7UuypYL0/fi_workdir/microH.dat /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_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.La7UuypYL0/fi_workdir/microH.dat /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.La7UuypYL0 --json_outfile /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.La7UuypYL0 --json_outfile /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.La7UuypYL0/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.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1 --html_output /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-01c779-R1_A23YTGFLT4_1 --html_output /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000176826.15] WARNING, no entry stored in dbm for [ENSG00000176826.15] WARNING, no entry stored in dbm for [ENSG00000176826.15] WARNING, no entry stored in dbm for [ENSG00000176826.15] WARNING, no entry stored in dbm for [ENSG00000176826.15] WARNING, no entry stored in dbm for [ENSG00000176826.15] WARNING, no entry stored in dbm for [ENSG00000234428.2] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000225535.7] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.La7UuypYL0/ctat_genome_lib_build_dir > /tmp/nxf.La7UuypYL0/aih-tih-sc-01c779-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.La7UuypYL0/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory