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
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[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.
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[10000] -fusion SPANNING read extraction for scaff: BAD--AC024405.1
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[10000] -fusion SPANNING read extraction for scaff: BAD--OR4C50P
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[7000] -fusion SPANNING read extraction for scaff: CEP89--AKR1B1P7
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[318000] -fusion SPANNING read extraction for scaff: CIZ1--GOLGA2
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[228000] -fusion SPANNING read extraction for scaff: CYB5B--MPP2
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[45000] -fusion SPANNING read extraction for scaff: CYLD--NKD1
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[121000] -fusion SPANNING read extraction for scaff: DHX9--LINC01720
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[82000] -fusion SPANNING read extraction for scaff: EXPH5--TSPAN18
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[114000] -fusion SPANNING read extraction for scaff: EXT2--EXPH5
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[168000] -fusion SPANNING read extraction for scaff: ITPR2--TM7SF3
[1000]
[2000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
[1000]
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[90000] -fusion SPANNING read extraction for scaff: LAMTOR2--HDGF
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[69000] -fusion SPANNING read extraction for scaff: MARK2--CCDC82
[1000]
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[5000] -fusion SPANNING read extraction for scaff: MED21--AC023051.1
[1000]
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[12000] -fusion SPANNING read extraction for scaff: MRPS14--LINC01724
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[62000] -fusion SPANNING read extraction for scaff: PAPOLA--AK7
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[47000] -fusion SPANNING read extraction for scaff: PCCA--CLYBL
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[34000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[35000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[34000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[63000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[34000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
[1000]
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[23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[36000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
[1000]
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
[1000]
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[36000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[35000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[28000] -fusion SPANNING read extraction for scaff: PGAP1--ANKRD44
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[14000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146
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[59000] -fusion SPANNING read extraction for scaff: PTPRK--GRID2
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[63000] -fusion SPANNING read extraction for scaff: SIPA1L2--ANKRD29
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[51000] -fusion SPANNING read extraction for scaff: TMEM241--NPC1
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[14000] -fusion SPANNING read extraction for scaff: TMEM241--ANKRD29
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[93000] -fusion SPANNING read extraction for scaff: USP50--TRPM7
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[292000] -fusion SPANNING read extraction for scaff: UTRN--STX11
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[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: Round [310] log likelihood: -11378.413053
EM: Round [311] log likelihood: -11378.411541
EM: Round [312] log likelihood: -11378.410033
EM: Round [313] log likelihood: -11378.408530
EM: Round [314] log likelihood: -11378.407032
EM: Round [315] log likelihood: -11378.405538
EM: Round [316] log likelihood: -11378.404049
EM: Round [317] log likelihood: -11378.402565
EM: Round [318] log likelihood: -11378.401085
EM: Round [319] log likelihood: -11378.399609
EM: Round [320] log likelihood: -11378.398138
EM: Round [321] log likelihood: -11378.396672
EM: Round [322] log likelihood: -11378.395210
EM: Round [323] log likelihood: -11378.393752
EM: Round [324] log likelihood: -11378.392299
EM: Round [325] log likelihood: -11378.390850
EM: Round [326] log likelihood: -11378.389405
EM: Round [327] log likelihood: -11378.387965
EM: Round [328] log likelihood: -11378.386530
EM: Round [329] log likelihood: -11378.385098
EM: Round [330] log likelihood: -11378.383671
EM: Round [331] log likelihood: -11378.382248
EM: Round [332] log likelihood: -11378.380830
EM: Round [333] log likelihood: -11378.379415
EM: Round [334] log likelihood: -11378.378005
EM: Round [335] log likelihood: -11378.376600
EM: Round [336] log likelihood: -11378.375198
EM: Round [337] log likelihood: -11378.373800
EM: Round [338] log likelihood: -11378.372407
EM: Round [339] log likelihood: -11378.371018
EM: Round [340] log likelihood: -11378.369633
EM: Round [341] log likelihood: -11378.368252
EM: Round [342] log likelihood: -11378.366875
EM: Round [343] log likelihood: -11378.365502
EM: Round [344] log likelihood: -11378.364133
EM: Round [345] log likelihood: -11378.362768
EM: Round [346] log likelihood: -11378.361408
EM: Round [347] log likelihood: -11378.360051
EM: Round [348] log likelihood: -11378.358698
EM: Round [349] log likelihood: -11378.357349
EM: Round [350] log likelihood: -11378.356004
EM: Round [351] log likelihood: -11378.354663
EM: Round [352] log likelihood: -11378.353326
EM: Round [353] log likelihood: -11378.351993
EM: Round [354] log likelihood: -11378.350664
EM: Round [355] log likelihood: -11378.349338
EM: Round [356] log likelihood: -11378.348017
EM: Round [357] log likelihood: -11378.346699
EM: Round [358] log likelihood: -11378.345385
EM: Round [359] log likelihood: -11378.344075
EM: Round [360] log likelihood: -11378.342768
EM: Round [361] log likelihood: -11378.341466
EM: Round [362] log likelihood: -11378.340167
EM: Round [363] log likelihood: -11378.338872
EM: Round [364] log likelihood: -11378.337580
EM: Round [365] log likelihood: -11378.336293
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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: -10694.308216
EM: Round [75] log likelihood: -10694.302722
EM: Round [76] log likelihood: -10694.297266
EM: Round [77] log likelihood: -10694.291848
EM: Round [78] log likelihood: -10694.286468
EM: Round [79] log likelihood: -10694.281126
EM: Round [80] log likelihood: -10694.275820
EM: Round [81] log likelihood: -10694.270550
EM: Round [82] log likelihood: -10694.265316
EM: Round [83] log likelihood: -10694.260118
EM: Round [84] log likelihood: -10694.254955
EM: Round [85] log likelihood: -10694.249826
EM: Round [86] log likelihood: -10694.244732
EM: Round [87] log likelihood: -10694.239671
EM: Round [88] log likelihood: -10694.234644
EM: Round [89] log likelihood: -10694.229650
EM: Round [90] log likelihood: -10694.224688
EM: Round [91] log likelihood: -10694.219759
EM: Round [92] log likelihood: -10694.214861
EM: Round [93] log likelihood: -10694.209996
EM: Round [94] log likelihood: -10694.205161
EM: Round [95] log likelihood: -10694.200357
EM: Round [96] log likelihood: -10694.195584
EM: Round [97] log likelihood: -10694.190841
EM: Round [98] log likelihood: -10694.186128
EM: Round [99] log likelihood: -10694.181444
EM: Round [100] log likelihood: -10694.176789
EM: Round [101] log likelihood: -10694.172163
EM: Round [102] log likelihood: -10694.167566
EM: Round [103] log likelihood: -10694.162997
EM: Round [104] log likelihood: -10694.158456
EM: Round [105] log likelihood: -10694.153943
EM: Round [106] log likelihood: -10694.149457
EM: Round [107] log likelihood: -10694.144998
EM: Round [108] log likelihood: -10694.140566
EM: Round [109] log likelihood: -10694.136161
EM: Round [110] log likelihood: -10694.131781
EM: Round [111] log likelihood: -10694.127428
EM: Round [112] log likelihood: -10694.123100
EM: Round [113] log likelihood: -10694.118798
EM: Round [114] log likelihood: -10694.114521
EM: Round [115] log likelihood: -10694.110269
EM: Round [116] log likelihood: -10694.106041
EM: Round [117] log likelihood: -10694.101838
EM: Round [118] log likelihood: -10694.097660
EM: Round [119] log likelihood: -10694.093505
EM: Round [120] log likelihood: -10694.089374
EM: Round [121] log likelihood: -10694.085266
EM: Round [122] log likelihood: -10694.081181
EM: Round [123] log likelihood: -10694.077120
EM: Round [124] log likelihood: -10694.073082
EM: Round [125] log likelihood: -10694.069066
EM: Round [126] log likelihood: -10694.065072
EM: Round [127] log likelihood: -10694.061100
EM: Round [128] log likelihood: -10694.057151
EM: Round [129] log likelihood: -10694.053223
EM: Round [130] log likelihood: -10694.049317
EM: Round [131] log likelihood: -10694.045432
EM: Round [132] log likelihood: -10694.041568
EM: Round [133] log likelihood: -10694.037725
EM: Round [134] log likelihood: -10694.033903
EM: Round [135] log likelihood: -10694.030102
EM: Round [136] log likelihood: -10694.026321
EM: Round [137] log likelihood: -10694.022560
EM: Round [138] log likelihood: -10694.018819
EM: Round [139] log likelihood: -10694.015097
EM: Round [140] log likelihood: -10694.011396
EM: Round [141] log likelihood: -10694.007714
EM: Round [142] log likelihood: -10694.004051
EM: Round [143] log likelihood: -10694.000408
EM: Round [144] log likelihood: -10693.996783
EM: Round [145] log likelihood: -10693.993177
EM: Round [146] log likelihood: -10693.989590
EM: Round [147] log likelihood: -10693.986021
EM: Round [148] log likelihood: -10693.982470
EM: Round [149] log likelihood: -10693.978938
EM: Round [150] log likelihood: -10693.975424
EM: Round [151] log likelihood: -10693.971927
EM: Round [152] log likelihood: -10693.968448
EM: Round [153] log likelihood: -10693.964987
EM: Round [154] log likelihood: -10693.961543
EM: Round [155] log likelihood: -10693.958116
EM: Round [156] log likelihood: -10693.954706
EM: Round [157] log likelihood: -10693.951314
EM: Round [158] log likelihood: -10693.947938
EM: Round [159] log likelihood: -10693.944579
EM: Round [160] log likelihood: -10693.941236
EM: Round [161] log likelihood: -10693.937909
EM: Round [162] log likelihood: -10693.934599
EM: Round [163] log likelihood: -10693.931305
EM: Round [164] log likelihood: -10693.928028
EM: Round [165] log likelihood: -10693.924765
EM: Round [166] log likelihood: -10693.921519
EM: Round [167] log likelihood: -10693.918288
EM: Round [168] log likelihood: -10693.915073
EM: Round [169] log likelihood: -10693.911873
EM: Round [170] log likelihood: -10693.908689
EM: Round [171] log likelihood: -10693.905519
EM: Round [172] log likelihood: -10693.902364
EM: Round [173] log likelihood: -10693.899225
EM: Round [174] log likelihood: -10693.896100
EM: Round [175] log likelihood: -10693.892990
EM: Round [176] log likelihood: -10693.889894
EM: Round [177] log likelihood: -10693.886813
EM: Round [178] log likelihood: -10693.883746
EM: Round [179] log likelihood: -10693.880693
EM: Round [180] log likelihood: -10693.877654
EM: Round [181] log likelihood: -10693.874629
EM: Round [182] log likelihood: -10693.871619
EM: Round [183] log likelihood: -10693.868622
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EM: Round [646] log likelihood: -10693.184664
EM: Round [647] log likelihood: -10693.183939
EM: Round [648] log likelihood: -10693.183216
EM: Round [649] log likelihood: -10693.182495
EM: Round [650] log likelihood: -10693.181775
EM: Round [651] log likelihood: -10693.181056
EM: Round [652] log likelihood: -10693.180340
EM: Round [653] log likelihood: -10693.179625
EM: Round [654] log likelihood: -10693.178912
EM: Round [655] log likelihood: -10693.178200
EM: Round [656] log likelihood: -10693.177490
EM: Round [657] log likelihood: -10693.176782
EM: Round [658] log likelihood: -10693.176075
EM: Round [659] log likelihood: -10693.175370
EM: Round [660] log likelihood: -10693.174666
EM: Round [661] log likelihood: -10693.173964
EM: Round [662] log likelihood: -10693.173264
EM: Round [663] log likelihood: -10693.172565
EM: Round [664] log likelihood: -10693.171868
EM: Round [665] log likelihood: -10693.171172
EM: Round [666] log likelihood: -10693.170478
EM: Round [667] log likelihood: -10693.169786
EM: Round [668] log likelihood: -10693.169095
EM: Round [669] log likelihood: -10693.168406
EM: Round [670] log likelihood: -10693.167718
EM: Round [671] log likelihood: -10693.167032
EM: Round [672] log likelihood: -10693.166347
EM: Round [673] log likelihood: -10693.165664
EM: Round [674] log likelihood: -10693.164983
EM: Round [675] log likelihood: -10693.164303
EM: Round [676] log likelihood: -10693.163624
EM: Round [677] log likelihood: -10693.162948
EM: Round [678] log likelihood: -10693.162272
EM: Round [679] log likelihood: -10693.161598
EM: Round [680] log likelihood: -10693.160926
EM: Round [681] log likelihood: -10693.160255
EM: Round [682] log likelihood: -10693.159586
EM: Round [683] log likelihood: -10693.158918
EM: Round [684] log likelihood: -10693.158252
EM: Round [685] log likelihood: -10693.157587
EM: Round [686] log likelihood: -10693.156924
EM: Round [687] log likelihood: -10693.156262
EM: Round [688] log likelihood: -10693.155601
EM: Round [689] log likelihood: -10693.154943
EM: Round [690] log likelihood: -10693.154285
EM: Round [691] log likelihood: -10693.153629
EM: Round [692] log likelihood: -10693.152975
EM: Round [693] log likelihood: -10693.152322
EM: Round [694] log likelihood: -10693.151670
EM: Round [695] log likelihood: -10693.151020
EM: Round [696] log likelihood: -10693.150371
EM: Round [697] log likelihood: -10693.149724
EM: Round [698] log likelihood: -10693.149078
EM: Round [699] log likelihood: -10693.148434
EM: Round [700] log likelihood: -10693.147791
EM: Round [701] log likelihood: -10693.147150
EM: Round [702] log likelihood: -10693.146510
EM: Round [703] log likelihood: -10693.145871
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EM: Round [705] log likelihood: -10693.144598
EM: Round [706] log likelihood: -10693.143964
EM: Round [707] log likelihood: -10693.143331
EM: Round [708] log likelihood: -10693.142699
EM: Round [709] log likelihood: -10693.142069
EM: Round [710] log likelihood: -10693.141440
EM: Round [711] log likelihood: -10693.140813
EM: Round [712] log likelihood: -10693.140187
EM: Round [713] log likelihood: -10693.139562
EM: Round [714] log likelihood: -10693.138939
EM: Round [715] log likelihood: -10693.138317
EM: Round [716] log likelihood: -10693.137696
EM: Round [717] log likelihood: -10693.137077
EM: Round [718] log likelihood: -10693.136459
EM: Round [719] log likelihood: -10693.135843
EM: Round [720] log likelihood: -10693.135228
EM: Round [721] log likelihood: -10693.134614
EM: Round [722] log likelihood: -10693.134002
EM: Round [723] log likelihood: -10693.133390
EM: Round [724] log likelihood: -10693.132781
EM: Round [725] log likelihood: -10693.132172
EM: Round [726] log likelihood: -10693.131565
EM: Round [727] log likelihood: -10693.130960
EM: Round [728] log likelihood: -10693.130355
EM: Round [729] log likelihood: -10693.129752
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EM: Round [731] log likelihood: -10693.128550
EM: Round [732] log likelihood: -10693.127951
EM: Round [733] log likelihood: -10693.127353
EM: Round [734] log likelihood: -10693.126756
EM: Round [735] log likelihood: -10693.126161
EM: Round [736] log likelihood: -10693.125567
EM: Round [737] log likelihood: -10693.124974
EM: Round [738] log likelihood: -10693.124383
EM: Round [739] log likelihood: -10693.123793
EM: Round [740] log likelihood: -10693.123204
EM: Round [741] log likelihood: -10693.122616
EM: Round [742] log likelihood: -10693.122030
EM: Round [743] log likelihood: -10693.121445
EM: Round [744] log likelihood: -10693.120861
EM: Round [745] log likelihood: -10693.120279
EM: Round [746] log likelihood: -10693.119698
EM: Round [747] log likelihood: -10693.119118
EM: Round [748] log likelihood: -10693.118539
EM: Round [749] log likelihood: -10693.117961
EM: Round [750] log likelihood: -10693.117385
EM: Round [751] log likelihood: -10693.116810
EM: Round [752] log likelihood: -10693.116237
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EM: Round [754] log likelihood: -10693.115093
EM: Round [755] log likelihood: -10693.114523
EM: Round [756] log likelihood: -10693.113954
EM: Round [757] log likelihood: -10693.113386
EM: Round [758] log likelihood: -10693.112820
EM: Round [759] log likelihood: -10693.112255
EM: Round [760] log likelihood: -10693.111691
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EM: Round [762] log likelihood: -10693.110566
EM: Round [763] log likelihood: -10693.110006
EM: Round [764] log likelihood: -10693.109447
EM: Round [765] log likelihood: -10693.108889
EM: Round [766] log likelihood: -10693.108332
EM: Round [767] log likelihood: -10693.107777
EM: Round [768] log likelihood: -10693.107222
EM: Round [769] log likelihood: -10693.106669
EM: Round [770] log likelihood: -10693.106117
EM: Round [771] log likelihood: -10693.105566
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EM: Round [773] log likelihood: -10693.104468
EM: Round [774] log likelihood: -10693.103921
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EM: Round [777] log likelihood: -10693.102286
EM: Round [778] log likelihood: -10693.101743
EM: Round [779] log likelihood: -10693.101201
EM: Round [780] log likelihood: -10693.100661
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EM: Round [782] log likelihood: -10693.099584
EM: Round [783] log likelihood: -10693.099047
EM: Round [784] log likelihood: -10693.098511
EM: Round [785] log likelihood: -10693.097976
EM: Round [786] log likelihood: -10693.097442
EM: Round [787] log likelihood: -10693.096910
EM: Round [788] log likelihood: -10693.096379
EM: Round [789] log likelihood: -10693.095848
EM: Round [790] log likelihood: -10693.095319
EM: Round [791] log likelihood: -10693.094791
EM: Round [792] log likelihood: -10693.094264
EM: Round [793] log likelihood: -10693.093739
EM: Round [794] log likelihood: -10693.093214
EM: Round [795] log likelihood: -10693.092690
EM: Round [796] log likelihood: -10693.092168
EM: Round [797] log likelihood: -10693.091647
EM: Round [798] log likelihood: -10693.091126
EM: Round [799] log likelihood: -10693.090607
EM: Round [800] log likelihood: -10693.090089
EM: Round [801] log likelihood: -10693.089572
EM: Round [802] log likelihood: -10693.089056
EM: Round [803] log likelihood: -10693.088541
EM: Round [804] log likelihood: -10693.088028
EM: Round [805] log likelihood: -10693.087515
EM: Round [806] log likelihood: -10693.087003
EM: Round [807] log likelihood: -10693.086493
EM: Round [808] log likelihood: -10693.085983
EM: Round [809] log likelihood: -10693.085475
EM: Round [810] log likelihood: -10693.084968
EM: Round [811] log likelihood: -10693.084461
EM: Round [812] log likelihood: -10693.083956
EM: Round [813] log likelihood: -10693.083452
EM: Round [814] log likelihood: -10693.082949
EM: Round [815] log likelihood: -10693.082447
EM: Round [816] log likelihood: -10693.081946
EM: Round [817] log likelihood: -10693.081446
EM: Round [818] log likelihood: -10693.080947
EM: Round [819] log likelihood: -10693.080449
EM: Round [820] log likelihood: -10693.079952
EM: Round [821] log likelihood: -10693.079456
EM: Round [822] log likelihood: -10693.078961
EM: Round [823] log likelihood: -10693.078468
EM: Round [824] log likelihood: -10693.077975
EM: Round [825] log likelihood: -10693.077483
EM: Round [826] log likelihood: -10693.076992
EM: Round [827] log likelihood: -10693.076503
EM: Round [828] log likelihood: -10693.076014
EM: Round [829] log likelihood: -10693.075526
EM: Round [830] log likelihood: -10693.075039
EM: Round [831] log likelihood: -10693.074554
EM: Round [832] log likelihood: -10693.074069
EM: Round [833] log likelihood: -10693.073585
EM: Round [834] log likelihood: -10693.073103
EM: Round [835] log likelihood: -10693.072621
EM: Round [836] log likelihood: -10693.072140
EM: Round [837] log likelihood: -10693.071661
EM: Round [838] log likelihood: -10693.071182
EM: Round [839] log likelihood: -10693.070704
EM: Round [840] log likelihood: -10693.070227
EM: Round [841] log likelihood: -10693.069752
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EM: Round [843] log likelihood: -10693.068803
EM: Round [844] log likelihood: -10693.068330
EM: Round [845] log likelihood: -10693.067858
EM: Round [846] log likelihood: -10693.067387
EM: Round [847] log likelihood: -10693.066917
EM: Round [848] log likelihood: -10693.066448
EM: Round [849] log likelihood: -10693.065980
EM: Round [850] log likelihood: -10693.065513
EM: Round [851] log likelihood: -10693.065047
EM: Round [852] log likelihood: -10693.064582
EM: Round [853] log likelihood: -10693.064118
EM: Round [854] log likelihood: -10693.063655
EM: Round [855] log likelihood: -10693.063192
EM: Round [856] log likelihood: -10693.062731
EM: Round [857] log likelihood: -10693.062271
EM: Round [858] log likelihood: -10693.061811
EM: Round [859] log likelihood: -10693.061353
EM: Round [860] log likelihood: -10693.060895
EM: Round [861] log likelihood: -10693.060438
EM: Round [862] log likelihood: -10693.059982
EM: Round [863] log likelihood: -10693.059528
EM: Round [864] log likelihood: -10693.059074
EM: Round [865] log likelihood: -10693.058621
EM: Round [866] log likelihood: -10693.058169
EM: Round [867] log likelihood: -10693.057718
EM: Round [868] log likelihood: -10693.057267
EM: Round [869] log likelihood: -10693.056818
EM: Round [870] log likelihood: -10693.056370
EM: Round [871] log likelihood: -10693.055922
EM: Round [872] log likelihood: -10693.055476
EM: Round [873] log likelihood: -10693.055030
EM: Round [874] log likelihood: -10693.054585
EM: Round [875] log likelihood: -10693.054141
EM: Round [876] log likelihood: -10693.053698
EM: Round [877] log likelihood: -10693.053256
EM: Round [878] log likelihood: -10693.052815
EM: Round [879] log likelihood: -10693.052375
EM: Round [880] log likelihood: -10693.051935
EM: Round [881] log likelihood: -10693.051497
EM: Round [882] log likelihood: -10693.051059
EM: Round [883] log likelihood: -10693.050622
EM: Round [884] log likelihood: -10693.050186
EM: Round [885] log likelihood: -10693.049751
EM: Round [886] log likelihood: -10693.049317
EM: Round [887] log likelihood: -10693.048884
EM: Round [888] log likelihood: -10693.048452
EM: Round [889] log likelihood: -10693.048020
EM: Round [890] log likelihood: -10693.047589
EM: Round [891] log likelihood: -10693.047160
EM: Round [892] log likelihood: -10693.046731
EM: Round [893] log likelihood: -10693.046303
EM: Round [894] log likelihood: -10693.045875
EM: Round [895] log likelihood: -10693.045449
EM: Round [896] log likelihood: -10693.045024
EM: Round [897] log likelihood: -10693.044599
EM: Round [898] log likelihood: -10693.044175
EM: Round [899] log likelihood: -10693.043752
EM: Round [900] log likelihood: -10693.043330
EM: Round [901] log likelihood: -10693.042909
EM: Round [902] log likelihood: -10693.042489
EM: Round [903] log likelihood: -10693.042069
EM: Round [904] log likelihood: -10693.041650
EM: Round [905] log likelihood: -10693.041232
EM: Round [906] log likelihood: -10693.040815
EM: Round [907] log likelihood: -10693.040399
EM: Round [908] log likelihood: -10693.039984
EM: Round [909] log likelihood: -10693.039569
EM: Round [910] log likelihood: -10693.039155
EM: Round [911] log likelihood: -10693.038743
EM: Round [912] log likelihood: -10693.038330
EM: Round [913] log likelihood: -10693.037919
EM: Round [914] log likelihood: -10693.037509
EM: Round [915] log likelihood: -10693.037099
EM: Round [916] log likelihood: -10693.036690
EM: Round [917] log likelihood: -10693.036282
EM: Round [918] log likelihood: -10693.035875
EM: Round [919] log likelihood: -10693.035469
EM: Round [920] log likelihood: -10693.035063
EM: Round [921] log likelihood: -10693.034658
EM: Round [922] log likelihood: -10693.034254
EM: Round [923] log likelihood: -10693.033851
EM: Round [924] log likelihood: -10693.033449
EM: Round [925] log likelihood: -10693.033047
EM: Round [926] log likelihood: -10693.032646
EM: Round [927] log likelihood: -10693.032246
EM: Round [928] log likelihood: -10693.031847
EM: Round [929] log likelihood: -10693.031449
EM: Round [930] log likelihood: -10693.031051
EM: Round [931] log likelihood: -10693.030654
EM: Round [932] log likelihood: -10693.030258
EM: Round [933] log likelihood: -10693.029863
EM: Round [934] log likelihood: -10693.029469
EM: Round [935] log likelihood: -10693.029075
EM: Round [936] log likelihood: -10693.028682
EM: Round [937] log likelihood: -10693.028290
EM: Round [938] log likelihood: -10693.027898
EM: Round [939] log likelihood: -10693.027508
EM: Round [940] log likelihood: -10693.027118
EM: Round [941] log likelihood: -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
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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