Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/73b2f6ec6a8b5424e1d07d6b49ecbe/aih-tih-sc-06a169-R1_A23WJ53LT4_1_2.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/bd/b91878d73718e9ad9441d25883b44f/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/b91878d73718e9ad9441d25883b44f/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/ff482f719378a042a1d8d7c4e36761/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/73b2f6ec6a8b5424e1d07d6b49ecbe/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/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 = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf > /tmp/nxf.6tRU5QxEjn/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf > /tmp/nxf.6tRU5QxEjn/cytoBand.txt
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed
-parsing GTF file: /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.sorted.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-06a169-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.6tRU5QxEjn/fi_workdir --reads "/tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:04:22 ..... started STAR run
Jun 08 10:04:22 ..... loading genome
Jun 08 10:05:29 ... generating Suffix Array index
Jun 08 10:09:12 ... completed Suffix Array index
Jun 08 10:09:12 ..... processing annotations GTF
Jun 08 10:09:13 ..... inserting junctions into the genome indices
Jun 08 10:09:57 ..... started mapping
Jun 08 10:48:34 ..... finished mapping
Jun 08 10:48:36 ..... started sorting BAM
Jun 08 10:48:36 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam
Execution Time = 44.25 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-06a169-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.6tRU5QxEjn/fi_workdir --reads "/tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
10:48:43 : INFO : Done.
Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf
-parsing /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam
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[1400000] -done parsing /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 18,
'small anchor length' => 23,
'low complexity anchor region' => 2,
'excessive soft clipping' => 8478,
'per_id < 96' => 4188,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 88,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
'num genes matched < 2' => 8,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8,
' ** passed ** ' => 3021
};
-writing fusion junction support info.
Execution Time = 0.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[11000] -fusion SPANNING read extraction for scaff: APPL1--LINC02531
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[116000] -fusion SPANNING read extraction for scaff: ARHGEF10L--NKAIN1
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[96000] -fusion SPANNING read extraction for scaff: TP53--CLDN7
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 10188
};
Execution Time = 1.40 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -4340.079626
EM: Round [1] log likelihood: -4340.072222
EM: Round [2] log likelihood: -4340.072196
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam"
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam
Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.25 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa > /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir
-done, see /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -4235.082197
EM: Round [1] log likelihood: -4235.074794
EM: Round [2] log likelihood: -4235.074767
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 274831184
Execution Time = 3.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf > /tmp/nxf.6tRU5QxEjn/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gtf > /tmp/nxf.6tRU5QxEjn/fi_workdir/microH.dat
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.6tRU5QxEjn/fi_workdir/microH.dat /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_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.6tRU5QxEjn/fi_workdir/microH.dat /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.6tRU5QxEjn --json_outfile /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-06a169-R1_A23WJ53LT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.6tRU5QxEjn --json_outfile /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-06a169-R1_A23WJ53LT4_1
Running: touch /tmp/nxf.6tRU5QxEjn/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.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-06a169-R1_A23WJ53LT4_1 --html_output /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-06a169-R1_A23WJ53LT4_1 --html_output /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000253787.1]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.6tRU5QxEjn/ctat_genome_lib_build_dir > /tmp/nxf.6tRU5QxEjn/aih-tih-sc-06a169-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.6tRU5QxEjn/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory