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/25/cadfa99ce2a7fe23902e1d090dc27c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/cadfa99ce2a7fe23902e1d090dc27c/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/f6c01154df515156512720cec1e7a2/tih_rna_sample_00614_B23MVV7LT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ac1192f8cc58b9961a13bc75df0053/tih_rna_sample_00614_B23MVV7LT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/ac1192f8cc58b9961a13bc75df0053/tih_rna_sample_00614_B23MVV7LT4_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 tih_rna_sample_00614_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00614_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fa Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf > /tmp/nxf.uMS6WptGv5/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf > /tmp/nxf.uMS6WptGv5/cytoBand.txt Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed -parsing GTF file: /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00614_B23MVV7LT4_1.star --out_dir /tmp/nxf.uMS6WptGv5/fi_workdir --reads "/tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:34:19 ..... started STAR run Jun 08 10:34:19 ..... loading genome Jun 08 10:36:08 ... generating Suffix Array index Jun 08 10:40:01 ... completed Suffix Array index Jun 08 10:40:01 ..... processing annotations GTF Jun 08 10:40:02 ..... inserting junctions into the genome indices Jun 08 10:41:03 ..... started mapping Jun 08 11:43:26 ..... finished mapping Jun 08 11:43:28 ..... started sorting BAM Jun 08 11:43:31 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00614_B23MVV7LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00614_B23MVV7LT4_1.star.sortedByCoord.out.bam Execution Time = 69.30 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00614_B23MVV7LT4_1.star --out_dir /tmp/nxf.uMS6WptGv5/fi_workdir --reads "/tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:44:03 : INFO : Done. Execution Time = 0.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf -parsing /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] 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[5270000] [5280000] [5290000] [5300000] [5310000] [5320000] [5330000] -done parsing /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 360, 'seq-similar region overlap' => 273, 'excessive soft clipping' => 44795, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 143, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 146, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 30, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 56, ' ** passed ** ' => 17832, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18, 'per_id < 96' => 16838, 'low complexity anchor region' => 8, 'num genes matched < 2' => 24, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2, 'small anchor length' => 104 }; -writing fusion junction support info. Execution Time = 3.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] -fusion SPANNING read extraction for scaff: AC110588.1--GABRG3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: AC239859.5--AC013734.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] -fusion SPANNING read extraction for scaff: AFAP1--KCNIP4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] -fusion SPANNING read extraction for scaff: AFAP1--LINC02501 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] -fusion SPANNING read extraction for scaff: AFAP1--LINC02506 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] -fusion SPANNING read extraction for scaff: AFAP1--AC027369.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] -fusion SPANNING read extraction for scaff: AFAP1--TRIM53CP [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] -fusion SPANNING read extraction for scaff: AKAP10--RB1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] -fusion SPANNING read extraction for scaff: ANKRD27--ZNF507 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: AOPEP--AL450426.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] -fusion SPANNING read extraction for scaff: APBB2--AC093878.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] -fusion SPANNING read extraction for scaff: APBB2--AC097535.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] -fusion SPANNING read extraction for scaff: C11orf49--TTC17 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: CCNE1--CDH9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] -fusion SPANNING read extraction for scaff: CCNL2--LINC01837 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] -fusion SPANNING read extraction for scaff: CHCHD6--ZBTB20 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] -fusion SPANNING read extraction for scaff: CWC27--CPLANE1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] -fusion SPANNING read extraction for scaff: CWC27--RGS7BP [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] -fusion SPANNING read extraction for scaff: CWC27--MRPL49P1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: DARS2--ESRRG [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: DARS2--GPATCH2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: DNAJC3--ADPRHL1 [1000] -fusion SPANNING read extraction for scaff: FAM149B1P1--GABRG3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: GPATCH2--LRRC7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] -fusion SPANNING read extraction for scaff: KCTD8--RELL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: LIMCH1--TRIM64C [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: LIMCH1--AC116611.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: LIMCH1--LINC02353 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] -fusion SPANNING read extraction for scaff: LSM14A--ZNF460 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] -fusion SPANNING read extraction for scaff: LSM14A--ZNF460-AS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] -fusion SPANNING read extraction for scaff: MED13--RIPK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: NDUFS4--AC010327.4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] -fusion SPANNING read extraction for scaff: NRDC--AGBL4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] -fusion SPANNING read extraction for scaff: NUP155--SHISAL2B [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] -fusion SPANNING read extraction for scaff: PHLDB2--KCNAB1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] -fusion SPANNING read extraction for scaff: PHLDB2--AC091607.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] -fusion SPANNING read extraction for scaff: PLCH2--ITGB3BP [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] -fusion SPANNING read extraction for scaff: PPP1R8--STX12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PSG8--CD177 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] -fusion SPANNING read extraction for scaff: QKI--RNF217-AS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] -fusion SPANNING read extraction for scaff: RRAS2--COPB1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] -fusion SPANNING read extraction for scaff: SCP2--COPB1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] -fusion SPANNING read extraction for scaff: SLIT2--AC024230.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] -fusion SPANNING read extraction for scaff: SMIM14--PI4K2B [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: SMIM14--AC007106.1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: SMIM14--AC093791.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] -fusion SPANNING read extraction for scaff: SNX29--MARF1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] -fusion SPANNING read extraction for scaff: SUSD1--PTBP3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] -fusion SPANNING read extraction for scaff: TLK2--CCDC144NL-AS1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: TP53--DLEU1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] -fusion SPANNING read extraction for scaff: XPO6--ZP2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] -fusion SPANNING read extraction for scaff: XPO6--ANKS4B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] -fusion SPANNING read extraction for scaff: ZNF507--AC010485.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] -fusion SPANNING read extraction for scaff: ZNF507--RPL21P131 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] -fusion SPANNING read extraction for scaff: ZNF785--ADD1 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 25415, 'seq similar region alignment' => 15902 }; Execution Time = 8.62 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -13984.250979 EM: Round [1] log likelihood: -13981.328137 EM: Round [2] log likelihood: -13979.551462 EM: Round [3] log likelihood: -13978.108621 EM: Round [4] log likelihood: -13976.929530 EM: Round [5] log likelihood: -13975.960836 EM: Round [6] log likelihood: -13975.161185 EM: Round [7] log likelihood: -13974.498142 EM: Round [8] log likelihood: -13973.946034 EM: Round [9] log likelihood: -13973.484393 EM: Round [10] log likelihood: -13973.096811 EM: Round [11] log likelihood: -13972.770068 EM: Round [12] log likelihood: -13972.493471 EM: Round [13] log likelihood: -13972.258340 EM: Round [14] log likelihood: -13972.057602 EM: Round [15] log likelihood: -13971.885483 EM: Round [16] log likelihood: -13971.737250 EM: Round [17] log likelihood: -13971.609015 EM: Round [18] log likelihood: -13971.497574 EM: Round [19] log likelihood: -13971.400282 EM: Round [20] log likelihood: -13971.314949 EM: Round [21] log likelihood: -13971.239753 EM: Round [22] log likelihood: -13971.173180 EM: Round [23] log likelihood: -13971.113964 EM: Round [24] log likelihood: -13971.061046 EM: Round [25] log likelihood: -13971.013537 EM: Round [26] log likelihood: -13970.970686 EM: Round [27] log likelihood: -13970.931862 EM: Round [28] log likelihood: -13970.896528 EM: Round [29] log likelihood: -13970.864230 EM: Round [30] log likelihood: -13970.834581 EM: Round [31] log likelihood: -13970.807248 EM: Round [32] log likelihood: -13970.781949 EM: Round [33] log likelihood: -13970.758440 EM: Round [34] log likelihood: -13970.736510 EM: Round [35] log likelihood: -13970.715980 EM: Round [36] log likelihood: -13970.696692 EM: Round [37] log likelihood: -13970.678509 EM: Round [38] log likelihood: -13970.661313 EM: Round [39] log likelihood: -13970.645000 EM: Round [40] log likelihood: -13970.629480 EM: Round [41] log likelihood: -13970.614673 EM: Round [42] log likelihood: -13970.600510 EM: Round [43] log likelihood: -13970.586928 EM: Round [44] log likelihood: -13970.573875 EM: Round [45] log likelihood: -13970.561301 EM: Round [46] log likelihood: -13970.549165 EM: Round [47] log likelihood: -13970.537428 EM: Round [48] log likelihood: -13970.526057 EM: Round [49] log likelihood: -13970.515023 EM: Round [50] log likelihood: -13970.504297 EM: Round [51] log likelihood: -13970.493858 EM: Round [52] log likelihood: -13970.483683 EM: Round [53] log likelihood: -13970.473752 EM: Round [54] log likelihood: -13970.464050 EM: Round [55] log likelihood: -13970.454560 EM: Round [56] log likelihood: -13970.445269 EM: Round [57] log likelihood: -13970.436164 EM: Round [58] log likelihood: -13970.427233 EM: Round [59] log likelihood: -13970.418467 EM: Round [60] log likelihood: -13970.409855 EM: Round [61] log likelihood: -13970.401391 EM: Round [62] log likelihood: -13970.393065 EM: Round [63] log likelihood: -13970.384870 EM: Round [64] log likelihood: -13970.376802 EM: Round [65] log likelihood: -13970.368853 EM: Round [66] log likelihood: -13970.361018 EM: Round [67] log likelihood: -13970.353292 EM: Round [68] log likelihood: -13970.345671 EM: Round [69] log likelihood: -13970.338151 EM: Round [70] log likelihood: -13970.330728 EM: Round [71] log likelihood: -13970.323399 EM: Round [72] log likelihood: -13970.316159 EM: Round [73] log likelihood: -13970.309006 EM: Round [74] log likelihood: -13970.301938 EM: Round [75] log likelihood: -13970.294951 EM: Round [76] log likelihood: -13970.288044 EM: Round [77] log likelihood: -13970.281213 EM: Round [78] log likelihood: -13970.274458 EM: Round [79] log likelihood: -13970.267775 EM: Round [80] log likelihood: -13970.261163 EM: Round [81] log likelihood: -13970.254620 EM: Round [82] log likelihood: -13970.248145 EM: Round [83] log likelihood: -13970.241736 EM: Round [84] log likelihood: -13970.235391 EM: Round [85] log likelihood: -13970.229110 EM: Round [86] log likelihood: -13970.222890 EM: Round [87] log likelihood: -13970.216730 EM: Round [88] log likelihood: -13970.210630 EM: Round [89] log likelihood: -13970.204588 EM: Round [90] log likelihood: -13970.198602 EM: Round [91] log likelihood: -13970.192673 EM: Round [92] log likelihood: -13970.186798 EM: Round [93] log likelihood: -13970.180978 EM: Round [94] log likelihood: -13970.175210 EM: Round [95] log likelihood: -13970.169494 EM: Round [96] log likelihood: -13970.163830 EM: Round [97] log likelihood: -13970.158216 EM: Round [98] log likelihood: -13970.152651 EM: Round [99] log likelihood: -13970.147135 EM: Round [100] log likelihood: -13970.141667 EM: Round [101] log likelihood: -13970.136246 EM: Round [102] log likelihood: -13970.130872 EM: Round [103] log likelihood: -13970.125544 EM: Round [104] log likelihood: -13970.120260 EM: Round [105] log likelihood: -13970.115021 EM: Round [106] log likelihood: -13970.109826 EM: Round [107] log likelihood: -13970.104674 EM: Round [108] log likelihood: -13970.099565 EM: Round [109] log likelihood: -13970.094498 EM: Round [110] log likelihood: -13970.089472 EM: Round [111] log likelihood: -13970.084487 EM: Round [112] log likelihood: -13970.079542 EM: Round [113] log likelihood: -13970.074637 EM: Round [114] log likelihood: -13970.069771 EM: Round [115] log likelihood: -13970.064944 EM: Round [116] log likelihood: -13970.060155 EM: Round [117] log likelihood: -13970.055403 EM: Round [118] log likelihood: -13970.050689 EM: Round [119] log likelihood: -13970.046012 EM: Round [120] log likelihood: -13970.041371 EM: Round [121] log likelihood: -13970.036766 EM: Round [122] log likelihood: -13970.032196 EM: Round [123] log likelihood: -13970.027661 EM: Round [124] log likelihood: -13970.023161 EM: Round [125] log likelihood: -13970.018695 EM: Round [126] log likelihood: -13970.014262 EM: Round [127] log likelihood: -13970.009863 EM: Round [128] log likelihood: -13970.005496 EM: Round [129] log likelihood: -13970.001162 EM: Round [130] log likelihood: -13969.996860 EM: Round [131] log likelihood: -13969.992590 EM: Round [132] log likelihood: -13969.988351 EM: Round [133] log likelihood: -13969.984144 EM: Round [134] log likelihood: -13969.979966 EM: Round [135] log likelihood: -13969.975820 EM: Round [136] log likelihood: -13969.971703 EM: Round [137] log likelihood: -13969.967615 EM: Round [138] log likelihood: -13969.963557 EM: Round [139] log likelihood: -13969.959528 EM: Round [140] log likelihood: -13969.955527 EM: Round [141] log likelihood: -13969.951555 EM: Round [142] log likelihood: -13969.947611 EM: Round [143] log likelihood: -13969.943694 EM: Round [144] log likelihood: -13969.939805 EM: Round [145] log likelihood: -13969.935943 EM: Round [146] log likelihood: -13969.932108 EM: Round [147] log likelihood: -13969.928299 EM: Round [148] log likelihood: -13969.924516 EM: Round [149] log likelihood: -13969.920759 EM: Round [150] log likelihood: -13969.917028 EM: Round [151] log likelihood: -13969.913323 EM: Round [152] log likelihood: -13969.909642 EM: Round [153] log likelihood: -13969.905986 EM: Round [154] log likelihood: -13969.902355 EM: Round [155] log likelihood: -13969.898749 EM: Round [156] log likelihood: -13969.895166 EM: Round [157] log likelihood: -13969.891607 EM: Round [158] log likelihood: -13969.888072 EM: Round [159] log likelihood: -13969.884560 EM: Round [160] log likelihood: -13969.881072 EM: Round [161] log likelihood: -13969.877606 EM: Round [162] log likelihood: -13969.874163 EM: Round [163] log likelihood: -13969.870742 EM: Round [164] log likelihood: -13969.867344 EM: Round [165] log likelihood: -13969.863968 EM: Round [166] log likelihood: -13969.860613 EM: Round [167] log likelihood: -13969.857280 EM: Round [168] log likelihood: -13969.853969 EM: Round [169] log likelihood: -13969.850678 EM: Round [170] log likelihood: -13969.847409 EM: Round [171] log likelihood: -13969.844160 EM: Round [172] log likelihood: -13969.840932 EM: Round [173] log likelihood: -13969.837724 EM: Round [174] log likelihood: -13969.834536 EM: Round [175] log likelihood: -13969.831368 EM: Round [176] log likelihood: -13969.828221 EM: Round [177] log likelihood: -13969.825092 EM: Round [178] log likelihood: -13969.821983 EM: Round [179] log likelihood: -13969.818894 EM: Round [180] log likelihood: -13969.815823 EM: Round [181] log likelihood: -13969.812772 EM: Round [182] log likelihood: -13969.809739 EM: Round [183] log likelihood: -13969.806724 EM: Round [184] log likelihood: -13969.803728 EM: Round [185] log likelihood: -13969.800750 EM: Round [186] log likelihood: -13969.797791 EM: Round [187] log likelihood: -13969.794849 EM: Round [188] log likelihood: -13969.791925 EM: Round [189] log likelihood: -13969.789018 EM: Round [190] log likelihood: -13969.786129 EM: Round [191] log likelihood: -13969.783257 EM: Round [192] log likelihood: -13969.780402 EM: Round [193] log likelihood: -13969.777564 EM: Round [194] log likelihood: -13969.774743 EM: Round [195] log likelihood: -13969.771939 EM: Round [196] log likelihood: -13969.769151 EM: Round [197] log likelihood: -13969.766379 EM: Round [198] log likelihood: -13969.763624 EM: Round [199] log likelihood: -13969.760885 EM: Round [200] log likelihood: -13969.758162 EM: Round [201] log likelihood: -13969.755454 EM: Round [202] log likelihood: -13969.752762 EM: Round [203] log likelihood: -13969.750086 EM: Round [204] log likelihood: -13969.747425 EM: Round [205] log likelihood: -13969.744780 EM: Round [206] log likelihood: -13969.742149 EM: Round [207] log likelihood: -13969.739534 EM: Round [208] log likelihood: -13969.736934 EM: Round [209] log likelihood: -13969.734348 EM: Round [210] log likelihood: -13969.731777 EM: Round [211] log likelihood: -13969.729221 EM: Round [212] log likelihood: -13969.726679 EM: Round [213] log likelihood: -13969.724151 EM: Round [214] log likelihood: -13969.721638 EM: Round [215] log likelihood: -13969.719138 EM: Round [216] log likelihood: -13969.716653 EM: Round [217] log likelihood: -13969.714181 EM: Round [218] log likelihood: -13969.711724 EM: Round [219] log likelihood: -13969.709279 EM: Round [220] log likelihood: -13969.706849 EM: Round [221] log likelihood: -13969.704431 EM: Round [222] log likelihood: -13969.702027 EM: Round [223] log likelihood: -13969.699637 EM: Round [224] log likelihood: -13969.697259 EM: Round [225] log likelihood: -13969.694894 EM: Round [226] log likelihood: -13969.692542 EM: Round [227] log likelihood: -13969.690204 EM: Round [228] log likelihood: -13969.687877 EM: Round [229] log likelihood: -13969.685564 EM: Round [230] log likelihood: -13969.683262 EM: Round [231] log likelihood: -13969.680974 EM: Round [232] log likelihood: -13969.678697 EM: Round [233] log likelihood: -13969.676433 EM: Round [234] log likelihood: -13969.674181 EM: Round [235] log likelihood: -13969.671941 EM: Round [236] log likelihood: -13969.669712 EM: Round [237] log likelihood: -13969.667496 EM: Round [238] log likelihood: -13969.665291 EM: Round [239] log likelihood: -13969.663099 EM: Round [240] log likelihood: -13969.660917 EM: Round [241] log likelihood: -13969.658747 EM: Round [242] log likelihood: -13969.656589 EM: Round [243] log likelihood: -13969.654442 EM: Round [244] log likelihood: -13969.652306 EM: Round [245] log likelihood: -13969.650182 EM: Round [246] log likelihood: -13969.648068 EM: Round [247] log likelihood: -13969.645965 EM: Round [248] log likelihood: -13969.643874 EM: Round [249] log likelihood: -13969.641793 EM: Round [250] log likelihood: -13969.639723 EM: Round [251] log likelihood: -13969.637663 EM: Round [252] log likelihood: -13969.635615 EM: Round [253] log likelihood: -13969.633576 EM: Round [254] log likelihood: -13969.631549 EM: Round [255] log likelihood: -13969.629531 EM: Round [256] log likelihood: -13969.627524 EM: Round [257] log likelihood: -13969.625527 EM: Round [258] log likelihood: -13969.623541 EM: Round [259] log likelihood: -13969.621564 EM: Round [260] log likelihood: -13969.619597 EM: Round [261] log likelihood: -13969.617641 EM: Round [262] log likelihood: -13969.615694 EM: Round [263] log likelihood: -13969.613757 EM: Round [264] log likelihood: -13969.611830 EM: Round [265] log likelihood: -13969.609912 EM: Round [266] log likelihood: -13969.608004 EM: Round [267] log likelihood: -13969.606106 EM: Round [268] log likelihood: -13969.604217 EM: Round [269] log likelihood: -13969.602338 EM: Round [270] log likelihood: -13969.600467 EM: Round [271] log likelihood: -13969.598607 EM: Round [272] log likelihood: -13969.596755 EM: Round [273] log likelihood: -13969.594912 EM: Round [274] log likelihood: -13969.593079 EM: Round [275] log likelihood: -13969.591255 EM: Round [276] log likelihood: -13969.589439 EM: Round [277] log likelihood: -13969.587633 EM: Round [278] log likelihood: -13969.585835 EM: Round [279] log likelihood: -13969.584046 EM: Round [280] log likelihood: -13969.582266 EM: Round [281] log likelihood: -13969.580495 EM: Round [282] log likelihood: -13969.578732 EM: Round [283] log likelihood: -13969.576977 EM: Round [284] log likelihood: -13969.575232 EM: Round [285] log likelihood: -13969.573494 EM: Round [286] log likelihood: -13969.571765 EM: Round [287] log likelihood: -13969.570045 EM: Round [288] log 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likelihood: -13969.400568 EM: Round [419] log likelihood: -13969.399606 EM: Round [420] log likelihood: -13969.398648 EM: Round [421] log likelihood: -13969.397694 EM: Round [422] log likelihood: -13969.396743 EM: Round [423] log likelihood: -13969.395797 EM: Round [424] log likelihood: -13969.394854 EM: Round [425] log likelihood: -13969.393915 EM: Round [426] log likelihood: -13969.392980 EM: Round [427] log likelihood: -13969.392049 EM: Round [428] log likelihood: -13969.391121 EM: Round [429] log likelihood: -13969.390197 EM: Round [430] log likelihood: -13969.389277 EM: Round [431] log likelihood: -13969.388361 EM: Round [432] log likelihood: -13969.387448 EM: Round [433] log likelihood: -13969.386539 EM: Round [434] log likelihood: -13969.385633 EM: Round [435] log likelihood: -13969.384732 EM: Round [436] log likelihood: -13969.383833 EM: Round [437] log likelihood: -13969.382939 EM: Round [438] log likelihood: -13969.382048 EM: Round [439] log likelihood: -13969.381160 EM: Round [440] log likelihood: -13969.380276 EM: Round [441] log likelihood: -13969.379396 EM: Round [442] log likelihood: -13969.378519 EM: Round [443] log likelihood: -13969.377645 EM: Round [444] log likelihood: -13969.376775 EM: Round [445] log likelihood: -13969.375909 EM: Round [446] log likelihood: -13969.375046 EM: Round [447] log likelihood: -13969.374186 EM: Round [448] log likelihood: -13969.373330 EM: Round [449] log likelihood: -13969.372477 EM: Round [450] log likelihood: -13969.371628 EM: Round [451] log likelihood: -13969.370781 EM: Round [452] log likelihood: -13969.369939 EM: Round [453] log likelihood: -13969.369099 EM: Round [454] log likelihood: -13969.368263 EM: Round [455] log likelihood: -13969.367430 EM: Round [456] log likelihood: -13969.366601 EM: Round [457] log likelihood: -13969.365774 EM: Round [458] log likelihood: -13969.364951 EM: Round [459] log likelihood: -13969.364131 EM: Round [460] log likelihood: -13969.363315 EM: Round [461] log likelihood: 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likelihood: -13969.345385 EM: Round [484] log likelihood: -13969.344641 EM: Round [485] log likelihood: -13969.343900 EM: Round [486] log likelihood: -13969.343162 EM: Round [487] log likelihood: -13969.342427 EM: Round [488] log likelihood: -13969.341694 EM: Round [489] log likelihood: -13969.340964 EM: Round [490] log likelihood: -13969.340238 EM: Round [491] log likelihood: -13969.339513 EM: Round [492] log likelihood: -13969.338792 EM: Round [493] log likelihood: -13969.338073 EM: Round [494] log likelihood: -13969.337358 EM: Round [495] log likelihood: -13969.336645 EM: Round [496] log likelihood: -13969.335934 EM: Round [497] log likelihood: -13969.335226 EM: Round [498] log likelihood: -13969.334521 EM: Round [499] log likelihood: -13969.333819 EM: Round [500] log likelihood: -13969.333120 EM: Round [501] log likelihood: -13969.332423 EM: Round [502] log likelihood: -13969.331728 EM: Round [503] log likelihood: -13969.331037 EM: Round [504] log likelihood: -13969.330348 EM: Round [505] log likelihood: -13969.329661 EM: Round [506] log likelihood: -13969.328977 EM: Round [507] log likelihood: -13969.328296 EM: Round [508] log likelihood: -13969.327617 EM: Round [509] log likelihood: -13969.326941 EM: Round [510] log likelihood: -13969.326268 EM: Round [511] log likelihood: -13969.325597 EM: Round [512] log likelihood: -13969.324928 EM: Round [513] log likelihood: -13969.324262 EM: Round [514] log likelihood: -13969.323599 EM: Round [515] log likelihood: -13969.322938 EM: Round [516] log likelihood: -13969.322279 EM: Round [517] log likelihood: -13969.321623 EM: Round [518] log likelihood: -13969.320970 EM: Round [519] log likelihood: -13969.320319 EM: Round [520] log likelihood: -13969.319670 EM: Round [521] log likelihood: -13969.319024 EM: Round [522] log likelihood: -13969.318380 EM: Round [523] log likelihood: -13969.317739 EM: Round [524] log likelihood: -13969.317100 EM: Round [525] log likelihood: -13969.316463 EM: Round [526] log likelihood: -13969.315829 EM: Round [527] log likelihood: -13969.315197 EM: Round [528] log likelihood: -13969.314568 EM: Round [529] log likelihood: -13969.313940 EM: Round [530] log likelihood: -13969.313316 EM: Round [531] log likelihood: -13969.312693 EM: Round [532] log likelihood: -13969.312073 EM: Round [533] log likelihood: -13969.311455 EM: Round [534] log likelihood: -13969.310840 EM: Round [535] log likelihood: -13969.310226 EM: Round [536] log likelihood: -13969.309615 EM: Round [537] log likelihood: -13969.309007 EM: Round [538] log likelihood: -13969.308400 EM: Round [539] log likelihood: -13969.307796 EM: Round [540] log likelihood: -13969.307194 EM: Round [541] log likelihood: -13969.306594 EM: Round [542] log likelihood: -13969.305997 EM: Round [543] log likelihood: -13969.305402 EM: Round [544] log likelihood: -13969.304809 EM: Round [545] log likelihood: -13969.304218 EM: Round [546] log likelihood: -13969.303629 EM: Round [547] log likelihood: -13969.303042 EM: Round [548] log 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Round [570] log likelihood: -13969.290131 EM: Round [571] log likelihood: -13969.289594 EM: Round [572] log likelihood: -13969.289059 EM: Round [573] log likelihood: -13969.288526 EM: Round [574] log likelihood: -13969.287994 EM: Round [575] log likelihood: -13969.287465 EM: Round [576] log likelihood: -13969.286938 EM: Round [577] log likelihood: -13969.286412 EM: Round [578] log likelihood: -13969.285889 EM: Round [579] log likelihood: -13969.285367 EM: Round [580] log likelihood: -13969.284847 EM: Round [581] log likelihood: -13969.284329 EM: Round [582] log likelihood: -13969.283813 EM: Round [583] log likelihood: -13969.283299 EM: Round [584] log likelihood: -13969.282787 EM: Round [585] log likelihood: -13969.282277 EM: Round [586] log likelihood: -13969.281768 EM: Round [587] log likelihood: -13969.281261 EM: Round [588] log likelihood: -13969.280756 EM: Round [589] log likelihood: -13969.280253 EM: Round [590] log likelihood: -13969.279752 EM: Round [591] log likelihood: -13969.279253 EM: Round [592] log likelihood: -13969.278755 EM: Round [593] log likelihood: -13969.278259 EM: Round [594] log likelihood: -13969.277765 EM: Round [595] log likelihood: -13969.277273 EM: Round [596] log likelihood: -13969.276782 EM: Round [597] log likelihood: -13969.276293 EM: Round [598] log likelihood: -13969.275806 EM: Round [599] log likelihood: -13969.275321 EM: Round [600] log likelihood: -13969.274837 EM: Round [601] log likelihood: -13969.274356 EM: Round [602] log likelihood: -13969.273875 EM: Round [603] log likelihood: -13969.273397 EM: Round [604] log likelihood: -13969.272920 EM: Round [605] log likelihood: -13969.272445 EM: Round [606] log likelihood: -13969.271972 EM: Round [607] log likelihood: -13969.271501 EM: Round [608] log likelihood: -13969.271031 EM: Round [609] log likelihood: -13969.270563 EM: Round [610] log likelihood: -13969.270096 EM: Round [611] log likelihood: -13969.269631 EM: Round [612] log likelihood: -13969.269168 EM: Round [613] log 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Round [635] log likelihood: -13969.258957 EM: Round [636] log likelihood: -13969.258532 EM: Round [637] log likelihood: -13969.258108 EM: Round [638] log likelihood: -13969.257686 EM: Round [639] log likelihood: -13969.257265 EM: Round [640] log likelihood: -13969.256846 EM: Round [641] log likelihood: -13969.256428 EM: Round [642] log likelihood: -13969.256012 EM: Round [643] log likelihood: -13969.255597 EM: Round [644] log likelihood: -13969.255183 EM: Round [645] log likelihood: -13969.254771 EM: Round [646] log likelihood: -13969.254361 EM: Round [647] log likelihood: -13969.253951 EM: Round [648] log likelihood: -13969.253544 EM: Round [649] log likelihood: -13969.253137 EM: Round [650] log likelihood: -13969.252733 EM: Round [651] log likelihood: -13969.252329 EM: Round [652] log likelihood: -13969.251927 EM: Round [653] log likelihood: -13969.251527 EM: Round [654] log likelihood: -13969.251127 EM: Round [655] log likelihood: -13969.250730 EM: Round [656] log likelihood: -13969.250333 EM: Round [657] log likelihood: -13969.249938 EM: Round [658] log likelihood: -13969.249545 EM: Round [659] log likelihood: -13969.249152 EM: Round [660] log likelihood: -13969.248761 EM: Round [661] log likelihood: -13969.248372 EM: Round [662] log likelihood: -13969.247984 EM: Round [663] log likelihood: -13969.247597 EM: Round [664] log likelihood: -13969.247212 EM: Round [665] log likelihood: -13969.246827 EM: Round [666] log likelihood: -13969.246445 EM: Round [667] log likelihood: -13969.246063 EM: Round [668] log likelihood: -13969.245683 EM: Round [669] log likelihood: -13969.245304 EM: Round [670] log likelihood: -13969.244927 EM: Round [671] log likelihood: -13969.244551 EM: Round [672] log likelihood: -13969.244176 EM: Round [673] log likelihood: -13969.243802 EM: Round [674] log likelihood: -13969.243430 EM: Round [675] log likelihood: -13969.243059 EM: Round [676] log likelihood: -13969.242690 EM: Round [677] log likelihood: -13969.242321 EM: Round [678] log 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Round [700] log likelihood: -13969.234192 EM: Round [701] log likelihood: -13969.233853 EM: Round [702] log likelihood: -13969.233515 EM: Round [703] log likelihood: -13969.233179 EM: Round [704] log likelihood: -13969.232843 EM: Round [705] log likelihood: -13969.232509 EM: Round [706] log likelihood: -13969.232176 EM: Round [707] log likelihood: -13969.231843 EM: Round [708] log likelihood: -13969.231513 EM: Round [709] log likelihood: -13969.231183 EM: Round [710] log likelihood: -13969.230854 EM: Round [711] log likelihood: -13969.230527 EM: Round [712] log likelihood: -13969.230200 EM: Round [713] log likelihood: -13969.229875 EM: Round [714] log likelihood: -13969.229551 EM: Round [715] log likelihood: -13969.229228 EM: Round [716] log likelihood: -13969.228906 EM: Round [717] log likelihood: -13969.228585 EM: Round [718] log likelihood: -13969.228265 EM: Round [719] log likelihood: -13969.227947 EM: Round [720] log likelihood: -13969.227629 EM: Round [721] log likelihood: -13969.227313 EM: Round [722] log likelihood: -13969.226997 EM: Round [723] log likelihood: -13969.226683 EM: Round [724] log likelihood: -13969.226370 EM: Round [725] log likelihood: -13969.226058 EM: Round [726] log likelihood: -13969.225747 EM: Round [727] log likelihood: -13969.225437 EM: Round [728] log likelihood: -13969.225128 EM: Round [729] log likelihood: -13969.224820 EM: Round [730] log likelihood: -13969.224513 EM: Round [731] log likelihood: -13969.224207 EM: Round [732] log likelihood: -13969.223902 EM: Round [733] log likelihood: -13969.223598 EM: Round [734] log likelihood: -13969.223296 EM: Round [735] log likelihood: -13969.222994 EM: Round [736] log likelihood: -13969.222693 EM: Round [737] log likelihood: -13969.222394 EM: Round [738] log likelihood: -13969.222095 EM: Round [739] log likelihood: -13969.221798 EM: Round [740] log likelihood: -13969.221501 EM: Round [741] log likelihood: -13969.221206 EM: Round [742] log likelihood: -13969.220911 EM: Round [743] log likelihood: -13969.220617 EM: Round [744] log likelihood: -13969.220325 EM: Round [745] log likelihood: -13969.220033 EM: Round [746] log likelihood: -13969.219743 EM: Round [747] log likelihood: -13969.219453 EM: Round [748] log likelihood: -13969.219165 EM: Round [749] log likelihood: -13969.218877 EM: Round [750] log likelihood: -13969.218590 EM: Round [751] log likelihood: -13969.218305 EM: Round [752] log likelihood: -13969.218020 EM: Round [753] log likelihood: -13969.217736 EM: Round [754] log likelihood: -13969.217453 EM: Round [755] log likelihood: -13969.217172 EM: Round [756] log likelihood: -13969.216891 EM: Round [757] log likelihood: -13969.216611 EM: Round [758] log likelihood: -13969.216332 EM: Round [759] log likelihood: -13969.216054 EM: Round [760] log likelihood: -13969.215777 EM: Round [761] log likelihood: -13969.215501 EM: Round [762] log likelihood: -13969.215225 EM: Round [763] log likelihood: -13969.214951 EM: Round [764] log likelihood: -13969.214678 EM: Round [765] log likelihood: -13969.214405 EM: Round [766] log likelihood: -13969.214134 EM: Round [767] log likelihood: -13969.213863 EM: Round [768] log likelihood: -13969.213593 EM: Round [769] log likelihood: -13969.213325 EM: Round [770] log likelihood: -13969.213057 EM: Round [771] log likelihood: -13969.212790 EM: Round [772] log likelihood: -13969.212524 EM: Round [773] log likelihood: -13969.212259 EM: Round [774] log likelihood: -13969.211994 EM: Round [775] log likelihood: -13969.211731 EM: Round [776] log likelihood: -13969.211468 EM: Round [777] log likelihood: -13969.211207 EM: Round [778] log likelihood: -13969.210946 EM: Round [779] log likelihood: -13969.210686 EM: Round [780] log likelihood: -13969.210427 EM: Round [781] log likelihood: -13969.210169 EM: Round [782] log likelihood: -13969.209912 EM: Round [783] log likelihood: -13969.209655 EM: Round [784] log likelihood: -13969.209400 EM: Round [785] log likelihood: -13969.209145 EM: Round [786] log likelihood: -13969.208891 EM: Round [787] log likelihood: -13969.208639 EM: Round [788] log likelihood: -13969.208386 EM: Round [789] log likelihood: -13969.208135 EM: Round [790] log likelihood: -13969.207885 EM: Round [791] log likelihood: -13969.207635 EM: Round [792] log likelihood: -13969.207386 EM: Round [793] log likelihood: -13969.207139 EM: Round [794] log likelihood: -13969.206891 EM: Round [795] log likelihood: -13969.206645 EM: Round [796] log likelihood: -13969.206400 EM: Round [797] log likelihood: -13969.206155 EM: Round [798] log likelihood: -13969.205911 EM: Round [799] log likelihood: -13969.205668 EM: Round [800] log likelihood: -13969.205426 EM: Round [801] log likelihood: -13969.205185 EM: Round [802] log likelihood: -13969.204944 EM: Round [803] log likelihood: -13969.204705 EM: Round [804] log likelihood: -13969.204466 EM: Round [805] log likelihood: -13969.204228 EM: Round [806] log likelihood: -13969.203990 EM: Round [807] log likelihood: -13969.203754 EM: Round [808] log likelihood: -13969.203518 EM: Round [809] log likelihood: -13969.203283 EM: Round [810] log likelihood: -13969.203049 EM: Round [811] log likelihood: -13969.202815 EM: Round [812] log likelihood: -13969.202583 EM: Round [813] log likelihood: -13969.202351 EM: Round [814] log likelihood: -13969.202120 EM: Round [815] log likelihood: -13969.201890 EM: Round [816] log likelihood: -13969.201660 EM: Round [817] log likelihood: -13969.201431 EM: Round [818] log likelihood: -13969.201203 EM: Round [819] log likelihood: -13969.200976 EM: Round [820] log likelihood: -13969.200750 EM: Round [821] log likelihood: -13969.200524 EM: Round [822] log likelihood: -13969.200299 EM: Round [823] log likelihood: -13969.200075 EM: Round [824] log likelihood: -13969.199851 EM: Round [825] log likelihood: -13969.199629 EM: Round [826] log likelihood: -13969.199407 EM: Round [827] log likelihood: -13969.199185 EM: Round [828] log likelihood: -13969.198965 EM: Round [829] log likelihood: -13969.198745 EM: Round [830] log likelihood: -13969.198526 EM: Round [831] log likelihood: -13969.198308 EM: Round [832] log likelihood: -13969.198090 EM: Round [833] log likelihood: -13969.197873 EM: Round [834] log likelihood: -13969.197657 EM: Round [835] log likelihood: -13969.197441 EM: Round [836] log likelihood: -13969.197227 EM: Round [837] log likelihood: -13969.197013 EM: Round [838] log likelihood: -13969.196799 EM: Round [839] log likelihood: -13969.196587 EM: Round [840] log likelihood: -13969.196375 EM: Round [841] log likelihood: -13969.196164 EM: Round [842] log likelihood: -13969.195953 EM: Round [843] log likelihood: -13969.195743 EM: Round [844] log likelihood: -13969.195534 EM: Round [845] log likelihood: -13969.195326 EM: Round [846] log likelihood: -13969.195118 EM: Round [847] log likelihood: -13969.194911 EM: Round [848] log likelihood: -13969.194705 EM: Round [849] log likelihood: -13969.194499 EM: Round [850] log likelihood: -13969.194294 EM: Round [851] log likelihood: -13969.194090 EM: Round [852] log likelihood: -13969.193886 EM: Round [853] log likelihood: -13969.193683 EM: Round [854] log likelihood: -13969.193481 EM: Round [855] log likelihood: -13969.193280 EM: Round [856] log likelihood: -13969.193079 EM: Round [857] log likelihood: -13969.192878 EM: Round [858] log likelihood: -13969.192679 EM: Round [859] log likelihood: -13969.192480 EM: Round [860] log likelihood: -13969.192281 EM: Round [861] log likelihood: -13969.192084 EM: Round [862] log likelihood: -13969.191887 EM: Round [863] log likelihood: -13969.191690 EM: Round [864] log likelihood: -13969.191495 EM: Round [865] log likelihood: -13969.191300 EM: Round [866] log likelihood: -13969.191105 EM: Round [867] log likelihood: -13969.190912 EM: Round [868] log likelihood: -13969.190718 EM: Round [869] log likelihood: -13969.190526 EM: Round [870] log likelihood: -13969.190334 EM: Round [871] log likelihood: -13969.190143 EM: Round [872] log likelihood: -13969.189952 EM: Round [873] log likelihood: -13969.189762 EM: Round [874] log likelihood: -13969.189573 EM: Round [875] log likelihood: -13969.189384 EM: Round [876] log likelihood: -13969.189196 EM: Round [877] log likelihood: -13969.189009 EM: Round [878] log likelihood: -13969.188822 EM: Round [879] log likelihood: -13969.188636 EM: Round [880] log likelihood: -13969.188450 EM: Round [881] log likelihood: -13969.188265 EM: Round [882] log likelihood: -13969.188081 EM: Round [883] log likelihood: -13969.187897 EM: Round [884] log likelihood: -13969.187714 EM: Round [885] log likelihood: -13969.187531 EM: Round [886] log likelihood: -13969.187349 EM: Round [887] log likelihood: -13969.187168 EM: Round [888] log likelihood: -13969.186987 EM: Round [889] log likelihood: -13969.186807 EM: Round [890] log likelihood: -13969.186627 EM: Round [891] log likelihood: -13969.186448 EM: Round [892] log likelihood: -13969.186270 EM: Round [893] log likelihood: -13969.186092 EM: Round [894] log likelihood: -13969.185915 EM: Round [895] log likelihood: -13969.185738 EM: Round [896] log likelihood: -13969.185562 EM: Round [897] log likelihood: -13969.185386 EM: Round [898] log likelihood: -13969.185211 EM: Round [899] log likelihood: -13969.185037 EM: Round [900] log likelihood: -13969.184863 EM: Round [901] log likelihood: -13969.184690 EM: Round [902] log likelihood: -13969.184517 EM: Round [903] log likelihood: -13969.184345 EM: Round [904] log likelihood: -13969.184174 EM: Round [905] log likelihood: -13969.184003 EM: Round [906] log likelihood: -13969.183832 EM: Round [907] log likelihood: -13969.183662 EM: Round [908] log likelihood: -13969.183493 EM: Round [909] log likelihood: -13969.183324 EM: Round [910] log likelihood: -13969.183156 EM: Round [911] log likelihood: -13969.182988 EM: Round [912] log likelihood: -13969.182821 EM: Round [913] log likelihood: -13969.182655 EM: Round [914] log likelihood: -13969.182489 EM: Round [915] log likelihood: -13969.182323 EM: Round [916] log likelihood: -13969.182158 EM: Round [917] log likelihood: -13969.181994 EM: Round [918] log likelihood: -13969.181830 EM: Round [919] log likelihood: -13969.181667 EM: Round [920] log likelihood: -13969.181504 EM: Round [921] log likelihood: -13969.181342 EM: Round [922] log likelihood: -13969.181180 EM: Round [923] log likelihood: -13969.181019 EM: Round [924] log likelihood: -13969.180858 EM: Round [925] log likelihood: -13969.180698 EM: Round [926] log likelihood: -13969.180539 EM: Round [927] log likelihood: -13969.180379 EM: Round [928] log likelihood: -13969.180221 EM: Round [929] log likelihood: -13969.180063 EM: Round [930] log likelihood: -13969.179905 EM: Round [931] log likelihood: -13969.179748 EM: Round [932] log likelihood: -13969.179592 EM: Round [933] log likelihood: -13969.179436 EM: Round [934] log likelihood: -13969.179280 EM: Round [935] log likelihood: -13969.179125 EM: Round [936] log likelihood: -13969.178971 EM: Round [937] log likelihood: -13969.178817 EM: Round [938] log likelihood: -13969.178663 EM: Round [939] log likelihood: -13969.178510 EM: Round [940] log likelihood: -13969.178358 EM: Round [941] log likelihood: -13969.178206 EM: Round [942] log likelihood: -13969.178055 EM: Round [943] log likelihood: -13969.177904 EM: Round [944] log likelihood: -13969.177753 EM: Round [945] log likelihood: -13969.177603 EM: Round [946] log likelihood: -13969.177454 EM: Round [947] log likelihood: -13969.177304 EM: Round [948] log likelihood: -13969.177156 EM: Round [949] log likelihood: -13969.177008 EM: Round [950] log likelihood: -13969.176860 EM: Round [951] log likelihood: -13969.176713 EM: Round [952] log likelihood: -13969.176567 EM: Round [953] log likelihood: -13969.176420 EM: Round [954] log likelihood: -13969.176275 EM: Round [955] log likelihood: -13969.176130 EM: Round [956] log likelihood: -13969.175985 EM: Round [957] log likelihood: -13969.175841 EM: Round [958] log likelihood: -13969.175697 EM: Round [959] log likelihood: -13969.175553 EM: Round [960] log likelihood: -13969.175411 EM: Round [961] log likelihood: -13969.175268 EM: Round [962] log likelihood: -13969.175126 EM: Round [963] log likelihood: -13969.174985 EM: Round [964] log likelihood: -13969.174844 EM: Round [965] log likelihood: -13969.174703 EM: Round [966] log likelihood: -13969.174563 EM: Round [967] log likelihood: -13969.174424 EM: Round [968] log likelihood: -13969.174284 EM: Round [969] log likelihood: -13969.174146 EM: Round [970] log likelihood: -13969.174007 EM: Round [971] log likelihood: -13969.173869 EM: Round [972] log likelihood: -13969.173732 EM: Round [973] log likelihood: -13969.173595 EM: Round [974] log likelihood: -13969.173459 EM: Round [975] log likelihood: -13969.173323 EM: Round [976] log likelihood: -13969.173187 EM: Round [977] log likelihood: -13969.173052 EM: Round [978] log likelihood: -13969.172917 EM: Round [979] log likelihood: -13969.172783 EM: Round [980] log likelihood: -13969.172649 EM: Round [981] log likelihood: -13969.172515 EM: Round [982] log likelihood: -13969.172382 EM: Round [983] log likelihood: -13969.172250 EM: Round [984] log likelihood: -13969.172118 EM: Round [985] log likelihood: -13969.171986 EM: Round [986] log likelihood: -13969.171855 EM: Round [987] log likelihood: -13969.171724 EM: Round [988] log likelihood: -13969.171593 EM: Round [989] log likelihood: -13969.171463 EM: Round [990] log likelihood: -13969.171334 EM: Round [991] log likelihood: -13969.171205 EM: Round [992] log likelihood: -13969.171076 EM: Round [993] log likelihood: -13969.170948 EM: Round [994] log likelihood: -13969.170820 EM: Round [995] log likelihood: -13969.170692 EM: Round [996] log likelihood: -13969.170565 EM: Round [997] log likelihood: -13969.170438 EM: Round [998] log likelihood: -13969.170312 EM: Round [999] log likelihood: -13969.170186 EM: Round [1000] log likelihood: -13969.170061 EM: Round [1001] log likelihood: -13969.169936 Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam" Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/tih_rna_sample_00614_B23MVV7LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa > /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir -done, see /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -12221.393982 EM: Round [1] log likelihood: -12221.380464 EM: Round [2] log likelihood: -12221.380402 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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_1.fastp.fastq.gz: 253418477 Execution Time = 4.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa --gtf /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf > /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fa --gtf /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf > /tmp/nxf.uMS6WptGv5/fi_workdir/microH.dat Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.uMS6WptGv5/fi_workdir/microH.dat /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/microH.dat /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.uMS6WptGv5 --json_outfile /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00614_B23MVV7LT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.uMS6WptGv5 --json_outfile /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00614_B23MVV7LT4_1 Running: touch /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00614_B23MVV7LT4_1 --html_output /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.03 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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00614_B23MVV7LT4_1 --html_output /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000267489.5] WARNING, no entry stored in dbm for [ENSG00000267489.5] WARNING, no entry stored in dbm for [ENSG00000267489.5] WARNING, no entry stored in dbm for [ENSG00000267489.5] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000283001.2] 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 [ENSG00000236548.2] WARNING, no entry stored in dbm for [ENSG00000236548.2] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000277702.1] WARNING, no entry stored in dbm for [ENSG00000277146.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000286784.1] WARNING, no entry stored in dbm for [ENSG00000267577.1] WARNING, no entry stored in dbm for [ENSG00000267577.1] WARNING, no entry stored in dbm for [ENSG00000176124.15] WARNING, no entry stored in dbm for [ENSG00000176124.15] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.uMS6WptGv5/ctat_genome_lib_build_dir > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.uMS6WptGv5/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory