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/8d/affa4a10f0af05afab6983ebc42065/tih_rna_sample_00596_B23MVV7LT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/26efdc9fcae3c29e8b6e2eeb07293e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/d9fecba3758cc767aae61d03d46eab/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/26efdc9fcae3c29e8b6e2eeb07293e/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/d9fecba3758cc767aae61d03d46eab/tih_rna_sample_00596_B23MVV7LT4_1_2.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_00596_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00596_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/cytoBand.txt Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed -parsing GTF file: /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00596_B23MVV7LT4_1.star --out_dir /tmp/nxf.y4PgUajcQJ/fi_workdir --reads "/tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:15:59 ..... started STAR run Jun 08 10:15:59 ..... loading genome Jun 08 10:17:54 ... generating Suffix Array index Jun 08 10:22:06 ... completed Suffix Array index Jun 08 10:22:06 ..... processing annotations GTF Jun 08 10:22:07 ..... inserting junctions into the genome indices Jun 08 10:23:15 ..... started mapping Jun 08 11:49:07 ..... finished mapping Jun 08 11:49:11 ..... started sorting BAM Jun 08 11:49:15 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00596_B23MVV7LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00596_B23MVV7LT4_1.star.sortedByCoord.out.bam Execution Time = 93.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00596_B23MVV7LT4_1.star --out_dir /tmp/nxf.y4PgUajcQJ/fi_workdir --reads "/tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:50:04 : INFO : Done. Execution Time = 0.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf -parsing /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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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Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1056, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 47, ' ** passed ** ' => 16682, 'num_hits: 10 != num_counted_on_fusion_contigs 7 ' => 7, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 242, 'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 21, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 232, 'per_id < 96' => 26122, 'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 45, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 464, 'exons hit < 2' => 9, 'num_hits: 9 != num_counted_on_fusion_contigs 5 ' => 5, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 10, 'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 8, 'small anchor length' => 83, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 30, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 2137, 'num_hits: 8 != num_counted_on_fusion_contigs 3 ' => 3, 'low complexity anchor region' => 29, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 129, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 44, 'excessive soft clipping' => 67034, 'num genes matched < 2' => 157, 'num_hits: 8 != num_counted_on_fusion_contigs 5 ' => 10, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 48, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12 }; -writing fusion junction support info. Execution Time = 4.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [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] -fusion SPANNING read extraction for scaff: ADAP1--C7orf50 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: ADCY1--GCK [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] 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[144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] -fusion SPANNING read extraction for scaff: ADGRF1--TNFRSF21 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] -fusion SPANNING read extraction for scaff: AHCY--AL356299.1 [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] 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[391000] [392000] [393000] [394000] [395000] -fusion SPANNING read extraction for scaff: AKAP8L--BRD4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: ANKRD45--KLHL20 [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] -fusion SPANNING read extraction for scaff: ASPH--TACC2 [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] 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ATP7A--ATRX [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] -fusion SPANNING read extraction for scaff: ATP7A--MAGT1 [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] -fusion SPANNING read extraction for scaff: ATXN10--TTC38 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: AVL9--DPY19L1P2 [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] -fusion SPANNING read extraction for scaff: BPTF--LINC00674 [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] -fusion SPANNING read extraction for scaff: CCT2--FRS2 [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: CDC42--CELA3B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: CERS6--NOSTRIN [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] -fusion SPANNING read extraction for scaff: CLIP2--LAT2 [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: CNOT2--TPH2 [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] -fusion SPANNING read extraction for scaff: CNOT2--IRAK3 [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] -fusion SPANNING read extraction for scaff: COX19--C7orf50 [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] -fusion SPANNING read extraction for scaff: CPD--RIT1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: CPNE3--AC060765.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: DCUN1D2--GRTP1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: DIAPH3--RIOK3P1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: DIAPH3--RNU6-38P [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: FBXW7--SLC39A8 [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] -fusion SPANNING read extraction for scaff: FRS2--LYZ [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] -fusion SPANNING read extraction for scaff: FRS2--GRIP1 [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] -fusion SPANNING read extraction for scaff: GRIP1--CPSF6 [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] -fusion SPANNING read extraction for scaff: GRIP1--NUP107 [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] -fusion SPANNING read extraction for scaff: GTF2IRD1--POM121 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] -fusion SPANNING read extraction for scaff: HELB--GRIP1 [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: ITGB6--RBMS1 [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] -fusion SPANNING read extraction for scaff: JUP--P3H4 [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: KANSL1--ARL17B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: LINC02408--GRIP1 [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] -fusion SPANNING read extraction for scaff: MARK4--BRSK1 [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: MIA2--AL049828.1 [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] -fusion SPANNING read extraction for scaff: NBPF14--GNG12 [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] -fusion SPANNING read extraction for scaff: NOTCH2--GNG12 [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] -fusion SPANNING read extraction for scaff: OGT--AC008397.1 [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] -fusion SPANNING read extraction for scaff: OGT--IQCN [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] -fusion SPANNING read extraction for scaff: PAF1--PLEKHG2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -fusion SPANNING read extraction for scaff: PLEKHA2--ADAM2 [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] -fusion SPANNING read extraction for scaff: PRPF8--YWHAE [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: RBM4--PDPK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] -fusion SPANNING read extraction for scaff: RBM4B--PDPK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: RCOR1--TRAF3 [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: RPS6KB1--RNU6-450P [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: RPS6KB1--TUBD1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: SH2D4A--AC100849.1 [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] -fusion SPANNING read extraction for scaff: SKIL--PRKCI [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] -fusion SPANNING read extraction for scaff: SLC4A7--BSG [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: SLC9A2--IL18RAP [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] -fusion SPANNING read extraction for scaff: SPAG9--MBTD1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: STON1--GTF2A1L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] -fusion SPANNING read extraction for scaff: THADA--AC012409.2 [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] -fusion SPANNING read extraction for scaff: TLK2--FAM157A [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [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] -fusion SPANNING read extraction for scaff: TMED10--CENPT [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] -fusion SPANNING read extraction for scaff: TMED10--THAP11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: TMEM163--CCNT2-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] -fusion SPANNING read extraction for scaff: TRA2B--VPS8 [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] -fusion SPANNING read extraction for scaff: TRA2B--C3orf70 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -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] [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: UNC13D--FBF1 [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: ZNF552--RPS29P30 [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: ZNF552--LGALS16 [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: ZNF587--ZSCAN5C -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 5388, 'lacks exon overlap' => 72348 }; Execution Time = 11.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -27654.689121 EM: Round [1] log likelihood: -27613.951167 EM: Round [2] log likelihood: -27598.640474 EM: Round [3] log likelihood: -27586.664461 EM: Round [4] log likelihood: -27577.130748 EM: Round [5] log likelihood: -27569.451215 EM: Round [6] log likelihood: -27563.208906 EM: Round [7] log likelihood: -27558.098626 EM: Round [8] log likelihood: -27553.891292 EM: Round [9] log likelihood: -27550.411450 EM: Round [10] log likelihood: -27547.522502 EM: Round [11] log likelihood: -27545.116669 EM: Round [12] log likelihood: -27543.107971 EM: Round [13] log likelihood: -27541.427189 EM: Round [14] log likelihood: -27540.018177 EM: Round [15] log likelihood: -27538.835103 EM: Round [16] log likelihood: -27537.840354 EM: Round [17] log likelihood: -27537.002927 EM: Round [18] log likelihood: -27536.297174 EM: Round [19] log likelihood: -27535.701804 EM: Round [20] log likelihood: -27535.199100 EM: Round [21] log likelihood: -27534.774285 EM: Round [22] log likelihood: -27534.415009 EM: Round [23] log likelihood: -27534.110933 EM: Round [24] log likelihood: -27533.853389 EM: Round [25] log likelihood: -27533.635104 EM: Round [26] log likelihood: -27533.449964 EM: Round [27] log likelihood: -27533.292826 EM: Round [28] log likelihood: -27533.159363 EM: Round [29] log likelihood: -27533.045928 EM: Round [30] log likelihood: -27532.949445 EM: Round [31] log likelihood: -27532.867322 EM: Round [32] log likelihood: -27532.797369 EM: Round [33] log likelihood: -27532.737736 EM: Round [34] log likelihood: -27532.686860 EM: Round [35] log likelihood: -27532.643420 EM: Round [36] log likelihood: -27532.606298 EM: Round [37] log likelihood: -27532.574546 EM: Round [38] log likelihood: -27532.547365 EM: Round [39] log likelihood: -27532.524074 EM: Round [40] log likelihood: -27532.504097 EM: Round [41] log likelihood: -27532.486947 EM: Round [42] log likelihood: -27532.472208 EM: Round [43] log likelihood: -27532.459529 EM: Round [44] log likelihood: -27532.448609 EM: Round [45] log likelihood: -27532.439196 EM: Round [46] log likelihood: -27532.431071 EM: Round [47] log likelihood: -27532.424051 EM: Round [48] log likelihood: -27532.417979 EM: Round [49] log likelihood: -27532.412720 EM: Round [50] log likelihood: -27532.408160 EM: Round [51] log likelihood: -27532.404202 EM: Round [52] log likelihood: -27532.400763 EM: Round [53] log likelihood: -27532.397770 EM: Round [54] log likelihood: -27532.395162 EM: Round [55] log likelihood: -27532.392888 EM: Round [56] log likelihood: -27532.390902 EM: Round [57] log likelihood: -27532.389166 EM: Round [58] log likelihood: -27532.387646 EM: Round [59] log likelihood: -27532.386315 EM: Round [60] log likelihood: -27532.385146 EM: Round [61] log likelihood: -27532.384120 EM: Round [62] log likelihood: -27532.383218 EM: Round [63] log likelihood: -27532.382423 EM: Round [64] log likelihood: -27532.381723 EM: Round [65] log likelihood: -27532.381106 EM: Round [66] log likelihood: -27532.380560 EM: Round [67] log likelihood: -27532.380078 EM: Round [68] log likelihood: -27532.379652 EM: Round [69] log likelihood: -27532.379274 EM: Round [70] log likelihood: -27532.378939 EM: Round [71] log likelihood: -27532.378642 EM: Round [72] log likelihood: -27532.378378 EM: Round [73] log likelihood: -27532.378144 EM: Round [74] log likelihood: -27532.377935 EM: Round [75] log likelihood: -27532.377750 EM: Round [76] log likelihood: -27532.377585 EM: Round [77] log likelihood: -27532.377437 EM: Round [78] log likelihood: -27532.377306 EM: Round [79] log likelihood: -27532.377188 EM: Round [80] log likelihood: -27532.377084 EM: Round [81] log likelihood: -27532.376990 EM: Stopping iterations at round 81 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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam" Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/tih_rna_sample_00596_B23MVV7LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam Execution Time = 0.07 minutes. CMD: samtools index /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.FusionJuncSpan Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa > /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/tih_rna_sample_00596_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir -done, see /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -27053.256799 EM: Round [1] log likelihood: -27050.230377 EM: Round [2] log likelihood: -27050.223842 EM: Round [3] log likelihood: -27050.223829 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz: 295821566 Execution Time = 5.81 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa --gtf /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fa --gtf /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.gtf > /tmp/nxf.y4PgUajcQJ/fi_workdir/microH.dat Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.y4PgUajcQJ/fi_workdir/microH.dat /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/fi_workdir/microH.dat /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.y4PgUajcQJ --json_outfile /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00596_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.y4PgUajcQJ --json_outfile /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00596_B23MVV7LT4_1 Running: touch /tmp/nxf.y4PgUajcQJ/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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00596_B23MVV7LT4_1 --html_output /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_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.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00596_B23MVV7LT4_1 --html_output /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000231952.3] WARNING, no entry stored in dbm for [ENSG00000237854.3] WARNING, no entry stored in dbm for [ENSG00000237854.3] WARNING, no entry stored in dbm for [ENSG00000236438.7] 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 [ENSG00000224043.8] WARNING, no entry stored in dbm for [ENSG00000275443.2] WARNING, no entry stored in dbm for [ENSG00000203585.4] WARNING, no entry stored in dbm for [ENSG00000258526.7] WARNING, no entry stored in dbm for [ENSG00000258526.7] WARNING, no entry stored in dbm for [ENSG00000258526.7] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.y4PgUajcQJ/ctat_genome_lib_build_dir > /tmp/nxf.y4PgUajcQJ/tih_rna_sample_00596_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.y4PgUajcQJ/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory