Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/46df9a2220cf7ec57118f6d34762c7/659_bUs-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/2106c716cbc35c4cce4dadcd8f7d16/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/2106c716cbc35c4cce4dadcd8f7d16/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/46df9a2220cf7ec57118f6d34762c7/659_bUs-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/39c88e99264e98c8826368f5b8672a/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.27 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.lXs9IJKSup/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.lXs9IJKSup/cytoBand.txt Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed -parsing GTF file: /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bUs-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.lXs9IJKSup/fi_workdir --reads "/tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 04 22:10:26 ..... started STAR run Jun 04 22:10:26 ..... loading genome Jun 04 22:13:29 ... generating Suffix Array index Jun 04 22:19:34 ... completed Suffix Array index Jun 04 22:19:34 ..... processing annotations GTF Jun 04 22:19:35 ..... inserting junctions into the genome indices Jun 04 22:21:14 ..... started mapping Jun 04 23:28:30 ..... finished mapping Jun 04 23:28:32 ..... started sorting BAM Jun 04 23:28:37 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam Execution Time = 78.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bUs-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.lXs9IJKSup/fi_workdir --reads "/tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups 23:29:31 : INFO : Done. Execution Time = 0.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf -parsing /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] 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[7290000] [7300000] [7310000] [7320000] [7330000] [7340000] [7350000] [7360000] [7370000] [7380000] [7390000] [7400000] [7410000] [7420000] [7430000] [7440000] [7450000] [7460000] [7470000] [7480000] [7490000] [7500000] [7510000] [7520000] [7530000] [7540000] [7550000] [7560000] [7570000] [7580000] [7590000] [7600000] [7610000] [7620000] [7630000] [7640000] [7650000] [7660000] [7670000] [7680000] [7690000] [7700000] [7710000] [7720000] [7730000] [7740000] [7750000] [7760000] [7770000] [7780000] [7790000] [7800000] [7810000] [7820000] [7830000] [7840000] [7850000] [7860000] [7870000] [7880000] [7890000] [7900000] [7910000] [7920000] [7930000] [7940000] [7950000] -done parsing /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 321, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 42, 'small anchor length' => 182, 'exons hit < 2' => 4, 'excessive soft clipping' => 36469, 'num genes matched < 2' => 273, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 4662, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 26, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 40, 'per_id < 96' => 20764, ' ** passed ** ' => 42460, 'seq-similar region overlap' => 360, 'low complexity anchor region' => 59, 'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 74, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 524, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 147, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 6, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 474 }; -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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: AC006008.1--ACTR3B -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: AC092666.1--ACTR3B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: ADAM2--AP005902.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] 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[160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] -fusion SPANNING read extraction for scaff: AFF3--FLI1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: AL512590.2--CCDC180 [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] 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[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] -fusion SPANNING read extraction for scaff: AL512624.2--POTEH [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] 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[162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] -fusion SPANNING read extraction for scaff: AL929601.3--POTEG [1000] [2000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2 [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] -fusion SPANNING read extraction for scaff: DMXL1--SERBP1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] [489000] [490000] [491000] [492000] [493000] [494000] [495000] [496000] [497000] [498000] [499000] [500000] [501000] [502000] [503000] [504000] [505000] [506000] [507000] [508000] [509000] [510000] [511000] [512000] [513000] [514000] [515000] [516000] [517000] [518000] [519000] [520000] [521000] [522000] [523000] [524000] [525000] [526000] [527000] [528000] [529000] [530000] [531000] [532000] [533000] [534000] [535000] [536000] [537000] [538000] [539000] [540000] [541000] [542000] [543000] [544000] [545000] [546000] [547000] [548000] [549000] [550000] [551000] [552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] -fusion SPANNING read extraction for scaff: ERG--NEDD4L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [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: GOLPH3--ZNF273 [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] -fusion SPANNING read extraction for scaff: ITPKC--LTBP4 [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: ITPKC--SPTBN4 [1000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] -fusion SPANNING read extraction for scaff: NUMBL--SPTBN4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: NXPE4--TENM4 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PIP4K2B--RNF125 [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] -fusion SPANNING read extraction for scaff: PPCS--ERI3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: RBM7--TENM4 [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] -fusion SPANNING read extraction for scaff: RNF125--ACLY [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: RORA--ZNF774 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: RORA--GOLGA2P8 [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] -fusion SPANNING read extraction for scaff: SHKBP1--SPTBN4 [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] -fusion SPANNING read extraction for scaff: SLC45A2--AMACR [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] 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[527000] [528000] [529000] [530000] [531000] [532000] [533000] [534000] [535000] [536000] [537000] [538000] [539000] [540000] [541000] [542000] [543000] [544000] [545000] [546000] [547000] [548000] [549000] [550000] [551000] [552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] [589000] [590000] [591000] [592000] [593000] [594000] [595000] [596000] [597000] [598000] [599000] [600000] [601000] [602000] [603000] [604000] [605000] [606000] [607000] [608000] [609000] [610000] [611000] [612000] [613000] [614000] [615000] [616000] [617000] [618000] [619000] [620000] [621000] [622000] [623000] [624000] [625000] [626000] [627000] [628000] [629000] [630000] [631000] [632000] [633000] [634000] [635000] [636000] [637000] 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[860000] [861000] [862000] [863000] [864000] [865000] [866000] [867000] [868000] [869000] [870000] [871000] [872000] [873000] [874000] [875000] [876000] [877000] [878000] [879000] [880000] [881000] [882000] [883000] [884000] [885000] [886000] [887000] [888000] [889000] [890000] [891000] [892000] [893000] [894000] [895000] [896000] [897000] [898000] [899000] [900000] [901000] [902000] [903000] [904000] [905000] [906000] [907000] [908000] [909000] [910000] [911000] [912000] [913000] [914000] [915000] [916000] [917000] [918000] [919000] [920000] [921000] [922000] [923000] [924000] [925000] [926000] [927000] [928000] [929000] [930000] [931000] [932000] [933000] [934000] [935000] [936000] [937000] [938000] [939000] [940000] [941000] [942000] [943000] [944000] [945000] [946000] [947000] [948000] [949000] [950000] [951000] [952000] [953000] [954000] [955000] [956000] [957000] [958000] [959000] [960000] [961000] [962000] [963000] [964000] [965000] [966000] [967000] [968000] [969000] [970000] [971000] [972000] [973000] [974000] [975000] [976000] [977000] [978000] [979000] [980000] [981000] [982000] [983000] [984000] [985000] [986000] [987000] [988000] [989000] [990000] [991000] [992000] [993000] [994000] [995000] [996000] [997000] [998000] [999000] [1000000] [1001000] [1002000] [1003000] [1004000] [1005000] [1006000] [1007000] [1008000] [1009000] [1010000] [1011000] [1012000] [1013000] [1014000] [1015000] [1016000] [1017000] [1018000] [1019000] [1020000] [1021000] [1022000] [1023000] [1024000] [1025000] [1026000] [1027000] [1028000] [1029000] [1030000] [1031000] [1032000] [1033000] [1034000] [1035000] [1036000] [1037000] [1038000] [1039000] [1040000] [1041000] [1042000] [1043000] [1044000] [1045000] [1046000] [1047000] [1048000] [1049000] [1050000] [1051000] [1052000] [1053000] [1054000] [1055000] [1056000] [1057000] [1058000] [1059000] [1060000] [1061000] [1062000] [1063000] [1064000] [1065000] [1066000] [1067000] [1068000] [1069000] [1070000] [1071000] [1072000] [1073000] [1074000] [1075000] [1076000] [1077000] [1078000] [1079000] [1080000] [1081000] [1082000] [1083000] [1084000] [1085000] [1086000] [1087000] [1088000] [1089000] [1090000] [1091000] [1092000] [1093000] [1094000] [1095000] [1096000] [1097000] [1098000] [1099000] [1100000] [1101000] [1102000] [1103000] [1104000] [1105000] [1106000] [1107000] [1108000] [1109000] [1110000] [1111000] [1112000] [1113000] [1114000] -fusion SPANNING read extraction for scaff: SLC45A3--ERG [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: SNED1--RAD51C [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: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A [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] 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[813000] [814000] [815000] [816000] [817000] [818000] [819000] [820000] [821000] [822000] [823000] [824000] [825000] [826000] [827000] [828000] [829000] [830000] [831000] [832000] [833000] [834000] [835000] [836000] [837000] [838000] [839000] [840000] [841000] [842000] [843000] [844000] [845000] [846000] [847000] [848000] [849000] [850000] [851000] [852000] [853000] [854000] [855000] [856000] [857000] [858000] [859000] [860000] [861000] [862000] [863000] [864000] [865000] [866000] [867000] [868000] [869000] [870000] [871000] [872000] [873000] [874000] [875000] [876000] [877000] [878000] [879000] [880000] [881000] [882000] [883000] [884000] [885000] [886000] [887000] [888000] [889000] [890000] [891000] [892000] [893000] [894000] [895000] [896000] [897000] [898000] [899000] [900000] [901000] [902000] [903000] [904000] [905000] [906000] [907000] [908000] [909000] [910000] [911000] [912000] [913000] [914000] [915000] [916000] [917000] [918000] [919000] [920000] [921000] [922000] [923000] 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[2631000] [2632000] [2633000] [2634000] [2635000] [2636000] [2637000] -fusion SPANNING read extraction for scaff: TMPRSS2--ERG [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: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: ZW10--NXPE4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 269592, 'seq similar region alignment' => 123854 }; Execution Time = 11.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -33487.684003 EM: Round [1] log likelihood: -33469.732471 EM: Round [2] log likelihood: -33464.160721 EM: Round [3] log likelihood: -33459.992059 EM: Round [4] log likelihood: -33456.623892 EM: Round [5] log likelihood: -33453.788970 EM: Round [6] log likelihood: -33451.336210 EM: Round [7] log likelihood: -33449.175788 EM: Round [8] log likelihood: -33447.251358 EM: Round [9] log likelihood: -33445.525136 EM: Round [10] log likelihood: -33443.969816 EM: Round [11] log likelihood: -33442.564202 EM: Round [12] log likelihood: -33441.290875 EM: Round [13] log likelihood: -33440.134946 EM: Round [14] log likelihood: -33439.083391 EM: Round [15] log likelihood: -33438.124687 EM: Round [16] log likelihood: -33437.248590 EM: Round [17] log likelihood: -33436.445996 EM: Round [18] log likelihood: -33435.708819 EM: Round [19] log likelihood: -33435.029899 EM: Round [20] log likelihood: -33434.402908 EM: Round [21] log likelihood: -33433.822265 EM: Round [22] log likelihood: -33433.283056 EM: Round [23] log likelihood: -33432.780961 EM: Round [24] log likelihood: -33432.312179 EM: Round [25] log likelihood: -33431.873373 EM: Round [26] log likelihood: -33431.461603 EM: Round [27] log likelihood: -33431.074287 EM: Round [28] log likelihood: -33430.709145 EM: Round [29] log likelihood: -33430.364168 EM: Round [30] log likelihood: -33430.037579 EM: Round [31] log likelihood: -33429.727801 EM: Round [32] log likelihood: -33429.433438 EM: Round [33] log likelihood: -33429.153244 EM: Round [34] log likelihood: -33428.886110 EM: Round [35] log likelihood: -33428.631043 EM: Round [36] log likelihood: -33428.387151 EM: Round [37] log likelihood: -33428.153636 EM: Round [38] log likelihood: -33427.929775 EM: Round [39] log likelihood: -33427.714917 EM: Round [40] log likelihood: -33427.508470 EM: Round [41] log likelihood: -33427.309899 EM: Round [42] log likelihood: -33427.118715 EM: Round [43] log likelihood: -33426.934473 EM: Round [44] log likelihood: -33426.756765 EM: Round [45] log likelihood: -33426.585218 EM: Round [46] log likelihood: -33426.419489 EM: Round [47] log likelihood: -33426.259261 EM: Round [48] log likelihood: -33426.104244 EM: Round [49] log likelihood: -33425.954169 EM: Round [50] log likelihood: -33425.808785 EM: Round [51] log likelihood: -33425.667863 EM: Round [52] log likelihood: -33425.531187 EM: Round [53] log likelihood: -33425.398558 EM: Round [54] log likelihood: -33425.269789 EM: Round [55] log likelihood: -33425.144708 EM: Round [56] log likelihood: -33425.023150 EM: Round [57] log likelihood: -33424.904964 EM: Round [58] log likelihood: -33424.790008 EM: Round [59] log likelihood: -33424.678148 EM: Round [60] log likelihood: -33424.569257 EM: Round [61] log likelihood: -33424.463218 EM: Round [62] log likelihood: -33424.359918 EM: Round [63] log likelihood: -33424.259254 EM: Round [64] log likelihood: -33424.161124 EM: Round [65] log likelihood: -33424.065436 EM: Round [66] log likelihood: -33423.972100 EM: Round [67] log likelihood: -33423.881032 EM: Round [68] log likelihood: -33423.792152 EM: Round [69] log likelihood: -33423.705384 EM: Round [70] log likelihood: -33423.620657 EM: Round [71] log likelihood: -33423.537901 EM: Round [72] log likelihood: -33423.457052 EM: Round [73] log likelihood: -33423.378047 EM: Round [74] log likelihood: -33423.300827 EM: Round [75] log likelihood: -33423.225335 EM: Round [76] log likelihood: -33423.151518 EM: Round [77] log likelihood: -33423.079323 EM: Round [78] log likelihood: -33423.008702 EM: Round [79] log likelihood: -33422.939607 EM: Round [80] log likelihood: -33422.871993 EM: Round [81] log likelihood: -33422.805816 EM: Round [82] log likelihood: -33422.741034 EM: Round [83] log likelihood: -33422.677609 EM: Round [84] log likelihood: -33422.615501 EM: Round [85] log likelihood: -33422.554674 EM: Round [86] log likelihood: -33422.495092 EM: Round [87] log likelihood: -33422.436722 EM: Round [88] log likelihood: -33422.379529 EM: Round [89] log likelihood: -33422.323483 EM: Round [90] log likelihood: -33422.268554 EM: Round [91] log likelihood: -33422.214712 EM: Round [92] log likelihood: -33422.161928 EM: Round [93] log likelihood: -33422.110176 EM: Round [94] log likelihood: -33422.059429 EM: Round [95] log likelihood: -33422.009661 EM: Round [96] log likelihood: -33421.960849 EM: Round [97] log likelihood: -33421.912968 EM: Round [98] log likelihood: -33421.865995 EM: Round [99] log likelihood: -33421.819908 EM: Round [100] log likelihood: -33421.774686 EM: Round [101] log likelihood: -33421.730308 EM: Round [102] log likelihood: -33421.686754 EM: Round [103] log likelihood: -33421.644004 EM: Round [104] log likelihood: -33421.602039 EM: Round [105] log likelihood: -33421.560841 EM: Round [106] log likelihood: -33421.520392 EM: Round [107] log likelihood: -33421.480676 EM: Round [108] log likelihood: -33421.441674 EM: Round [109] log likelihood: -33421.403372 EM: Round [110] log likelihood: -33421.365753 EM: Round [111] log likelihood: -33421.328803 EM: Round [112] log likelihood: -33421.292505 EM: Round [113] log likelihood: -33421.256847 EM: Round [114] log likelihood: -33421.221813 EM: Round [115] log likelihood: -33421.187391 EM: Round [116] log likelihood: -33421.153566 EM: Round [117] log likelihood: -33421.120327 EM: Round [118] log likelihood: -33421.087661 EM: Round [119] log likelihood: -33421.055555 EM: Round [120] log likelihood: -33421.023997 EM: Round [121] log likelihood: -33420.992977 EM: Round [122] log likelihood: -33420.962483 EM: Round [123] log likelihood: -33420.932504 EM: Round [124] log likelihood: -33420.903029 EM: Round [125] log likelihood: -33420.874048 EM: Round [126] log likelihood: -33420.845552 EM: Round [127] log likelihood: -33420.817529 EM: Round [128] log likelihood: -33420.789971 EM: Round [129] log likelihood: -33420.762869 EM: Round [130] log likelihood: -33420.736212 EM: Round [131] log likelihood: -33420.709993 EM: Round [132] log likelihood: -33420.684202 EM: Round [133] log likelihood: -33420.658832 EM: Round [134] log likelihood: -33420.633874 EM: Round [135] log likelihood: -33420.609320 EM: Round [136] log likelihood: -33420.585162 EM: Round [137] log likelihood: -33420.561392 EM: Round [138] log likelihood: -33420.538004 EM: Round [139] log likelihood: -33420.514989 EM: Round [140] log likelihood: -33420.492341 EM: Round [141] log likelihood: -33420.470053 EM: Round [142] log likelihood: -33420.448118 EM: Round [143] log likelihood: -33420.426529 EM: Round [144] log likelihood: -33420.405280 EM: Round [145] log likelihood: -33420.384365 EM: Round [146] log likelihood: -33420.363777 EM: Round [147] log likelihood: -33420.343510 EM: Round [148] log likelihood: -33420.323559 EM: Round [149] log likelihood: -33420.303918 EM: Round [150] log likelihood: -33420.284581 EM: Round [151] log likelihood: -33420.265543 EM: Round [152] log likelihood: -33420.246797 EM: Round [153] log likelihood: -33420.228340 EM: Round [154] log likelihood: -33420.210165 EM: Round [155] log likelihood: -33420.192269 EM: Round [156] log likelihood: -33420.174645 EM: Round [157] log likelihood: -33420.157289 EM: Round [158] log likelihood: -33420.140197 EM: Round [159] log likelihood: -33420.123363 EM: Round [160] log likelihood: -33420.106783 EM: Round [161] log likelihood: -33420.090453 EM: Round [162] log likelihood: -33420.074369 EM: Round [163] log likelihood: -33420.058525 EM: Round [164] log likelihood: -33420.042919 EM: Round [165] log likelihood: -33420.027546 EM: Round [166] log likelihood: -33420.012401 EM: Round [167] log likelihood: -33419.997482 EM: Round [168] log likelihood: -33419.982784 EM: Round [169] log likelihood: -33419.968304 EM: Round [170] log likelihood: -33419.954037 EM: Round [171] log likelihood: -33419.939981 EM: Round [172] log likelihood: -33419.926132 EM: Round [173] log likelihood: -33419.912486 EM: Round [174] log likelihood: -33419.899039 EM: Round [175] log likelihood: -33419.885790 EM: Round [176] log likelihood: -33419.872734 EM: Round [177] log likelihood: -33419.859867 EM: Round [178] log likelihood: -33419.847189 EM: Round [179] log likelihood: -33419.834694 EM: Round [180] log likelihood: -33419.822380 EM: Round [181] log likelihood: -33419.810244 EM: Round [182] log likelihood: -33419.798283 EM: Round [183] log likelihood: -33419.786495 EM: Round [184] log likelihood: -33419.774876 EM: Round [185] log likelihood: -33419.763424 EM: Round [186] log likelihood: -33419.752137 EM: Round [187] log likelihood: -33419.741010 EM: Round [188] log likelihood: -33419.730043 EM: Round [189] log likelihood: -33419.719233 EM: Round [190] log likelihood: -33419.708576 EM: Round [191] log likelihood: -33419.698071 EM: Round [192] log likelihood: -33419.687715 EM: Round [193] log likelihood: -33419.677506 EM: Round [194] log likelihood: -33419.667441 EM: Round [195] log likelihood: -33419.657519 EM: Round [196] log likelihood: -33419.647737 EM: Round [197] log likelihood: -33419.638092 EM: Round [198] log likelihood: -33419.628583 EM: Round [199] log likelihood: -33419.619208 EM: Round [200] log likelihood: -33419.609965 EM: Round [201] log likelihood: -33419.600851 EM: Round [202] log likelihood: -33419.591865 EM: Round [203] log likelihood: -33419.583004 EM: Round [204] log likelihood: -33419.574267 EM: Round [205] log likelihood: -33419.565651 EM: Round [206] log likelihood: -33419.557156 EM: Round [207] log likelihood: -33419.548779 EM: Round [208] log likelihood: -33419.540518 EM: Round [209] log likelihood: -33419.532372 EM: Round [210] log likelihood: -33419.524339 EM: Round [211] log likelihood: -33419.516416 EM: Round [212] log likelihood: -33419.508604 EM: Round [213] log likelihood: -33419.500899 EM: Round [214] log likelihood: -33419.493300 EM: Round [215] log likelihood: -33419.485806 EM: Round [216] log likelihood: -33419.478415 EM: Round [217] log likelihood: -33419.471126 EM: Round [218] log likelihood: -33419.463937 EM: Round [219] log likelihood: -33419.456846 EM: Round [220] log likelihood: -33419.449853 EM: Round [221] log likelihood: -33419.442955 EM: Round [222] log likelihood: -33419.436151 EM: Round [223] log likelihood: -33419.429441 EM: Round [224] log likelihood: -33419.422821 EM: Round [225] log likelihood: -33419.416293 EM: Round [226] log likelihood: -33419.409853 EM: Round [227] log likelihood: -33419.403500 EM: Round [228] log likelihood: -33419.397234 EM: Round [229] log likelihood: -33419.391053 EM: Round [230] log likelihood: -33419.384956 EM: Round [231] log likelihood: -33419.378942 EM: Round [232] log likelihood: -33419.373009 EM: Round [233] log likelihood: -33419.367156 EM: Round [234] log likelihood: -33419.361382 EM: Round [235] log likelihood: -33419.355686 EM: Round [236] log likelihood: -33419.350067 EM: Round [237] log likelihood: -33419.344524 EM: Round [238] log likelihood: -33419.339056 EM: Round [239] log likelihood: -33419.333661 EM: Round [240] log likelihood: -33419.328338 EM: Round [241] log likelihood: -33419.323088 EM: Round [242] log likelihood: -33419.317907 EM: Round [243] log likelihood: -33419.312796 EM: Round [244] log likelihood: -33419.307754 EM: Round [245] log likelihood: -33419.302779 EM: Round [246] log likelihood: -33419.297871 EM: Round [247] log likelihood: -33419.293028 EM: Round [248] log likelihood: -33419.288251 EM: Round [249] log likelihood: -33419.283537 EM: Round [250] log likelihood: -33419.278885 EM: Round [251] log likelihood: -33419.274296 EM: Round [252] log likelihood: -33419.269768 EM: Round [253] log likelihood: -33419.265301 EM: Round [254] log likelihood: -33419.260893 EM: Round [255] log likelihood: -33419.256543 EM: Round [256] log likelihood: -33419.252251 EM: Round [257] log likelihood: -33419.248017 EM: Round [258] log likelihood: -33419.243838 EM: Round [259] log likelihood: -33419.239715 EM: Round [260] log likelihood: -33419.235647 EM: Round [261] log likelihood: -33419.231632 EM: Round [262] log likelihood: -33419.227671 EM: Round [263] log likelihood: -33419.223762 EM: Round [264] log likelihood: -33419.219905 EM: Round [265] log likelihood: -33419.216099 EM: Round [266] log likelihood: -33419.212343 EM: Round [267] log likelihood: -33419.208636 EM: Round [268] log likelihood: -33419.204979 EM: Round [269] log likelihood: -33419.201370 EM: Round [270] log likelihood: -33419.197808 EM: Round [271] log likelihood: -33419.194293 EM: Round [272] log likelihood: -33419.190825 EM: Round [273] log likelihood: -33419.187402 EM: Round [274] log likelihood: -33419.184024 EM: Round [275] log likelihood: -33419.180691 EM: Round [276] log likelihood: -33419.177401 EM: Round [277] log likelihood: -33419.174155 EM: Round [278] log likelihood: -33419.170951 EM: Round [279] log likelihood: -33419.167790 EM: Round [280] log likelihood: -33419.164669 EM: Round [281] log likelihood: -33419.161590 EM: Round [282] log likelihood: -33419.158551 EM: Round [283] log likelihood: -33419.155552 EM: Round [284] log likelihood: -33419.152592 EM: Round [285] log likelihood: -33419.149671 EM: Round [286] log likelihood: -33419.146788 EM: Round [287] log likelihood: -33419.143943 EM: Round [288] log likelihood: -33419.141134 EM: Round [289] log likelihood: -33419.138363 EM: Round [290] log likelihood: -33419.135628 EM: Round [291] log likelihood: -33419.132928 EM: Round [292] log likelihood: -33419.130264 EM: Round [293] log likelihood: -33419.127634 EM: Round [294] log likelihood: -33419.125039 EM: Round [295] log likelihood: -33419.122477 EM: Round [296] log likelihood: -33419.119949 EM: Round [297] log likelihood: -33419.117454 EM: Round [298] log likelihood: -33419.114991 EM: Round [299] log likelihood: -33419.112560 EM: Round [300] log likelihood: -33419.110161 EM: Round [301] log likelihood: -33419.107793 EM: Round [302] log likelihood: -33419.105456 EM: Round [303] log likelihood: -33419.103149 EM: Round [304] log likelihood: -33419.100873 EM: Round [305] log likelihood: -33419.098625 EM: Round [306] log likelihood: -33419.096407 EM: Round [307] log likelihood: -33419.094218 EM: Round [308] log likelihood: -33419.092057 EM: Round [309] log likelihood: -33419.089924 EM: Round [310] log likelihood: -33419.087818 EM: Round [311] log likelihood: -33419.085740 EM: Round [312] log likelihood: -33419.083689 EM: Round [313] log likelihood: -33419.081665 EM: Round [314] log likelihood: -33419.079666 EM: Round [315] log likelihood: -33419.077694 EM: Round [316] log likelihood: -33419.075747 EM: Round [317] log likelihood: -33419.073825 EM: Round [318] log likelihood: -33419.071928 EM: Round [319] log likelihood: -33419.070055 EM: Round [320] log likelihood: -33419.068207 EM: Round [321] log likelihood: -33419.066383 EM: Round [322] log likelihood: -33419.064582 EM: Round [323] log likelihood: -33419.062804 EM: Round [324] log likelihood: -33419.061049 EM: Round [325] log likelihood: -33419.059317 EM: Round [326] log likelihood: -33419.057608 EM: Round [327] log likelihood: -33419.055920 EM: Round [328] log likelihood: -33419.054254 EM: Round [329] log likelihood: -33419.052610 EM: Round [330] log likelihood: -33419.050986 EM: Round [331] log likelihood: -33419.049384 EM: Round [332] log likelihood: -33419.047802 EM: Round [333] log likelihood: -33419.046241 EM: Round [334] log likelihood: -33419.044700 EM: Round [335] log likelihood: -33419.043178 EM: Round [336] log likelihood: -33419.041676 EM: Round [337] log likelihood: -33419.040194 EM: Round [338] log likelihood: -33419.038730 EM: Round [339] log likelihood: -33419.037285 EM: Round [340] log likelihood: -33419.035859 EM: Round [341] log likelihood: -33419.034451 EM: Round [342] log likelihood: -33419.033062 EM: Round [343] log likelihood: -33419.031690 EM: Round [344] log likelihood: -33419.030336 EM: Round [345] log likelihood: -33419.028999 EM: Round [346] log likelihood: -33419.027679 EM: Round [347] log likelihood: -33419.026376 EM: Round [348] log likelihood: -33419.025090 EM: Round [349] log likelihood: -33419.023820 EM: Round [350] log likelihood: -33419.022567 EM: Round [351] log likelihood: -33419.021330 EM: Round [352] log likelihood: -33419.020108 EM: Round [353] log likelihood: -33419.018903 EM: Round [354] log likelihood: -33419.017712 EM: Round [355] log likelihood: -33419.016537 EM: Round [356] log likelihood: -33419.015377 EM: Round [357] log likelihood: -33419.014232 EM: Round [358] log likelihood: -33419.013102 EM: Round [359] log likelihood: -33419.011986 EM: Round [360] log likelihood: -33419.010884 EM: Round [361] log likelihood: -33419.009796 EM: Round [362] log likelihood: -33419.008722 EM: Round [363] log likelihood: -33419.007662 EM: Round [364] log likelihood: -33419.006616 EM: Round [365] log likelihood: -33419.005583 EM: Round [366] log likelihood: -33419.004563 EM: Round [367] log likelihood: -33419.003556 EM: Round [368] log likelihood: -33419.002562 EM: Round [369] log likelihood: -33419.001581 EM: Round [370] log likelihood: -33419.000612 EM: Round [371] log likelihood: -33418.999656 EM: Round [372] log likelihood: -33418.998711 EM: Round [373] log likelihood: -33418.997779 EM: Round [374] log likelihood: -33418.996859 EM: Round [375] log likelihood: -33418.995951 EM: Round [376] log likelihood: -33418.995054 EM: Round [377] log likelihood: -33418.994168 EM: Round [378] log likelihood: -33418.993294 EM: Round [379] log likelihood: -33418.992431 EM: Round [380] log likelihood: -33418.991579 EM: Round [381] log likelihood: -33418.990738 EM: Round [382] log likelihood: -33418.989907 EM: Round [383] log likelihood: -33418.989088 EM: Round [384] log likelihood: -33418.988278 EM: Round [385] log likelihood: -33418.987479 EM: Round [386] log likelihood: -33418.986690 EM: Round [387] log likelihood: -33418.985911 EM: Round [388] log likelihood: -33418.985142 EM: Round [389] log likelihood: -33418.984383 EM: Round [390] log likelihood: -33418.983634 EM: Round [391] log likelihood: -33418.982894 EM: Round [392] log likelihood: -33418.982163 EM: Round [393] log likelihood: -33418.981442 EM: Round [394] log likelihood: -33418.980730 EM: Round [395] log likelihood: -33418.980027 EM: Round [396] log likelihood: -33418.979333 EM: Round [397] log likelihood: -33418.978648 EM: Round [398] log likelihood: -33418.977971 EM: Round [399] log likelihood: -33418.977303 EM: Round [400] log likelihood: -33418.976644 EM: Round [401] log likelihood: -33418.975993 EM: Round [402] log likelihood: -33418.975350 EM: Round [403] log likelihood: -33418.974715 EM: Round [404] log likelihood: -33418.974089 EM: Round [405] log likelihood: -33418.973470 EM: Round [406] log likelihood: -33418.972860 EM: Round [407] log likelihood: -33418.972257 EM: Round [408] log likelihood: -33418.971661 EM: Round [409] log likelihood: -33418.971074 EM: Round [410] log likelihood: -33418.970493 EM: Round [411] log likelihood: -33418.969920 EM: Round [412] log likelihood: -33418.969355 EM: Round [413] log likelihood: -33418.968796 EM: Round [414] log likelihood: -33418.968245 EM: Round [415] log likelihood: -33418.967700 EM: Round [416] log likelihood: -33418.967163 EM: Round [417] log likelihood: -33418.966632 EM: Round [418] log likelihood: -33418.966108 EM: Round [419] log likelihood: -33418.965591 EM: Round [420] log likelihood: -33418.965080 EM: Round [421] log likelihood: -33418.964576 EM: Round [422] log likelihood: -33418.964078 EM: Round [423] log likelihood: -33418.963587 EM: Round [424] log likelihood: -33418.963101 EM: Round [425] log likelihood: -33418.962622 EM: Round [426] log likelihood: -33418.962149 EM: Round [427] log likelihood: -33418.961682 EM: Round [428] log likelihood: -33418.961221 EM: Round [429] log likelihood: -33418.960765 EM: Round [430] log likelihood: -33418.960316 EM: Round [431] log likelihood: -33418.959872 EM: Round [432] log likelihood: -33418.959434 EM: Round [433] log likelihood: -33418.959001 EM: Round [434] log likelihood: -33418.958574 EM: Round [435] log likelihood: -33418.958152 EM: Round [436] log likelihood: -33418.957735 EM: Round [437] log likelihood: -33418.957324 EM: Round [438] log likelihood: -33418.956918 EM: Round [439] log likelihood: -33418.956517 EM: Round [440] log likelihood: -33418.956122 EM: Round [441] log likelihood: -33418.955731 EM: Round [442] log likelihood: -33418.955345 EM: Round [443] log likelihood: -33418.954964 EM: Round [444] log likelihood: -33418.954588 EM: Round [445] log likelihood: -33418.954216 EM: Round [446] log likelihood: -33418.953850 EM: Round [447] log likelihood: -33418.953488 EM: Round [448] log likelihood: -33418.953130 EM: Round [449] log likelihood: -33418.952777 EM: Round [450] log likelihood: -33418.952429 EM: Round [451] log likelihood: -33418.952084 EM: Round [452] log likelihood: -33418.951745 EM: Round [453] log likelihood: -33418.951409 EM: Round [454] log likelihood: -33418.951078 EM: Round [455] log likelihood: -33418.950751 EM: Round [456] log likelihood: -33418.950428 EM: Round [457] log likelihood: -33418.950109 EM: Round [458] log likelihood: -33418.949794 EM: Round [459] log likelihood: -33418.949484 EM: Round [460] log likelihood: -33418.949177 EM: Round [461] log likelihood: -33418.948874 EM: Round [462] log likelihood: -33418.948574 EM: Round [463] log likelihood: -33418.948279 EM: Round [464] log likelihood: -33418.947987 EM: Round [465] log likelihood: -33418.947699 EM: Round [466] log likelihood: -33418.947415 EM: Round [467] log likelihood: -33418.947134 EM: Round [468] log likelihood: -33418.946857 EM: Round [469] log likelihood: -33418.946583 EM: Round [470] log likelihood: -33418.946313 EM: Round [471] log likelihood: -33418.946046 EM: Round [472] log likelihood: -33418.945782 EM: Round [473] log likelihood: -33418.945522 EM: Round [474] log likelihood: -33418.945265 EM: Round [475] log likelihood: -33418.945012 EM: Round [476] log likelihood: -33418.944761 EM: Round [477] log likelihood: -33418.944514 EM: Round [478] log likelihood: -33418.944270 EM: Round [479] log likelihood: -33418.944028 EM: Round [480] log likelihood: -33418.943790 EM: Round [481] log likelihood: -33418.943555 EM: Round [482] log likelihood: -33418.943323 EM: Round [483] log likelihood: -33418.943094 EM: Round [484] log likelihood: -33418.942868 EM: Round [485] log likelihood: -33418.942644 EM: Round [486] log likelihood: -33418.942423 EM: Round [487] log likelihood: -33418.942206 EM: Round [488] log likelihood: -33418.941990 EM: Round [489] log likelihood: -33418.941778 EM: Round [490] log likelihood: -33418.941568 EM: Round [491] log likelihood: -33418.941361 EM: Round [492] log likelihood: -33418.941157 EM: Round [493] log likelihood: -33418.940955 EM: Round [494] log likelihood: -33418.940755 EM: Round [495] log likelihood: -33418.940558 EM: Round [496] log likelihood: -33418.940364 EM: Round [497] log likelihood: -33418.940172 EM: Round [498] log likelihood: -33418.939983 EM: Round [499] log likelihood: -33418.939795 EM: Round [500] log likelihood: -33418.939611 EM: Round [501] log likelihood: -33418.939428 EM: Round [502] log likelihood: -33418.939248 EM: Round [503] log likelihood: -33418.939070 EM: Round [504] log likelihood: -33418.938894 EM: Round [505] log likelihood: -33418.938721 EM: Round [506] log likelihood: -33418.938550 EM: Round [507] log likelihood: -33418.938381 EM: Round [508] log likelihood: -33418.938214 EM: Round [509] log likelihood: -33418.938049 EM: Round [510] log likelihood: -33418.937886 EM: Round [511] log likelihood: -33418.937725 EM: Round [512] log likelihood: -33418.937566 EM: Round [513] log likelihood: -33418.937410 EM: Round [514] log likelihood: -33418.937255 EM: Round [515] log likelihood: -33418.937102 EM: Round [516] log likelihood: -33418.936951 EM: Round [517] log likelihood: -33418.936802 EM: Round [518] log likelihood: -33418.936655 EM: Round [519] log likelihood: -33418.936509 EM: Round [520] log likelihood: -33418.936366 EM: Round [521] log likelihood: -33418.936224 EM: Round [522] log likelihood: -33418.936084 EM: Round [523] log likelihood: -33418.935946 EM: Round [524] log likelihood: -33418.935810 EM: Round [525] log likelihood: -33418.935675 EM: Round [526] log likelihood: -33418.935542 EM: Round [527] log likelihood: -33418.935411 EM: Round [528] log likelihood: -33418.935281 EM: Round [529] log likelihood: -33418.935153 EM: Round [530] log likelihood: -33418.935026 EM: Round [531] log likelihood: -33418.934902 EM: Round [532] log likelihood: -33418.934778 EM: Round [533] log likelihood: -33418.934657 EM: Round [534] log likelihood: -33418.934536 EM: Round [535] log likelihood: -33418.934418 EM: Round [536] log likelihood: -33418.934300 EM: Round [537] log likelihood: -33418.934185 EM: Round [538] log likelihood: -33418.934070 EM: Round [539] log likelihood: -33418.933957 EM: Round [540] log likelihood: -33418.933846 EM: Round [541] log likelihood: -33418.933736 EM: Round [542] log likelihood: -33418.933627 EM: Round [543] log likelihood: -33418.933520 EM: Round [544] log likelihood: -33418.933414 EM: Round [545] log likelihood: -33418.933309 EM: Round [546] log likelihood: -33418.933206 EM: Round [547] log likelihood: -33418.933104 EM: Round [548] log likelihood: -33418.933003 EM: Round [549] log likelihood: -33418.932904 EM: Stopping iterations at round 549 due to insufficient improvement in likelihood. Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam" Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Execution Time = 0.09 minutes. CMD: samtools index /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 2.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir -done, see /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -29541.099422 EM: Round [1] log likelihood: -29536.362526 EM: Round [2] log likelihood: -29536.257033 EM: Round [3] log likelihood: -29536.255205 EM: Round [4] log likelihood: -29536.255177 EM: Stopping iterations at round 4 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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 296142999 Execution Time = 6.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.lXs9IJKSup/fi_workdir/microH.dat Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.lXs9IJKSup/fi_workdir/microH.dat /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/fi_workdir/microH.dat /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.lXs9IJKSup --json_outfile /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bUs-T1-TRNA-1_B23MHV2LT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.lXs9IJKSup --json_outfile /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bUs-T1-TRNA-1_B23MHV2LT4_1 Running: touch /tmp/nxf.lXs9IJKSup/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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bUs-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_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.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bUs-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000236438.7] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000276888.1] WARNING, no entry stored in dbm for [ENSG00000276888.1] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286065.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000275563.1] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.lXs9IJKSup/ctat_genome_lib_build_dir > /tmp/nxf.lXs9IJKSup/659_bUs-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.lXs9IJKSup/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory