Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/22f3c54ac812cd522077040cd8ce6b/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/cb284b7627e3634bdf3895d78c7d6b/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv 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/7a/72b214263274602061f9ad2f755e57/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/72b214263274602061f9ad2f755e57/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/22f3c54ac812cd522077040cd8ce6b/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.kHKFBso9Iw/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.kHKFBso9Iw/cytoBand.txt Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed -parsing GTF file: /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --CPU 8 --out_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star --out_dir /tmp/nxf.kHKFBso9Iw/fi_workdir --reads "/tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' May 28 22:37:28 ..... started STAR run May 28 22:37:28 ..... loading genome May 28 22:39:13 ... generating Suffix Array index May 28 22:43:07 ... completed Suffix Array index May 28 22:43:07 ..... processing annotations GTF May 28 22:43:08 ..... inserting junctions into the genome indices May 28 22:44:12 ..... started mapping May 28 23:49:47 ..... finished mapping May 28 23:49:49 ..... started sorting BAM May 28 23:49:52 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam Execution Time = 72.48 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --CPU 8 --out_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star --out_dir /tmp/nxf.kHKFBso9Iw/fi_workdir --reads "/tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups 23:50:27 : INFO : Done. Execution Time = 0.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf -parsing /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] 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[5270000] [5280000] [5290000] [5300000] [5310000] [5320000] [5330000] [5340000] [5350000] [5360000] -done parsing /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { ' ** passed ** ' => 46859, 'low complexity anchor region' => 34, 'exons hit < 2' => 2, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 2, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2, 'num genes matched < 2' => 53, 'seq-similar region overlap' => 260, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3, 'small anchor length' => 291, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 29, 'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 20, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 427, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 60, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 66, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38, 'per_id < 96' => 31470, 'excessive soft clipping' => 39148 }; -writing fusion junction support info. Execution Time = 3.07 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] -fusion SPANNING read extraction for scaff: AC002066.1--SYK [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: AC004917.1--SLC26A3 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: AC005050.1--SLC26A3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] -fusion SPANNING read extraction for scaff: AC015712.1--FBXL2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: AC015712.1--FAM13C [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [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] -fusion SPANNING read extraction for scaff: AL033504.1--SASH1 [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] 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[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] -fusion SPANNING read extraction for scaff: BIRC6--ITGA9 [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] -fusion SPANNING read extraction for scaff: CENPP--ASZ1 [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: CHST11--SYK [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: CHST11--DIRAS2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: CHST11--OR7E109P [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] 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[23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -fusion SPANNING read extraction for scaff: COBL--RN7SKP168 [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] -fusion SPANNING read extraction for scaff: CUX1--PCBP1-AS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: DGCR2--WARS2-AS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] -fusion SPANNING read extraction for scaff: EPHB2--TMEM39B [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: ERCC6L2--PPP1R9A [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] -fusion SPANNING read extraction for scaff: ERCC6L2--PPP1R9A-AS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] -fusion SPANNING read extraction for scaff: FAF1--CDKN2C [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: FAF1--MIR4421 [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] -fusion SPANNING read extraction for scaff: FOSL1--SLC30A8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] -fusion SPANNING read extraction for scaff: GLIS3--FGF7P4 [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] -fusion SPANNING read extraction for scaff: GLIS3--FGF7P6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] -fusion SPANNING read extraction for scaff: GTF2H2--FAM114A1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: LPAR1--SUSD1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] -fusion SPANNING read extraction for scaff: MMP24OS--PTPRT [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] -fusion SPANNING read extraction for scaff: NEK10--CCBE1 -fusion SPANNING read extraction for scaff: NTM-AS1--OPCML [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] -fusion SPANNING read extraction for scaff: PARD3--AL392046.1 [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] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6 [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--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [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] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [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] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] -fusion SPANNING read extraction for scaff: POLR2J3--KIF16B [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: PSG9--CD177 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] -fusion SPANNING read extraction for scaff: PSMB2--CELF4 [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] -fusion SPANNING read extraction for scaff: PXN--PLA2G1B [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] -fusion SPANNING read extraction for scaff: RBBP4--FBXL2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: SDHAF3--AC025614.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: SDHAF3--LINC01985 [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] -fusion SPANNING read extraction for scaff: SLC11A2--CASKP1 [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] -fusion SPANNING read extraction for scaff: SLC11A2--SFPQP1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: SLC30A7--UROC1 [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] -fusion SPANNING read extraction for scaff: SLC34A2--ROS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] -fusion SPANNING read extraction for scaff: SMARCA2--TRIM72 [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: SOGA3--KIAA0408 [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] -fusion SPANNING read extraction for scaff: ST7--AC006001.3 [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: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2 [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] 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[1311000] [1312000] [1313000] [1314000] [1315000] [1316000] [1317000] [1318000] [1319000] [1320000] [1321000] [1322000] [1323000] [1324000] [1325000] [1326000] [1327000] [1328000] [1329000] [1330000] [1331000] [1332000] [1333000] [1334000] [1335000] [1336000] [1337000] [1338000] [1339000] [1340000] [1341000] [1342000] [1343000] [1344000] [1345000] [1346000] [1347000] [1348000] [1349000] [1350000] [1351000] [1352000] [1353000] [1354000] [1355000] [1356000] [1357000] [1358000] [1359000] [1360000] [1361000] [1362000] [1363000] [1364000] [1365000] [1366000] [1367000] [1368000] [1369000] [1370000] [1371000] [1372000] [1373000] [1374000] [1375000] [1376000] [1377000] [1378000] [1379000] [1380000] [1381000] [1382000] [1383000] [1384000] [1385000] [1386000] [1387000] [1388000] [1389000] [1390000] [1391000] [1392000] [1393000] [1394000] [1395000] [1396000] [1397000] [1398000] [1399000] [1400000] [1401000] [1402000] [1403000] [1404000] [1405000] [1406000] [1407000] [1408000] [1409000] [1410000] [1411000] [1412000] [1413000] [1414000] [1415000] [1416000] [1417000] [1418000] [1419000] [1420000] [1421000] [1422000] [1423000] [1424000] [1425000] [1426000] [1427000] [1428000] [1429000] [1430000] [1431000] [1432000] [1433000] [1434000] [1435000] [1436000] [1437000] [1438000] [1439000] [1440000] [1441000] [1442000] [1443000] [1444000] [1445000] [1446000] [1447000] [1448000] [1449000] [1450000] [1451000] [1452000] [1453000] [1454000] [1455000] [1456000] [1457000] [1458000] [1459000] [1460000] [1461000] [1462000] [1463000] [1464000] [1465000] [1466000] [1467000] [1468000] [1469000] [1470000] [1471000] [1472000] [1473000] [1474000] [1475000] [1476000] [1477000] [1478000] [1479000] [1480000] [1481000] [1482000] -fusion SPANNING read extraction for scaff: TRIO--TMEM272 [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] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] -fusion SPANNING read extraction for scaff: UHRF2--SLC1A1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] -fusion SPANNING read extraction for scaff: XYLB--GOLGA4 [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] -fusion SPANNING read extraction for scaff: ZBTB40--ZMYM4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] -fusion SPANNING read extraction for scaff: ZFP62--SIMC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: ZNF559--ZNF177 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 27008, 'lacks exon overlap' => 197115 }; Execution Time = 8.53 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -21862.591218 EM: Round [1] log likelihood: -21849.927542 EM: Round [2] log likelihood: -21847.366049 EM: Round [3] log likelihood: -21845.411933 EM: Round [4] log likelihood: -21843.866492 EM: Round [5] log likelihood: -21842.635458 EM: Round [6] log likelihood: -21841.649222 EM: Round [7] log likelihood: -21840.854872 EM: Round [8] log likelihood: -21840.211792 EM: Round [9] log likelihood: -21839.688562 EM: Round [10] log likelihood: -21839.260718 EM: Round [11] log likelihood: -21838.909097 EM: Round [12] log likelihood: -21838.618620 EM: Round [13] log likelihood: -21838.377364 EM: Round [14] log likelihood: -21838.175865 EM: Round [15] log likelihood: -21838.006580 EM: Round [16] log likelihood: -21837.863481 EM: Round [17] log likelihood: -21837.741731 EM: Round [18] log likelihood: -21837.637439 EM: Round [19] log likelihood: -21837.547463 EM: Round [20] log likelihood: -21837.469261 EM: Round [21] log likelihood: -21837.400770 EM: Round [22] log likelihood: -21837.340311 EM: Round [23] log likelihood: -21837.286513 EM: Round [24] log likelihood: -21837.238256 EM: Round [25] log likelihood: -21837.194621 EM: Round [26] log likelihood: -21837.154851 EM: Round [27] log likelihood: -21837.118324 EM: Round [28] log likelihood: -21837.084526 EM: Round [29] log likelihood: -21837.053032 EM: Round [30] log likelihood: -21837.023489 EM: Round [31] log likelihood: -21836.995603 EM: Round [32] log likelihood: -21836.969130 EM: Round [33] log likelihood: -21836.943867 EM: Round [34] log likelihood: -21836.919643 EM: Round [35] log likelihood: -21836.896316 EM: Round [36] log likelihood: -21836.873766 EM: Round [37] log likelihood: -21836.851892 EM: Round [38] log likelihood: -21836.830611 EM: Round [39] log likelihood: -21836.809850 EM: Round [40] log likelihood: -21836.789550 EM: Round [41] log likelihood: -21836.769659 EM: Round [42] log likelihood: -21836.750134 EM: Round [43] log likelihood: -21836.730940 EM: Round [44] log likelihood: -21836.712043 EM: Round [45] log likelihood: -21836.693418 EM: Round [46] log likelihood: -21836.675043 EM: Round [47] log likelihood: -21836.656897 EM: Round [48] log likelihood: -21836.638964 EM: Round [49] log likelihood: -21836.621229 EM: Round [50] log likelihood: -21836.603681 EM: Round [51] log likelihood: -21836.586308 EM: Round [52] log likelihood: -21836.569102 EM: Round [53] log likelihood: -21836.552053 EM: Round [54] log likelihood: -21836.535155 EM: Round [55] log likelihood: -21836.518403 EM: Round [56] log likelihood: -21836.501789 EM: Round [57] log likelihood: -21836.485310 EM: Round [58] log likelihood: -21836.468960 EM: Round [59] log likelihood: -21836.452737 EM: Round [60] log likelihood: -21836.436637 EM: Round [61] log likelihood: -21836.420656 EM: Round [62] log likelihood: -21836.404793 EM: Round [63] log likelihood: -21836.389043 EM: Round [64] log likelihood: -21836.373405 EM: Round [65] log likelihood: -21836.357877 EM: Round [66] log likelihood: -21836.342456 EM: Round [67] log likelihood: -21836.327141 EM: Round [68] log likelihood: -21836.311930 EM: Round [69] log likelihood: -21836.296821 EM: Round [70] log likelihood: -21836.281813 EM: Round [71] log likelihood: -21836.266904 EM: Round [72] log likelihood: -21836.252092 EM: Round [73] log likelihood: -21836.237377 EM: Round [74] log likelihood: -21836.222757 EM: Round [75] log likelihood: -21836.208231 EM: Round [76] log likelihood: -21836.193797 EM: Round [77] log likelihood: -21836.179455 EM: Round [78] log likelihood: -21836.165203 EM: Round [79] log likelihood: -21836.151040 EM: Round [80] log likelihood: -21836.136966 EM: Round [81] log likelihood: -21836.122978 EM: Round [82] log likelihood: -21836.109076 EM: Round [83] log likelihood: -21836.095260 EM: Round [84] log likelihood: -21836.081528 EM: Round [85] log likelihood: -21836.067879 EM: Round [86] log likelihood: -21836.054312 EM: Round [87] log likelihood: -21836.040826 EM: Round [88] log likelihood: -21836.027421 EM: Round [89] log likelihood: -21836.014095 EM: Round [90] log likelihood: -21836.000849 EM: Round [91] log likelihood: -21835.987680 EM: Round [92] log likelihood: -21835.974588 EM: Round [93] log likelihood: -21835.961573 EM: Round [94] log likelihood: -21835.948632 EM: Round [95] log likelihood: -21835.935767 EM: Round [96] log likelihood: -21835.922976 EM: Round [97] log likelihood: -21835.910257 EM: Round [98] log likelihood: -21835.897612 EM: Round [99] log likelihood: -21835.885038 EM: Round [100] log likelihood: -21835.872534 EM: Round [101] log likelihood: -21835.860102 EM: Round [102] log likelihood: -21835.847738 EM: Round [103] log likelihood: -21835.835444 EM: Round [104] log likelihood: -21835.823218 EM: Round [105] log likelihood: -21835.811059 EM: Round [106] log likelihood: -21835.798968 EM: Round [107] log likelihood: -21835.786942 EM: Round [108] log likelihood: -21835.774983 EM: Round [109] log likelihood: -21835.763088 EM: Round [110] log likelihood: -21835.751258 EM: Round [111] log likelihood: -21835.739491 EM: Round [112] log likelihood: -21835.727788 EM: Round [113] log likelihood: -21835.716147 EM: Round [114] log likelihood: -21835.704568 EM: Round [115] log likelihood: -21835.693051 EM: Round [116] log likelihood: -21835.681594 EM: Round [117] log likelihood: -21835.670198 EM: Round [118] log likelihood: -21835.658861 EM: Round [119] log likelihood: -21835.647584 EM: Round [120] log likelihood: -21835.636366 EM: Round [121] log likelihood: -21835.625205 EM: Round [122] log likelihood: -21835.614102 EM: Round [123] log likelihood: -21835.603057 EM: Round [124] log likelihood: -21835.592068 EM: Round [125] log likelihood: -21835.581135 EM: Round [126] log likelihood: -21835.570257 EM: Round [127] log likelihood: -21835.559435 EM: Round [128] log likelihood: -21835.548668 EM: Round [129] log likelihood: -21835.537954 EM: Round [130] log likelihood: -21835.527294 EM: Round [131] log likelihood: -21835.516688 EM: Round [132] log likelihood: -21835.506134 EM: Round [133] log likelihood: -21835.495633 EM: Round [134] log likelihood: -21835.485184 EM: Round [135] log likelihood: -21835.474786 EM: Round [136] log likelihood: -21835.464439 EM: Round [137] log likelihood: -21835.454143 EM: Round [138] log likelihood: -21835.443896 EM: Round [139] log likelihood: -21835.433700 EM: Round [140] log likelihood: -21835.423553 EM: Round [141] log likelihood: -21835.413455 EM: Round [142] log likelihood: -21835.403405 EM: Round [143] log likelihood: -21835.393404 EM: Round [144] log likelihood: -21835.383450 EM: Round [145] log likelihood: -21835.373544 EM: Round [146] log likelihood: -21835.363685 EM: Round [147] log likelihood: -21835.353872 EM: Round [148] log likelihood: -21835.344106 EM: Round [149] log likelihood: -21835.334385 EM: Round [150] log likelihood: -21835.324710 EM: Round [151] log likelihood: -21835.315080 EM: Round [152] log likelihood: -21835.305495 EM: Round [153] log likelihood: -21835.295954 EM: Round [154] log likelihood: -21835.286458 EM: Round [155] log likelihood: -21835.277005 EM: Round [156] log likelihood: -21835.267595 EM: Round [157] log likelihood: -21835.258229 EM: Round [158] log likelihood: -21835.248905 EM: Round [159] log likelihood: -21835.239624 EM: Round [160] log likelihood: -21835.230385 EM: Round [161] log likelihood: -21835.221188 EM: Round [162] log likelihood: -21835.212032 EM: Round [163] log likelihood: -21835.202917 EM: Round [164] log likelihood: -21835.193843 EM: Round [165] log likelihood: -21835.184810 EM: Round [166] log likelihood: -21835.175817 EM: Round [167] log likelihood: -21835.166863 EM: Round [168] log likelihood: -21835.157950 EM: Round [169] log likelihood: -21835.149075 EM: Round [170] log likelihood: -21835.140240 EM: Round [171] log likelihood: -21835.131444 EM: Round [172] log likelihood: -21835.122686 EM: Round [173] log likelihood: -21835.113966 EM: Round [174] log likelihood: -21835.105284 EM: Round [175] log likelihood: -21835.096640 EM: Round [176] log likelihood: -21835.088033 EM: Round [177] log likelihood: -21835.079464 EM: Round [178] log likelihood: -21835.070931 EM: Round [179] log likelihood: -21835.062435 EM: Round [180] log likelihood: -21835.053975 EM: Round [181] log likelihood: -21835.045551 EM: Round [182] log likelihood: -21835.037163 EM: Round [183] log likelihood: -21835.028810 EM: Round [184] log likelihood: -21835.020493 EM: Round [185] log likelihood: -21835.012211 EM: Round [186] log likelihood: -21835.003964 EM: Round [187] log likelihood: -21834.995751 EM: Round [188] log likelihood: -21834.987573 EM: Round [189] log likelihood: -21834.979429 EM: Round [190] log likelihood: -21834.971319 EM: Round [191] log likelihood: -21834.963242 EM: Round [192] log likelihood: -21834.955199 EM: Round [193] log likelihood: -21834.947189 EM: Round [194] log likelihood: -21834.939212 EM: Round [195] log likelihood: -21834.931267 EM: Round [196] log likelihood: -21834.923356 EM: Round [197] log likelihood: -21834.915476 EM: Round [198] log likelihood: -21834.907629 EM: Round [199] log likelihood: -21834.899813 EM: Round [200] log likelihood: -21834.892029 EM: Round [201] log likelihood: -21834.884277 EM: Round [202] log likelihood: -21834.876556 EM: Round [203] log likelihood: -21834.868866 EM: Round [204] log likelihood: -21834.861207 EM: Round [205] log likelihood: -21834.853578 EM: Round [206] log likelihood: -21834.845980 EM: Round [207] log likelihood: -21834.838412 EM: Round [208] log likelihood: -21834.830875 EM: Round [209] log likelihood: -21834.823367 EM: Round [210] log likelihood: -21834.815888 EM: Round [211] log likelihood: -21834.808440 EM: Round [212] log likelihood: -21834.801020 EM: Round [213] log likelihood: -21834.793630 EM: Round [214] log likelihood: -21834.786268 EM: Round [215] log likelihood: -21834.778936 EM: Round [216] log likelihood: -21834.771632 EM: Round [217] log likelihood: -21834.764356 EM: Round [218] log likelihood: -21834.757108 EM: Round [219] log likelihood: -21834.749889 EM: Round [220] log likelihood: -21834.742697 EM: Round [221] log likelihood: -21834.735533 EM: Round [222] log likelihood: -21834.728397 EM: Round [223] log likelihood: -21834.721288 EM: Round [224] log likelihood: -21834.714206 EM: Round [225] log likelihood: -21834.707151 EM: Round [226] log likelihood: -21834.700123 EM: Round [227] log likelihood: -21834.693121 EM: Round [228] log likelihood: -21834.686146 EM: Round [229] log likelihood: -21834.679198 EM: Round [230] log likelihood: -21834.672276 EM: Round [231] log likelihood: -21834.665379 EM: Round [232] log likelihood: -21834.658509 EM: Round [233] log likelihood: -21834.651664 EM: Round [234] log likelihood: -21834.644845 EM: Round [235] log likelihood: -21834.638051 EM: Round [236] log likelihood: -21834.631283 EM: Round [237] log likelihood: -21834.624539 EM: Round [238] log likelihood: -21834.617821 EM: Round [239] log likelihood: -21834.611128 EM: Round [240] log likelihood: -21834.604459 EM: Round [241] log likelihood: -21834.597815 EM: Round [242] log likelihood: -21834.591195 EM: Round [243] log likelihood: -21834.584599 EM: Round [244] log likelihood: -21834.578027 EM: Round [245] log likelihood: -21834.571480 EM: Round [246] log likelihood: -21834.564956 EM: Round [247] log likelihood: -21834.558456 EM: Round [248] log likelihood: -21834.551980 EM: Round [249] log likelihood: -21834.545527 EM: Round [250] log likelihood: -21834.539097 EM: Round [251] log likelihood: -21834.532690 EM: Round [252] log likelihood: -21834.526307 EM: Round [253] log likelihood: -21834.519946 EM: Round [254] log likelihood: -21834.513608 EM: Round [255] log likelihood: -21834.507293 EM: Round [256] log likelihood: -21834.501000 EM: Round [257] log likelihood: -21834.494730 EM: Round [258] log likelihood: -21834.488482 EM: Round [259] log likelihood: -21834.482256 EM: Round [260] log likelihood: -21834.476052 EM: Round [261] log likelihood: -21834.469870 EM: Round [262] log likelihood: -21834.463709 EM: Round [263] log likelihood: -21834.457571 EM: Round [264] log likelihood: -21834.451454 EM: Round [265] log likelihood: -21834.445358 EM: Round [266] log likelihood: -21834.439284 EM: Round [267] log likelihood: -21834.433230 EM: Round [268] log likelihood: -21834.427198 EM: Round [269] log likelihood: -21834.421187 EM: Round [270] log likelihood: -21834.415197 EM: Round [271] log likelihood: -21834.409227 EM: Round [272] log likelihood: -21834.403278 EM: Round [273] log likelihood: -21834.397350 EM: Round [274] log likelihood: -21834.391442 EM: Round [275] log likelihood: -21834.385554 EM: Round [276] log likelihood: -21834.379686 EM: Round [277] log likelihood: -21834.373839 EM: Round [278] log likelihood: -21834.368011 EM: Round [279] log likelihood: -21834.362203 EM: Round [280] log likelihood: -21834.356415 EM: Round [281] log likelihood: -21834.350647 EM: Round [282] log likelihood: -21834.344898 EM: Round [283] log likelihood: -21834.339169 EM: Round [284] log likelihood: -21834.333459 EM: Round [285] log likelihood: -21834.327768 EM: Round [286] log likelihood: -21834.322097 EM: Round [287] log likelihood: -21834.316444 EM: Round [288] log 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Round [310] log likelihood: -21834.191473 EM: Round [311] log likelihood: -21834.186249 EM: Round [312] log likelihood: -21834.181043 EM: Round [313] log likelihood: -21834.175852 EM: Round [314] log likelihood: -21834.170679 EM: Round [315] log likelihood: -21834.165522 EM: Round [316] log likelihood: -21834.160382 EM: Round [317] log likelihood: -21834.155258 EM: Round [318] log likelihood: -21834.150150 EM: Round [319] log likelihood: -21834.145059 EM: Round [320] log likelihood: -21834.139983 EM: Round [321] log likelihood: -21834.134924 EM: Round [322] log likelihood: -21834.129881 EM: Round [323] log likelihood: -21834.124853 EM: Round [324] log likelihood: -21834.119842 EM: Round [325] log likelihood: -21834.114846 EM: Round [326] log likelihood: -21834.109866 EM: Round [327] log likelihood: -21834.104902 EM: Round [328] log likelihood: -21834.099953 EM: Round [329] log likelihood: -21834.095019 EM: Round [330] log likelihood: -21834.090101 EM: Round [331] log likelihood: 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Round [375] log likelihood: -21833.883631 EM: Round [376] log likelihood: -21833.879350 EM: Round [377] log likelihood: -21833.875082 EM: Round [378] log likelihood: -21833.870826 EM: Round [379] log likelihood: -21833.866582 EM: Round [380] log likelihood: -21833.862351 EM: Round [381] log likelihood: -21833.858132 EM: Round [382] log likelihood: -21833.853925 EM: Round [383] log likelihood: -21833.849730 EM: Round [384] log likelihood: -21833.845548 EM: Round [385] log likelihood: -21833.841377 EM: Round [386] log likelihood: -21833.837219 EM: Round [387] log likelihood: -21833.833072 EM: Round [388] log likelihood: -21833.828938 EM: Round [389] log likelihood: -21833.824815 EM: Round [390] log likelihood: -21833.820704 EM: Round [391] log likelihood: -21833.816604 EM: Round [392] log likelihood: -21833.812517 EM: Round [393] log likelihood: -21833.808441 EM: Round [394] log likelihood: -21833.804377 EM: Round [395] log likelihood: -21833.800324 EM: Round [396] log likelihood: 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Round [440] log likelihood: -21833.629178 EM: Round [441] log likelihood: -21833.625609 EM: Round [442] log likelihood: -21833.622050 EM: Round [443] log likelihood: -21833.618500 EM: Round [444] log likelihood: -21833.614960 EM: Round [445] log likelihood: -21833.611430 EM: Round [446] log likelihood: -21833.607908 EM: Round [447] log likelihood: -21833.604396 EM: Round [448] log likelihood: -21833.600894 EM: Round [449] log likelihood: -21833.597401 EM: Round [450] log likelihood: -21833.593917 EM: Round [451] log likelihood: -21833.590442 EM: Round [452] log likelihood: -21833.586977 EM: Round [453] log likelihood: -21833.583521 EM: Round [454] log likelihood: -21833.580074 EM: Round [455] log likelihood: -21833.576636 EM: Round [456] log likelihood: -21833.573207 EM: Round [457] log likelihood: -21833.569787 EM: Round [458] log likelihood: -21833.566376 EM: Round [459] log likelihood: -21833.562975 EM: Round [460] log likelihood: -21833.559582 EM: Round [461] log likelihood: 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likelihood: -21833.483942 EM: Round [484] log likelihood: -21833.480755 EM: Round [485] log likelihood: -21833.477575 EM: Round [486] log likelihood: -21833.474404 EM: Round [487] log likelihood: -21833.471241 EM: Round [488] log likelihood: -21833.468086 EM: Round [489] log likelihood: -21833.464939 EM: Round [490] log likelihood: -21833.461800 EM: Round [491] log likelihood: -21833.458669 EM: Round [492] log likelihood: -21833.455546 EM: Round [493] log likelihood: -21833.452430 EM: Round [494] log likelihood: -21833.449323 EM: Round [495] log likelihood: -21833.446224 EM: Round [496] log likelihood: -21833.443132 EM: Round [497] log likelihood: -21833.440049 EM: Round [498] log likelihood: -21833.436973 EM: Round [499] log likelihood: -21833.433905 EM: Round [500] log likelihood: -21833.430845 EM: Round [501] log likelihood: -21833.427792 EM: Round [502] log likelihood: -21833.424747 EM: Round [503] log likelihood: -21833.421710 EM: Round [504] log likelihood: -21833.418680 EM: Round [505] log likelihood: -21833.415658 EM: Round [506] log likelihood: -21833.412644 EM: Round [507] log likelihood: -21833.409637 EM: Round [508] log likelihood: -21833.406638 EM: Round [509] log likelihood: -21833.403646 EM: Round [510] log likelihood: -21833.400661 EM: Round [511] log likelihood: -21833.397684 EM: Round [512] log likelihood: -21833.394715 EM: Round [513] log likelihood: -21833.391753 EM: Round [514] log likelihood: -21833.388798 EM: Round [515] log likelihood: -21833.385851 EM: Round [516] log likelihood: -21833.382911 EM: Round [517] log likelihood: -21833.379978 EM: Round [518] log likelihood: -21833.377053 EM: Round [519] log likelihood: -21833.374135 EM: Round [520] log likelihood: -21833.371224 EM: Round [521] log likelihood: -21833.368320 EM: Round [522] log likelihood: -21833.365423 EM: Round [523] log likelihood: -21833.362534 EM: Round [524] log likelihood: -21833.359652 EM: Round [525] log likelihood: -21833.356777 EM: Round [526] log likelihood: 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likelihood: -21833.292555 EM: Round [549] log likelihood: -21833.289844 EM: Round [550] log likelihood: -21833.287139 EM: Round [551] log likelihood: -21833.284440 EM: Round [552] log likelihood: -21833.281748 EM: Round [553] log likelihood: -21833.279062 EM: Round [554] log likelihood: -21833.276383 EM: Round [555] log likelihood: -21833.273711 EM: Round [556] log likelihood: -21833.271044 EM: Round [557] log likelihood: -21833.268384 EM: Round [558] log likelihood: -21833.265731 EM: Round [559] log likelihood: -21833.263084 EM: Round [560] log likelihood: -21833.260443 EM: Round [561] log likelihood: -21833.257808 EM: Round [562] log likelihood: -21833.255180 EM: Round [563] log likelihood: -21833.252558 EM: Round [564] log likelihood: -21833.249942 EM: Round [565] log likelihood: -21833.247333 EM: Round [566] log likelihood: -21833.244730 EM: Round [567] log likelihood: -21833.242133 EM: Round [568] log likelihood: -21833.239542 EM: Round [569] log likelihood: -21833.236957 EM: Round [570] log likelihood: -21833.234378 EM: Round [571] log likelihood: -21833.231806 EM: Round [572] log likelihood: -21833.229239 EM: Round [573] log likelihood: -21833.226679 EM: Round [574] log likelihood: -21833.224124 EM: Round [575] log likelihood: -21833.221576 EM: Round [576] log likelihood: -21833.219034 EM: Round [577] log likelihood: -21833.216497 EM: Round [578] log likelihood: -21833.213967 EM: Round [579] log likelihood: -21833.211443 EM: Round [580] log likelihood: -21833.208924 EM: Round [581] log likelihood: -21833.206411 EM: Round [582] log likelihood: -21833.203905 EM: Round [583] log likelihood: -21833.201404 EM: Round [584] log likelihood: -21833.198909 EM: Round [585] log likelihood: -21833.196420 EM: Round [586] log likelihood: -21833.193937 EM: Round [587] log likelihood: -21833.191459 EM: Round [588] log likelihood: -21833.188988 EM: Round [589] log likelihood: -21833.186522 EM: Round [590] log likelihood: -21833.184062 EM: Round [591] log likelihood: 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Round [635] log likelihood: -21833.079030 EM: Round [636] log likelihood: -21833.076816 EM: Round [637] log likelihood: -21833.074607 EM: Round [638] log likelihood: -21833.072403 EM: Round [639] log likelihood: -21833.070204 EM: Round [640] log likelihood: -21833.068010 EM: Round [641] log likelihood: -21833.065821 EM: Round [642] log likelihood: -21833.063637 EM: Round [643] log likelihood: -21833.061458 EM: Round [644] log likelihood: -21833.059284 EM: Round [645] log likelihood: -21833.057114 EM: Round [646] log likelihood: -21833.054949 EM: Round [647] log likelihood: -21833.052790 EM: Round [648] log likelihood: -21833.050635 EM: Round [649] log likelihood: -21833.048485 EM: Round [650] log likelihood: -21833.046339 EM: Round [651] log likelihood: -21833.044199 EM: Round [652] log likelihood: -21833.042063 EM: Round [653] log likelihood: -21833.039932 EM: Round [654] log likelihood: -21833.037805 EM: Round [655] log likelihood: -21833.035684 EM: Round [656] log likelihood: -21833.033567 EM: Round [657] log likelihood: -21833.031455 EM: Round [658] log likelihood: -21833.029347 EM: Round [659] log likelihood: -21833.027244 EM: Round [660] log likelihood: -21833.025146 EM: Round [661] log likelihood: -21833.023053 EM: Round [662] log likelihood: -21833.020964 EM: Round [663] log likelihood: -21833.018880 EM: Round [664] log likelihood: -21833.016800 EM: Round [665] log likelihood: -21833.014725 EM: Round [666] log likelihood: -21833.012654 EM: Round [667] log likelihood: -21833.010589 EM: Round [668] log likelihood: -21833.008527 EM: Round [669] log likelihood: -21833.006470 EM: Round [670] log likelihood: -21833.004418 EM: Round [671] log likelihood: -21833.002370 EM: Round [672] log likelihood: -21833.000327 EM: Round [673] log likelihood: -21832.998288 EM: Round [674] log likelihood: -21832.996254 EM: Round [675] log likelihood: -21832.994224 EM: Round [676] log likelihood: -21832.992199 EM: Round [677] log likelihood: -21832.990178 EM: Round [678] log 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Round [700] log likelihood: -21832.944892 EM: Round [701] log likelihood: -21832.942974 EM: Round [702] log likelihood: -21832.941060 EM: Round [703] log likelihood: -21832.939150 EM: Round [704] log likelihood: -21832.937244 EM: Round [705] log likelihood: -21832.935342 EM: Round [706] log likelihood: -21832.933445 EM: Round [707] log likelihood: -21832.931551 EM: Round [708] log likelihood: -21832.929662 EM: Round [709] log likelihood: -21832.927776 EM: Round [710] log likelihood: -21832.925895 EM: Round [711] log likelihood: -21832.924018 EM: Round [712] log likelihood: -21832.922145 EM: Round [713] log likelihood: -21832.920275 EM: Round [714] log likelihood: -21832.918410 EM: Round [715] log likelihood: -21832.916549 EM: Round [716] log likelihood: -21832.914691 EM: Round [717] log likelihood: -21832.912838 EM: Round [718] log likelihood: -21832.910989 EM: Round [719] log likelihood: -21832.909143 EM: Round [720] log likelihood: -21832.907302 EM: Round [721] log likelihood: -21832.905464 EM: Round [722] log likelihood: -21832.903631 EM: Round [723] log likelihood: -21832.901801 EM: Round [724] log likelihood: -21832.899975 EM: Round [725] log likelihood: -21832.898153 EM: Round [726] log likelihood: -21832.896335 EM: Round [727] log likelihood: -21832.894521 EM: Round [728] log likelihood: -21832.892710 EM: Round [729] log likelihood: -21832.890904 EM: Round [730] log likelihood: -21832.889101 EM: Round [731] log likelihood: -21832.887302 EM: Round [732] log likelihood: -21832.885507 EM: Round [733] log likelihood: -21832.883716 EM: Round [734] log likelihood: -21832.881928 EM: Round [735] log likelihood: -21832.880145 EM: Round [736] log likelihood: -21832.878365 EM: Round [737] log likelihood: -21832.876589 EM: Round [738] log likelihood: -21832.874816 EM: Round [739] log likelihood: -21832.873047 EM: Round [740] log likelihood: -21832.871282 EM: Round [741] log likelihood: -21832.869521 EM: Round [742] log likelihood: -21832.867764 EM: Round [743] log likelihood: -21832.866010 EM: Round [744] log likelihood: -21832.864260 EM: Round [745] log likelihood: -21832.862513 EM: Round [746] log likelihood: -21832.860770 EM: Round [747] log likelihood: -21832.859031 EM: Round [748] log likelihood: -21832.857296 EM: Round [749] log likelihood: -21832.855564 EM: Round [750] log likelihood: -21832.853836 EM: Round [751] log likelihood: -21832.852111 EM: Round [752] log likelihood: -21832.850390 EM: Round [753] log likelihood: -21832.848673 EM: Round [754] log likelihood: -21832.846959 EM: Round [755] log likelihood: -21832.845248 EM: Round [756] log likelihood: -21832.843542 EM: Round [757] log likelihood: -21832.841839 EM: Round [758] log likelihood: -21832.840139 EM: Round [759] log likelihood: -21832.838443 EM: Round [760] log likelihood: -21832.836751 EM: Round [761] log likelihood: -21832.835062 EM: Round [762] log likelihood: -21832.833376 EM: Round [763] log likelihood: -21832.831694 EM: Round [764] log likelihood: -21832.830016 EM: Round [765] log likelihood: -21832.828341 EM: Round [766] log likelihood: -21832.826670 EM: Round [767] log likelihood: -21832.825002 EM: Round [768] log likelihood: -21832.823337 EM: Round [769] log likelihood: -21832.821676 EM: Round [770] log likelihood: -21832.820019 EM: Round [771] log likelihood: -21832.818364 EM: Round [772] log likelihood: -21832.816714 EM: Round [773] log likelihood: -21832.815066 EM: Round [774] log likelihood: -21832.813422 EM: Round [775] log likelihood: -21832.811782 EM: Round [776] log likelihood: -21832.810145 EM: Round [777] log likelihood: -21832.808511 EM: Round [778] log likelihood: -21832.806881 EM: Round [779] log likelihood: -21832.805253 EM: Round [780] log likelihood: -21832.803630 EM: Round [781] log likelihood: -21832.802009 EM: Round [782] log likelihood: -21832.800393 EM: Round [783] log likelihood: -21832.798779 EM: Round [784] log likelihood: -21832.797169 EM: Round [785] log likelihood: -21832.795561 EM: Round [786] log likelihood: -21832.793958 EM: Round [787] log likelihood: -21832.792357 EM: Round [788] log likelihood: -21832.790760 EM: Round [789] log likelihood: -21832.789166 EM: Round [790] log likelihood: -21832.787576 EM: Round [791] log likelihood: -21832.785988 EM: Round [792] log likelihood: -21832.784404 EM: Round [793] log likelihood: -21832.782823 EM: Round [794] log likelihood: -21832.781246 EM: Round [795] log likelihood: -21832.779671 EM: Round [796] log likelihood: -21832.778100 EM: Round [797] log likelihood: -21832.776532 EM: Round [798] log likelihood: -21832.774968 EM: Round [799] log likelihood: -21832.773406 EM: Round [800] log likelihood: -21832.771848 EM: Round [801] log likelihood: -21832.770293 EM: Round [802] log likelihood: -21832.768741 EM: Round [803] log likelihood: -21832.767192 EM: Round [804] log likelihood: -21832.765646 EM: Round [805] log likelihood: -21832.764103 EM: Round [806] log likelihood: -21832.762564 EM: Round [807] log likelihood: -21832.761028 EM: Round [808] log likelihood: -21832.759495 EM: Round [809] log likelihood: -21832.757965 EM: Round [810] log likelihood: -21832.756438 EM: Round [811] log likelihood: -21832.754914 EM: Round [812] log likelihood: -21832.753393 EM: Round [813] log likelihood: -21832.751875 EM: Round [814] log likelihood: -21832.750361 EM: Round [815] log likelihood: -21832.748849 EM: Round [816] log likelihood: -21832.747341 EM: Round [817] log likelihood: -21832.745835 EM: Round [818] log likelihood: -21832.744333 EM: Round [819] log likelihood: -21832.742834 EM: Round [820] log likelihood: -21832.741337 EM: Round [821] log likelihood: -21832.739844 EM: Round [822] log likelihood: -21832.738354 EM: Round [823] log likelihood: -21832.736867 EM: Round [824] log likelihood: -21832.735382 EM: Round [825] log likelihood: -21832.733901 EM: Round [826] log likelihood: -21832.732423 EM: Round [827] log likelihood: -21832.730947 EM: Round [828] log likelihood: -21832.729475 EM: Round [829] log likelihood: -21832.728006 EM: Round [830] log likelihood: -21832.726539 EM: Round [831] log likelihood: -21832.725076 EM: Round [832] log likelihood: -21832.723615 EM: Round [833] log likelihood: -21832.722158 EM: Round [834] log likelihood: -21832.720703 EM: Round [835] log likelihood: -21832.719251 EM: Round [836] log likelihood: -21832.717802 EM: Round [837] log likelihood: -21832.716356 EM: Round [838] log likelihood: -21832.714913 EM: Round [839] log likelihood: -21832.713473 EM: Round [840] log likelihood: -21832.712036 EM: Round [841] log likelihood: -21832.710601 EM: Round [842] log likelihood: -21832.709170 EM: Round [843] log likelihood: -21832.707741 EM: Round [844] log likelihood: -21832.706315 EM: Round [845] log likelihood: -21832.704892 EM: Round [846] log likelihood: -21832.703472 EM: Round [847] log likelihood: -21832.702055 EM: Round [848] log likelihood: -21832.700640 EM: Round [849] log likelihood: -21832.699229 EM: Round [850] log likelihood: -21832.697820 EM: Round [851] log likelihood: -21832.696414 EM: Round [852] log likelihood: -21832.695011 EM: Round [853] log likelihood: -21832.693610 EM: Round [854] log likelihood: -21832.692212 EM: Round [855] log likelihood: -21832.690818 EM: Round [856] log likelihood: -21832.689425 EM: Round [857] log likelihood: -21832.688036 EM: Round [858] log likelihood: -21832.686649 EM: Round [859] log likelihood: -21832.685266 EM: Round [860] log likelihood: -21832.683884 EM: Round [861] log likelihood: -21832.682506 EM: Round [862] log likelihood: -21832.681130 EM: Round [863] log likelihood: -21832.679757 EM: Round [864] log likelihood: -21832.678387 EM: Round [865] log likelihood: -21832.677020 EM: Round [866] log likelihood: -21832.675655 EM: Round [867] log likelihood: -21832.674293 EM: Round [868] log likelihood: -21832.672933 EM: Round [869] log likelihood: -21832.671577 EM: Round [870] log likelihood: -21832.670223 EM: Round [871] log likelihood: -21832.668871 EM: Round [872] log likelihood: -21832.667523 EM: Round [873] log likelihood: -21832.666177 EM: Round [874] log likelihood: -21832.664833 EM: Round [875] log likelihood: -21832.663492 EM: Round [876] log likelihood: -21832.662154 EM: Round [877] log likelihood: -21832.660819 EM: Round [878] log likelihood: -21832.659486 EM: Round [879] log likelihood: -21832.658156 EM: Round [880] log likelihood: -21832.656828 EM: Round [881] log likelihood: -21832.655503 EM: Round [882] log likelihood: -21832.654181 EM: Round [883] log likelihood: -21832.652861 EM: Round [884] log likelihood: -21832.651543 EM: Round [885] log likelihood: -21832.650229 EM: Round [886] log likelihood: -21832.648917 EM: Round [887] log likelihood: -21832.647607 EM: Round [888] log likelihood: -21832.646300 EM: Round [889] log likelihood: -21832.644996 EM: Round [890] log likelihood: -21832.643694 EM: Round [891] log likelihood: -21832.642395 EM: Round [892] log likelihood: -21832.641098 EM: Round [893] log likelihood: -21832.639804 EM: Round [894] log likelihood: -21832.638512 EM: Round [895] log likelihood: -21832.637223 EM: Round [896] log likelihood: -21832.635936 EM: Round [897] log likelihood: -21832.634652 EM: Round [898] log likelihood: -21832.633371 EM: Round [899] log likelihood: -21832.632091 EM: Round [900] log likelihood: -21832.630815 EM: Round [901] log likelihood: -21832.629541 EM: Round [902] log likelihood: -21832.628269 EM: Round [903] log likelihood: -21832.627000 EM: Round [904] log likelihood: -21832.625733 EM: Round [905] log likelihood: -21832.624469 EM: Round [906] log likelihood: -21832.623207 EM: Round [907] log likelihood: -21832.621947 EM: Round [908] log likelihood: -21832.620691 EM: Round [909] log likelihood: -21832.619436 EM: Round [910] log likelihood: -21832.618184 EM: Round [911] log likelihood: -21832.616934 EM: Round [912] log likelihood: -21832.615687 EM: Round [913] log likelihood: -21832.614442 EM: Round [914] log likelihood: -21832.613200 EM: Round [915] log likelihood: -21832.611960 EM: Round [916] log likelihood: -21832.610722 EM: Round [917] log likelihood: -21832.609487 EM: Round [918] log likelihood: -21832.608254 EM: Round [919] log likelihood: -21832.607024 EM: Round [920] log likelihood: -21832.605796 EM: Round [921] log likelihood: -21832.604570 EM: Round [922] log likelihood: -21832.603347 EM: Round [923] log likelihood: -21832.602126 EM: Round [924] log likelihood: -21832.600908 EM: Round [925] log likelihood: -21832.599691 EM: Round [926] log likelihood: -21832.598477 EM: Round [927] log likelihood: -21832.597266 EM: Round [928] log likelihood: -21832.596057 EM: Round [929] log likelihood: -21832.594850 EM: Round [930] log likelihood: -21832.593645 EM: Round [931] log likelihood: -21832.592443 EM: Round [932] log likelihood: -21832.591243 EM: Round [933] log likelihood: -21832.590045 EM: Round [934] log likelihood: -21832.588850 EM: Round [935] log likelihood: -21832.587657 EM: Round [936] log likelihood: -21832.586466 EM: Round [937] log likelihood: -21832.585278 EM: Round [938] log likelihood: -21832.584092 EM: Round [939] log likelihood: -21832.582908 EM: Round [940] log likelihood: -21832.581726 EM: Round [941] log likelihood: -21832.580547 EM: Round [942] log likelihood: -21832.579370 EM: Round [943] log likelihood: -21832.578195 EM: Round [944] log likelihood: -21832.577022 EM: Round [945] log likelihood: -21832.575852 EM: Round [946] log likelihood: -21832.574684 EM: Round [947] log likelihood: -21832.573518 EM: Round [948] log likelihood: -21832.572354 EM: Round [949] log likelihood: -21832.571192 EM: Round [950] log likelihood: -21832.570033 EM: Round [951] log likelihood: -21832.568876 EM: Round [952] log likelihood: -21832.567721 EM: Round [953] log likelihood: -21832.566569 EM: Round [954] log likelihood: -21832.565418 EM: Round [955] log likelihood: -21832.564270 EM: Round [956] log likelihood: -21832.563124 EM: Round [957] log likelihood: -21832.561980 EM: Round [958] log likelihood: -21832.560838 EM: Round [959] log likelihood: -21832.559699 EM: Round [960] log likelihood: -21832.558562 EM: Round [961] log likelihood: -21832.557426 EM: Round [962] log likelihood: -21832.556293 EM: Round [963] log likelihood: -21832.555163 EM: Round [964] log likelihood: -21832.554034 EM: Round [965] log likelihood: -21832.552907 EM: Round [966] log likelihood: -21832.551783 EM: Round [967] log likelihood: -21832.550660 EM: Round [968] log likelihood: -21832.549540 EM: Round [969] log likelihood: -21832.548422 EM: Round [970] log likelihood: -21832.547306 EM: Round [971] log likelihood: -21832.546192 EM: Round [972] log likelihood: -21832.545081 EM: Round [973] log likelihood: -21832.543971 EM: Round [974] log likelihood: -21832.542864 EM: Round [975] log likelihood: -21832.541758 EM: Round [976] log likelihood: -21832.540655 EM: Round [977] log likelihood: -21832.539553 EM: Round [978] log likelihood: -21832.538454 EM: Round [979] log likelihood: -21832.537357 EM: Round [980] log likelihood: -21832.536262 EM: Round [981] log likelihood: -21832.535169 EM: Round [982] log likelihood: -21832.534078 EM: Round [983] log likelihood: -21832.532989 EM: Round [984] log likelihood: -21832.531903 EM: Round [985] log likelihood: -21832.530818 EM: Round [986] log likelihood: -21832.529735 EM: Round [987] log likelihood: -21832.528654 EM: Round [988] log likelihood: -21832.527576 EM: Round [989] log likelihood: -21832.526499 EM: Round [990] log likelihood: -21832.525425 EM: Round [991] log likelihood: -21832.524352 EM: Round [992] log likelihood: -21832.523282 EM: Round [993] log likelihood: -21832.522213 EM: Round [994] log likelihood: -21832.521146 EM: Round [995] log likelihood: -21832.520082 EM: Round [996] log likelihood: -21832.519019 EM: Round [997] log likelihood: -21832.517959 EM: Round [998] log likelihood: -21832.516900 EM: Round [999] log likelihood: -21832.515844 EM: Round [1000] log likelihood: -21832.514789 EM: Round [1001] log likelihood: -21832.513737 Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam" Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.38 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa > /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir -done, see /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -21155.308005 EM: Round [1] log likelihood: -21154.310036 EM: Round [2] log likelihood: -21154.264257 EM: Round [3] log likelihood: -21154.229647 EM: Round [4] log likelihood: -21154.201081 EM: Round [5] log likelihood: -21154.176212 EM: Round [6] log likelihood: -21154.153629 EM: Round [7] log likelihood: -21154.132480 EM: Round [8] log likelihood: -21154.112250 EM: Round [9] log likelihood: -21154.092631 EM: Round [10] log likelihood: -21154.073438 EM: Round [11] log likelihood: -21154.054557 EM: Round [12] log likelihood: -21154.035921 EM: Round [13] log likelihood: -21154.017490 EM: Round [14] log likelihood: -21153.999237 EM: Round [15] log likelihood: -21153.981148 EM: Round [16] log likelihood: -21153.963211 EM: Round [17] log likelihood: -21153.945419 EM: Round [18] log likelihood: -21153.927769 EM: Round [19] log likelihood: -21153.910256 EM: Round [20] log likelihood: -21153.892877 EM: Round [21] log likelihood: -21153.875629 EM: Round [22] log likelihood: -21153.858511 EM: Round [23] log likelihood: -21153.841521 EM: Round [24] log likelihood: -21153.824656 EM: Round [25] log likelihood: -21153.807915 EM: Round [26] log likelihood: -21153.791297 EM: Round [27] log likelihood: -21153.774798 EM: Round [28] log likelihood: -21153.758418 EM: Round [29] log likelihood: -21153.742156 EM: Round [30] log likelihood: -21153.726009 EM: Round [31] log likelihood: -21153.709976 EM: Round [32] log likelihood: -21153.694056 EM: Round [33] log likelihood: -21153.678247 EM: Round [34] log likelihood: -21153.662547 EM: Round [35] log likelihood: -21153.646956 EM: Round [36] log likelihood: -21153.631471 EM: Round [37] log likelihood: -21153.616092 EM: Round [38] log likelihood: -21153.600818 EM: Round [39] log likelihood: -21153.585646 EM: Round [40] log likelihood: -21153.570575 EM: Round [41] log likelihood: -21153.555605 EM: Round [42] log likelihood: -21153.540735 EM: Round [43] log likelihood: -21153.525962 EM: Round [44] log likelihood: -21153.511286 EM: Round [45] log likelihood: -21153.496705 EM: Round [46] log likelihood: -21153.482219 EM: Round [47] log likelihood: -21153.467826 EM: Round [48] log likelihood: -21153.453525 EM: Round [49] log likelihood: -21153.439316 EM: Round [50] log likelihood: -21153.425197 EM: Round [51] log likelihood: -21153.411166 EM: Round [52] log likelihood: -21153.397224 EM: Round [53] log likelihood: -21153.383368 EM: Round [54] log likelihood: -21153.369599 EM: Round [55] log likelihood: -21153.355915 EM: Round [56] log likelihood: -21153.342315 EM: Round [57] log likelihood: -21153.328798 EM: Round [58] log likelihood: -21153.315363 EM: Round [59] log likelihood: -21153.302009 EM: Round [60] log likelihood: -21153.288736 EM: Round [61] log likelihood: -21153.275543 EM: Round [62] log likelihood: -21153.262428 EM: Round [63] log likelihood: -21153.249392 EM: Round [64] log likelihood: -21153.236432 EM: Round [65] log likelihood: -21153.223548 EM: Round [66] log likelihood: -21153.210740 EM: Round [67] log likelihood: -21153.198006 EM: Round [68] log likelihood: -21153.185347 EM: Round [69] log likelihood: -21153.172760 EM: Round [70] log likelihood: -21153.160246 EM: Round [71] log likelihood: -21153.147803 EM: Round [72] log likelihood: -21153.135431 EM: Round [73] log likelihood: -21153.123129 EM: Round [74] log likelihood: 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-21149.834218 EM: Round [942] log likelihood: -21149.833093 EM: Round [943] log likelihood: -21149.831970 EM: Round [944] log likelihood: -21149.830850 EM: Round [945] log likelihood: -21149.829731 EM: Round [946] log likelihood: -21149.828615 EM: Round [947] log likelihood: -21149.827501 EM: Round [948] log likelihood: -21149.826389 EM: Round [949] log likelihood: -21149.825279 EM: Round [950] log likelihood: -21149.824171 EM: Round [951] log likelihood: -21149.823065 EM: Round [952] log likelihood: -21149.821961 EM: Round [953] log likelihood: -21149.820859 EM: Round [954] log likelihood: -21149.819759 EM: Round [955] log likelihood: -21149.818661 EM: Round [956] log likelihood: -21149.817566 EM: Round [957] log likelihood: -21149.816472 EM: Round [958] log likelihood: -21149.815380 EM: Round [959] log likelihood: -21149.814291 EM: Round [960] log likelihood: -21149.813203 EM: Round [961] log likelihood: -21149.812117 EM: Round [962] log likelihood: -21149.811034 EM: Round [963] log likelihood: -21149.809952 EM: Round [964] log likelihood: -21149.808873 EM: Round [965] log likelihood: -21149.807795 EM: Round [966] log likelihood: -21149.806720 EM: Round [967] log likelihood: -21149.805646 EM: Round [968] log likelihood: -21149.804575 EM: Round [969] log likelihood: -21149.803505 EM: Round [970] log likelihood: -21149.802437 EM: Round [971] log likelihood: -21149.801372 EM: Round [972] log likelihood: -21149.800308 EM: Round [973] log likelihood: -21149.799246 EM: Round [974] log likelihood: -21149.798187 EM: Round [975] log likelihood: -21149.797129 EM: Round [976] log likelihood: -21149.796073 EM: Round [977] log likelihood: -21149.795019 EM: Round [978] log likelihood: -21149.793967 EM: Round [979] log likelihood: -21149.792917 EM: Round [980] log likelihood: -21149.791869 EM: Round [981] log likelihood: -21149.790823 EM: Round [982] log likelihood: -21149.789779 EM: Round [983] log likelihood: -21149.788736 EM: Round [984] log likelihood: -21149.787696 EM: Round [985] log likelihood: -21149.786658 EM: Round [986] log likelihood: -21149.785621 EM: Round [987] log likelihood: -21149.784586 EM: Round [988] log likelihood: -21149.783554 EM: Round [989] log likelihood: -21149.782523 EM: Round [990] log likelihood: -21149.781494 EM: Round [991] log likelihood: -21149.780467 EM: Round [992] log likelihood: -21149.779442 EM: Round [993] log likelihood: -21149.778418 EM: Round [994] log likelihood: -21149.777397 EM: Round [995] log likelihood: -21149.776377 EM: Round [996] log likelihood: -21149.775360 EM: Round [997] log likelihood: -21149.774344 EM: Round [998] log likelihood: -21149.773330 EM: Round [999] log likelihood: -21149.772318 EM: Round [1000] log likelihood: -21149.771308 EM: Round [1001] log likelihood: -21149.770299 Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz: 294765771 Execution Time = 5.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --gtf /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fa --gtf /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.kHKFBso9Iw/fi_workdir/microH.dat Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.kHKFBso9Iw/fi_workdir/microH.dat /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/fi_workdir/microH.dat /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.kHKFBso9Iw --json_outfile /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.kHKFBso9Iw --json_outfile /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 Running: touch /tmp/nxf.kHKFBso9Iw/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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --html_output /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_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.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix Hs746T_FFPE_RNA_0001_B23LG7FLT4_1 --html_output /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000231365.6] WARNING, no entry stored in dbm for [ENSG00000231365.6] WARNING, no entry stored in dbm for [ENSG00000231365.6] WARNING, no entry stored in dbm for [ENSG00000230534.6] WARNING, no entry stored in dbm for [ENSG00000216829.6] WARNING, no entry stored in dbm for [ENSG00000216829.6] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000229180.7] WARNING, no entry stored in dbm for [ENSG00000229180.7] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000227681.5] 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 [ENSG00000267052.3] WARNING, no entry stored in dbm for [ENSG00000267052.3] WARNING, no entry stored in dbm for [ENSG00000267052.3] WARNING, no entry stored in dbm for [ENSG00000237813.4] WARNING, no entry stored in dbm for [ENSG00000237813.4] WARNING, no entry stored in dbm for [ENSG00000237813.4] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000232386.9] WARNING, no entry stored in dbm for [ENSG00000232386.9] WARNING, no entry stored in dbm for [ENSG00000236197.4] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.kHKFBso9Iw/ctat_genome_lib_build_dir > /tmp/nxf.kHKFBso9Iw/Hs746T_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.kHKFBso9Iw/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory