Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/3a2d9a092683197e5e748dcb2f5919/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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/9d/cd458b46772546d8c3032f4c7e0fe4/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/cd458b46772546d8c3032f4c7e0fe4/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/e2e99a63ae6a2f460a2531917d1227/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/e2e99a63ae6a2f460a2531917d1227/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n5ewjTXfr6/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n5ewjTXfr6/cytoBand.txt Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed -parsing GTF file: /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.n5ewjTXfr6/fi_workdir --reads "/tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:52:51 ..... started STAR run Jun 08 10:52:51 ..... loading genome Jun 08 10:54:38 ... generating Suffix Array index Jun 08 10:58:45 ... completed Suffix Array index Jun 08 10:58:45 ..... processing annotations GTF Jun 08 10:58:45 ..... inserting junctions into the genome indices Jun 08 10:59:47 ..... started mapping Jun 08 11:52:38 ..... finished mapping Jun 08 11:52:40 ..... started sorting BAM Jun 08 11:52:43 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam Execution Time = 59.96 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.n5ewjTXfr6/fi_workdir --reads "/tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:53:19 : INFO : Done. Execution Time = 0.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf -parsing /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] 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[6260000] [6270000] [6280000] [6290000] [6300000] [6310000] [6320000] [6330000] [6340000] [6350000] [6360000] [6370000] [6380000] [6390000] [6400000] [6410000] [6420000] [6430000] [6440000] [6450000] [6460000] [6470000] [6480000] [6490000] [6500000] [6510000] [6520000] [6530000] [6540000] [6550000] [6560000] [6570000] [6580000] [6590000] [6600000] [6610000] [6620000] [6630000] [6640000] [6650000] [6660000] [6670000] [6680000] [6690000] [6700000] -done parsing /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num genes matched < 2' => 250, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 100, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 86, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 13, ' ** passed ** ' => 22995, 'per_id < 96' => 34735, 'seq-similar region overlap' => 2, 'small anchor length' => 90, 'low complexity anchor region' => 71, 'excessive soft clipping' => 110105, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 54, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 200, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1845, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 22, 'exons hit < 2' => 13, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 58 }; -writing fusion junction support info. Execution Time = 4.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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] -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] [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] 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[552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] [589000] [590000] [591000] [592000] [593000] [594000] [595000] [596000] [597000] [598000] [599000] [600000] [601000] [602000] [603000] [604000] [605000] [606000] [607000] [608000] [609000] [610000] [611000] -fusion SPANNING read extraction for scaff: ACTN1--DCAF5 [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: ANAPC2--CLIC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] 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-fusion SPANNING read extraction for scaff: ATF7--FMNL3 [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] 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[229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] [489000] [490000] [491000] [492000] [493000] [494000] [495000] [496000] [497000] [498000] [499000] [500000] [501000] [502000] [503000] [504000] [505000] [506000] [507000] [508000] [509000] -fusion SPANNING read extraction for scaff: COPS7B--ITGB1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] -fusion SPANNING read extraction for scaff: CSAD--ANO6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] -fusion SPANNING read extraction for scaff: FRS2--CCT2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: FYTTD1--AC024560.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: FYTTD1--AC024560.3 [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] [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: GNS--KRT87P [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] [489000] [490000] [491000] [492000] [493000] [494000] [495000] [496000] [497000] [498000] [499000] [500000] [501000] [502000] [503000] [504000] [505000] [506000] [507000] [508000] [509000] [510000] [511000] [512000] [513000] [514000] [515000] [516000] [517000] [518000] [519000] [520000] [521000] [522000] [523000] [524000] [525000] [526000] [527000] [528000] [529000] [530000] [531000] [532000] [533000] [534000] [535000] [536000] [537000] [538000] [539000] [540000] [541000] [542000] [543000] [544000] [545000] [546000] [547000] [548000] [549000] [550000] [551000] [552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] [589000] [590000] [591000] [592000] [593000] [594000] [595000] [596000] [597000] [598000] [599000] [600000] [601000] [602000] [603000] [604000] [605000] [606000] [607000] [608000] [609000] [610000] [611000] [612000] [613000] [614000] [615000] [616000] [617000] [618000] [619000] [620000] [621000] [622000] [623000] [624000] [625000] [626000] [627000] [628000] [629000] [630000] [631000] [632000] [633000] [634000] [635000] [636000] [637000] [638000] [639000] [640000] [641000] [642000] [643000] [644000] [645000] [646000] [647000] [648000] [649000] [650000] [651000] [652000] [653000] [654000] [655000] [656000] [657000] [658000] [659000] [660000] [661000] [662000] [663000] [664000] [665000] [666000] [667000] [668000] [669000] [670000] [671000] [672000] [673000] [674000] [675000] [676000] [677000] [678000] [679000] [680000] [681000] [682000] [683000] [684000] [685000] [686000] [687000] [688000] [689000] [690000] [691000] [692000] [693000] [694000] [695000] [696000] [697000] [698000] [699000] [700000] [701000] [702000] [703000] [704000] [705000] [706000] [707000] [708000] [709000] [710000] [711000] [712000] [713000] [714000] [715000] [716000] [717000] [718000] [719000] [720000] [721000] [722000] [723000] [724000] [725000] [726000] [727000] [728000] [729000] [730000] [731000] [732000] [733000] [734000] [735000] [736000] [737000] [738000] [739000] [740000] [741000] [742000] [743000] [744000] [745000] [746000] [747000] [748000] [749000] [750000] [751000] [752000] [753000] [754000] [755000] [756000] [757000] [758000] [759000] [760000] [761000] [762000] [763000] [764000] [765000] [766000] [767000] [768000] [769000] [770000] [771000] [772000] [773000] [774000] [775000] [776000] [777000] [778000] [779000] [780000] [781000] [782000] [783000] [784000] [785000] [786000] [787000] [788000] [789000] [790000] [791000] [792000] [793000] [794000] [795000] [796000] [797000] [798000] [799000] [800000] [801000] [802000] [803000] [804000] [805000] [806000] [807000] [808000] [809000] [810000] [811000] [812000] [813000] [814000] [815000] [816000] [817000] [818000] [819000] [820000] [821000] [822000] [823000] [824000] [825000] [826000] [827000] [828000] [829000] [830000] [831000] [832000] [833000] [834000] [835000] [836000] [837000] [838000] [839000] [840000] [841000] [842000] [843000] [844000] [845000] [846000] [847000] [848000] [849000] [850000] [851000] [852000] [853000] [854000] [855000] [856000] [857000] [858000] [859000] [860000] [861000] [862000] [863000] [864000] [865000] [866000] [867000] [868000] [869000] [870000] [871000] [872000] [873000] [874000] [875000] [876000] [877000] [878000] [879000] [880000] [881000] [882000] [883000] [884000] [885000] [886000] [887000] [888000] [889000] [890000] [891000] [892000] [893000] [894000] [895000] [896000] [897000] [898000] [899000] [900000] [901000] [902000] [903000] [904000] [905000] [906000] [907000] [908000] [909000] [910000] [911000] [912000] [913000] [914000] [915000] [916000] [917000] [918000] [919000] [920000] [921000] [922000] [923000] [924000] [925000] [926000] [927000] [928000] [929000] [930000] [931000] [932000] [933000] [934000] [935000] [936000] [937000] [938000] [939000] [940000] -fusion SPANNING read extraction for scaff: LIMA1--CAND1 [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] -fusion SPANNING read extraction for scaff: MAP3K12--TPH2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] [489000] [490000] [491000] [492000] [493000] [494000] [495000] [496000] [497000] [498000] [499000] [500000] [501000] [502000] [503000] [504000] [505000] [506000] [507000] [508000] [509000] [510000] [511000] [512000] [513000] [514000] [515000] [516000] [517000] [518000] [519000] [520000] [521000] [522000] [523000] [524000] [525000] [526000] [527000] [528000] [529000] [530000] [531000] [532000] [533000] [534000] [535000] [536000] [537000] [538000] [539000] [540000] [541000] [542000] [543000] [544000] [545000] [546000] [547000] [548000] [549000] [550000] [551000] [552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] [589000] [590000] [591000] [592000] [593000] [594000] [595000] [596000] [597000] [598000] [599000] [600000] [601000] [602000] [603000] [604000] [605000] [606000] [607000] [608000] [609000] [610000] [611000] [612000] [613000] [614000] [615000] [616000] [617000] [618000] [619000] [620000] [621000] [622000] [623000] [624000] [625000] [626000] [627000] [628000] [629000] [630000] [631000] [632000] [633000] [634000] [635000] [636000] [637000] [638000] [639000] [640000] [641000] [642000] [643000] [644000] [645000] [646000] [647000] [648000] [649000] [650000] [651000] [652000] [653000] [654000] [655000] [656000] [657000] [658000] [659000] [660000] [661000] [662000] [663000] [664000] [665000] [666000] [667000] [668000] [669000] [670000] [671000] [672000] [673000] [674000] [675000] [676000] [677000] [678000] [679000] [680000] [681000] [682000] [683000] [684000] [685000] [686000] [687000] [688000] [689000] [690000] [691000] [692000] [693000] [694000] [695000] [696000] [697000] [698000] [699000] [700000] [701000] [702000] [703000] [704000] [705000] [706000] [707000] [708000] [709000] [710000] [711000] [712000] [713000] [714000] [715000] [716000] [717000] [718000] -fusion SPANNING read extraction for scaff: MYH9--RBFOX2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] -fusion SPANNING read extraction for scaff: MYO18A--CCL5 [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] 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[614000] [615000] [616000] [617000] [618000] [619000] [620000] [621000] [622000] [623000] [624000] [625000] [626000] [627000] [628000] [629000] [630000] [631000] [632000] [633000] [634000] [635000] [636000] [637000] [638000] [639000] [640000] [641000] [642000] [643000] [644000] [645000] [646000] [647000] [648000] [649000] [650000] [651000] [652000] [653000] [654000] [655000] [656000] [657000] [658000] [659000] [660000] [661000] [662000] [663000] [664000] [665000] [666000] [667000] [668000] [669000] [670000] [671000] [672000] [673000] [674000] [675000] [676000] [677000] [678000] [679000] [680000] [681000] [682000] [683000] [684000] [685000] [686000] [687000] [688000] [689000] [690000] [691000] [692000] [693000] [694000] [695000] [696000] [697000] [698000] [699000] [700000] [701000] -fusion SPANNING read extraction for scaff: PCBP2--LINC02388 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [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: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [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] -fusion SPANNING read extraction for scaff: PPM1H--ZNF641 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PPM1H--AC090115.1 [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] 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[703000] [704000] [705000] [706000] [707000] [708000] [709000] [710000] [711000] [712000] [713000] [714000] [715000] [716000] [717000] [718000] [719000] [720000] [721000] [722000] [723000] [724000] [725000] [726000] [727000] [728000] [729000] [730000] [731000] [732000] [733000] [734000] [735000] [736000] [737000] [738000] [739000] [740000] [741000] [742000] [743000] [744000] [745000] [746000] [747000] [748000] [749000] [750000] [751000] [752000] [753000] [754000] [755000] [756000] [757000] [758000] [759000] [760000] [761000] [762000] [763000] [764000] [765000] [766000] [767000] [768000] [769000] [770000] [771000] [772000] [773000] [774000] [775000] [776000] [777000] [778000] [779000] [780000] [781000] [782000] [783000] [784000] [785000] [786000] [787000] [788000] [789000] [790000] [791000] [792000] [793000] [794000] [795000] [796000] [797000] [798000] [799000] [800000] [801000] [802000] [803000] [804000] [805000] [806000] [807000] [808000] [809000] [810000] [811000] [812000] [813000] [814000] [815000] [816000] [817000] [818000] [819000] [820000] [821000] [822000] [823000] [824000] [825000] [826000] [827000] [828000] [829000] [830000] [831000] [832000] [833000] [834000] [835000] [836000] [837000] [838000] [839000] [840000] [841000] [842000] [843000] [844000] [845000] [846000] [847000] [848000] [849000] [850000] [851000] [852000] [853000] [854000] [855000] [856000] [857000] [858000] [859000] [860000] [861000] [862000] [863000] [864000] [865000] [866000] [867000] [868000] [869000] [870000] [871000] [872000] [873000] [874000] [875000] [876000] [877000] [878000] [879000] [880000] [881000] [882000] [883000] [884000] [885000] [886000] [887000] [888000] [889000] [890000] [891000] [892000] [893000] [894000] [895000] [896000] [897000] -fusion SPANNING read extraction for scaff: SRF--RELA [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 96313, 'lacks exon overlap' => 21810 }; Execution Time = 9.97 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -12670.490584 EM: Round [1] log likelihood: -12670.482552 EM: Round [2] log likelihood: -12670.474600 EM: Round [3] log likelihood: -12670.466727 EM: Round [4] log likelihood: -12670.458931 EM: Round [5] log likelihood: -12670.451211 EM: Round [6] log likelihood: -12670.443566 EM: Round [7] log likelihood: -12670.435995 EM: Round [8] log likelihood: -12670.428495 EM: Round [9] log likelihood: -12670.421067 EM: Round [10] log likelihood: -12670.413708 EM: Round [11] log likelihood: -12670.406417 EM: Round [12] log likelihood: -12670.399195 EM: Round [13] log likelihood: -12670.392038 EM: Round [14] log likelihood: -12670.384947 EM: Round [15] log likelihood: -12670.377920 EM: Round [16] log likelihood: -12670.370956 EM: Round [17] log likelihood: -12670.364055 EM: Round [18] log likelihood: -12670.357214 EM: Round [19] log likelihood: -12670.350434 EM: Round [20] log likelihood: -12670.343713 EM: Round [21] log likelihood: -12670.337051 EM: Round [22] log likelihood: -12670.330446 EM: Round [23] log likelihood: -12670.323898 EM: Round [24] log likelihood: -12670.317405 EM: Round [25] log likelihood: -12670.310968 EM: Round [26] log likelihood: -12670.304585 EM: Round [27] log likelihood: -12670.298255 EM: Round [28] log likelihood: -12670.291978 EM: Round [29] log likelihood: -12670.285752 EM: Round [30] log likelihood: -12670.279578 EM: Round [31] log likelihood: -12670.273454 EM: Round [32] log likelihood: -12670.267379 EM: Round [33] log likelihood: -12670.261354 EM: Round [34] log likelihood: -12670.255377 EM: Round [35] log likelihood: -12670.249447 EM: Round [36] log likelihood: -12670.243564 EM: Round [37] log likelihood: -12670.237728 EM: Round [38] log likelihood: -12670.231937 EM: Round [39] log likelihood: -12670.226191 EM: Round [40] log likelihood: -12670.220490 EM: Round [41] log likelihood: -12670.214833 EM: Round [42] log likelihood: -12670.209218 EM: Round [43] log likelihood: -12670.203647 EM: Round [44] log likelihood: -12670.198117 EM: Round [45] log likelihood: -12670.192630 EM: Round [46] log likelihood: -12670.187183 EM: Round [47] log likelihood: -12670.181776 EM: Round [48] log likelihood: -12670.176410 EM: Round [49] log likelihood: -12670.171083 EM: Round [50] log likelihood: -12670.165795 EM: Round [51] log likelihood: -12670.160546 EM: Round [52] log likelihood: -12670.155335 EM: Round [53] log likelihood: -12670.150161 EM: Round [54] log likelihood: -12670.145024 EM: Round [55] log likelihood: -12670.139924 EM: Round [56] log likelihood: -12670.134860 EM: Round [57] log likelihood: -12670.129832 EM: Round [58] log likelihood: -12670.124840 EM: Round [59] log likelihood: -12670.119882 EM: Round [60] log likelihood: -12670.114958 EM: Round [61] log likelihood: -12670.110069 EM: Round [62] log likelihood: -12670.105213 EM: Round [63] log likelihood: -12670.100391 EM: Round [64] log likelihood: -12670.095601 EM: Round [65] log likelihood: -12670.090844 EM: Round [66] log likelihood: -12670.086120 EM: Round [67] log likelihood: -12670.081426 EM: Round [68] log likelihood: -12670.076765 EM: Round [69] log likelihood: -12670.072134 EM: Round [70] log likelihood: -12670.067534 EM: Round [71] log likelihood: -12670.062965 EM: Round [72] log likelihood: -12670.058425 EM: Round [73] log likelihood: -12670.053916 EM: Round [74] log likelihood: -12670.049435 EM: Round [75] log likelihood: -12670.044984 EM: Round [76] log likelihood: -12670.040561 EM: Round [77] log likelihood: -12670.036167 EM: Round [78] log likelihood: -12670.031801 EM: Round [79] log likelihood: -12670.027463 EM: Round [80] log likelihood: -12670.023152 EM: Round [81] log likelihood: -12670.018868 EM: Round [82] log likelihood: -12670.014612 EM: Round [83] log likelihood: -12670.010382 EM: Round [84] log likelihood: -12670.006178 EM: Round [85] log likelihood: -12670.002001 EM: Round [86] log likelihood: -12669.997849 EM: Round [87] log likelihood: -12669.993723 EM: Round [88] log likelihood: -12669.989622 EM: Round [89] log likelihood: -12669.985547 EM: Round [90] log likelihood: -12669.981496 EM: Round [91] log likelihood: -12669.977469 EM: Round [92] log likelihood: -12669.973467 EM: Round [93] log likelihood: -12669.969489 EM: Round [94] log likelihood: -12669.965535 EM: Round [95] log likelihood: -12669.961604 EM: Round [96] log likelihood: -12669.957697 EM: Round [97] log likelihood: -12669.953813 EM: Round [98] log likelihood: -12669.949952 EM: Round [99] log likelihood: -12669.946113 EM: Round [100] log likelihood: -12669.942297 EM: Round [101] log likelihood: -12669.938503 EM: Round [102] log likelihood: -12669.934731 EM: Round [103] log likelihood: -12669.930981 EM: Round [104] log likelihood: -12669.927253 EM: Round [105] log likelihood: -12669.923546 EM: Round [106] log likelihood: -12669.919860 EM: Round [107] log likelihood: -12669.916195 EM: Round [108] log likelihood: -12669.912551 EM: Round [109] log likelihood: -12669.908927 EM: Round [110] log likelihood: -12669.905324 EM: Round [111] log likelihood: -12669.901742 EM: Round [112] log likelihood: -12669.898179 EM: Round [113] log likelihood: -12669.894636 EM: Round [114] log likelihood: -12669.891113 EM: Round [115] log likelihood: -12669.887609 EM: Round [116] log likelihood: -12669.884125 EM: Round [117] log likelihood: -12669.880660 EM: Round [118] log likelihood: -12669.877213 EM: Round [119] log likelihood: -12669.873786 EM: Round [120] log likelihood: -12669.870377 EM: Round [121] log likelihood: -12669.866987 EM: Round [122] log likelihood: -12669.863615 EM: Round [123] log likelihood: -12669.860261 EM: Round [124] log likelihood: -12669.856926 EM: Round [125] log likelihood: -12669.853608 EM: Round [126] log likelihood: -12669.850307 EM: Round [127] log likelihood: -12669.847025 EM: Round [128] log likelihood: -12669.843760 EM: Round [129] log likelihood: -12669.840511 EM: Round [130] log likelihood: -12669.837281 EM: Round [131] log likelihood: -12669.834067 EM: Round [132] log likelihood: -12669.830869 EM: Round [133] log likelihood: -12669.827689 EM: Round [134] log likelihood: -12669.824525 EM: Round [135] log likelihood: -12669.821377 EM: Round [136] log likelihood: -12669.818246 EM: Round [137] log likelihood: -12669.815131 EM: Round [138] log likelihood: -12669.812032 EM: Round [139] log likelihood: -12669.808948 EM: Round [140] log likelihood: -12669.805881 EM: Round [141] log likelihood: -12669.802829 EM: Round [142] log likelihood: -12669.799792 EM: Round [143] log likelihood: -12669.796771 EM: Round [144] log likelihood: -12669.793765 EM: Round [145] log likelihood: -12669.790774 EM: Round [146] log likelihood: -12669.787798 EM: Round [147] log likelihood: -12669.784837 EM: Round [148] log likelihood: -12669.781891 EM: Round [149] log likelihood: -12669.778959 EM: Round [150] log likelihood: -12669.776042 EM: Round [151] log likelihood: -12669.773140 EM: Round [152] log likelihood: -12669.770251 EM: Round [153] log likelihood: -12669.767377 EM: Round [154] log likelihood: -12669.764517 EM: Round [155] log likelihood: -12669.761670 EM: Round [156] log likelihood: -12669.758838 EM: Round [157] log likelihood: -12669.756019 EM: Round [158] log likelihood: -12669.753214 EM: Round [159] log likelihood: -12669.750423 EM: Round [160] log likelihood: -12669.747645 EM: Round [161] log likelihood: -12669.744880 EM: Round [162] log likelihood: -12669.742129 EM: Round [163] log likelihood: -12669.739390 EM: Round [164] log likelihood: -12669.736665 EM: Round [165] log likelihood: -12669.733953 EM: Round [166] log likelihood: -12669.731253 EM: Round [167] log likelihood: -12669.728566 EM: Round [168] log likelihood: -12669.725892 EM: Round [169] log likelihood: -12669.723231 EM: Round [170] log likelihood: -12669.720582 EM: Round [171] log likelihood: -12669.717945 EM: Round [172] log likelihood: -12669.715320 EM: Round [173] log likelihood: -12669.712708 EM: Round [174] log likelihood: -12669.710108 EM: Round [175] log likelihood: -12669.707520 EM: Round [176] log likelihood: -12669.704944 EM: Round [177] log likelihood: -12669.702379 EM: Round [178] log likelihood: -12669.699827 EM: Round [179] log likelihood: -12669.697286 EM: Round [180] log likelihood: -12669.694756 EM: Round [181] log likelihood: -12669.692238 EM: Round [182] log likelihood: -12669.689732 EM: Round [183] log likelihood: -12669.687237 EM: Round [184] log likelihood: -12669.684753 EM: Round [185] log likelihood: -12669.682281 EM: Round [186] log likelihood: -12669.679819 EM: Round [187] log likelihood: -12669.677369 EM: Round [188] log likelihood: -12669.674929 EM: Round [189] log likelihood: -12669.672501 EM: Round [190] log likelihood: -12669.670083 EM: Round [191] log likelihood: -12669.667676 EM: Round [192] log likelihood: -12669.665280 EM: Round [193] log likelihood: -12669.662894 EM: Round [194] log likelihood: -12669.660519 EM: Round [195] log likelihood: -12669.658154 EM: Round [196] log likelihood: -12669.655799 EM: Round [197] log likelihood: -12669.653455 EM: Round [198] log likelihood: -12669.651122 EM: Round [199] log likelihood: -12669.648798 EM: Round [200] log likelihood: -12669.646484 EM: Round [201] log likelihood: -12669.644181 EM: Round [202] log likelihood: -12669.641887 EM: Round [203] log likelihood: -12669.639603 EM: Round [204] log likelihood: -12669.637330 EM: Round [205] log likelihood: -12669.635065 EM: Round [206] log likelihood: -12669.632811 EM: Round [207] log likelihood: -12669.630566 EM: Round [208] log likelihood: -12669.628331 EM: Round [209] log likelihood: -12669.626106 EM: Round [210] log likelihood: -12669.623890 EM: Round [211] log likelihood: -12669.621683 EM: Round [212] log likelihood: -12669.619485 EM: Round [213] log likelihood: -12669.617297 EM: Round [214] log likelihood: -12669.615118 EM: Round [215] log likelihood: -12669.612949 EM: Round [216] log likelihood: -12669.610788 EM: Round [217] log likelihood: -12669.608636 EM: Round [218] log likelihood: -12669.606494 EM: Round [219] log likelihood: -12669.604360 EM: Round [220] log likelihood: -12669.602235 EM: Round [221] log likelihood: -12669.600119 EM: Round [222] log likelihood: -12669.598012 EM: Round [223] log likelihood: -12669.595913 EM: Round [224] log likelihood: -12669.593824 EM: Round [225] log likelihood: -12669.591742 EM: Round [226] log likelihood: -12669.589670 EM: Round [227] log likelihood: -12669.587605 EM: Round [228] log likelihood: -12669.585550 EM: Round [229] log likelihood: -12669.583502 EM: Round [230] log likelihood: -12669.581463 EM: Round [231] log likelihood: -12669.579432 EM: Round [232] log likelihood: -12669.577410 EM: Round [233] log likelihood: -12669.575396 EM: Round [234] log likelihood: -12669.573389 EM: Round [235] log likelihood: -12669.571391 EM: Round [236] log likelihood: -12669.569401 EM: Round [237] log likelihood: -12669.567419 EM: Round [238] log likelihood: -12669.565445 EM: Round [239] log likelihood: -12669.563479 EM: Round [240] log likelihood: -12669.561520 EM: Round [241] log likelihood: -12669.559570 EM: Round [242] log likelihood: -12669.557627 EM: Round [243] log likelihood: -12669.555692 EM: Round [244] log likelihood: -12669.553765 EM: Round [245] log likelihood: -12669.551845 EM: Round [246] log likelihood: -12669.549933 EM: Round [247] log likelihood: -12669.548028 EM: Round [248] log likelihood: -12669.546131 EM: Round [249] log likelihood: -12669.544241 EM: Round [250] log likelihood: -12669.542359 EM: Round [251] log likelihood: -12669.540484 EM: Round [252] log likelihood: -12669.538616 EM: Round [253] log likelihood: -12669.536756 EM: Round [254] log likelihood: -12669.534902 EM: Round [255] log likelihood: -12669.533056 EM: Round [256] log likelihood: -12669.531218 EM: Round [257] log likelihood: -12669.529386 EM: Round [258] log likelihood: -12669.527561 EM: Round [259] log likelihood: -12669.525744 EM: Round [260] log likelihood: -12669.523933 EM: Round [261] log likelihood: -12669.522129 EM: Round [262] log likelihood: -12669.520332 EM: Round [263] log likelihood: -12669.518543 EM: Round [264] log likelihood: -12669.516760 EM: Round [265] log likelihood: -12669.514983 EM: Round [266] log likelihood: -12669.513214 EM: Round [267] log likelihood: -12669.511451 EM: Round [268] log likelihood: -12669.509695 EM: Round [269] log likelihood: -12669.507945 EM: Round [270] log likelihood: -12669.506203 EM: Round [271] log likelihood: -12669.504466 EM: Round [272] log likelihood: -12669.502737 EM: Round [273] log likelihood: -12669.501013 EM: Round [274] log likelihood: -12669.499296 EM: Round [275] log likelihood: -12669.497586 EM: Round [276] log likelihood: -12669.495882 EM: Round [277] log likelihood: -12669.494185 EM: Round [278] log likelihood: -12669.492493 EM: Round [279] log likelihood: -12669.490808 EM: Round [280] log likelihood: -12669.489130 EM: Round [281] log likelihood: -12669.487457 EM: Round [282] log likelihood: -12669.485791 EM: Round [283] log likelihood: -12669.484131 EM: Round [284] log likelihood: -12669.482477 EM: Round [285] log likelihood: -12669.480829 EM: Round [286] log likelihood: -12669.479187 EM: Round [287] log likelihood: -12669.477551 EM: Round [288] log likelihood: -12669.475921 EM: Round [289] log likelihood: -12669.474297 EM: Round [290] log likelihood: -12669.472679 EM: Round [291] log likelihood: -12669.471067 EM: Round [292] log likelihood: -12669.469461 EM: Round [293] log likelihood: -12669.467861 EM: Round [294] log likelihood: -12669.466266 EM: Round [295] log likelihood: -12669.464677 EM: Round [296] log likelihood: -12669.463094 EM: Round [297] log likelihood: -12669.461517 EM: Round [298] log likelihood: -12669.459946 EM: Round [299] log likelihood: -12669.458380 EM: Round [300] log likelihood: -12669.456819 EM: Round [301] log likelihood: -12669.455265 EM: Round [302] log likelihood: -12669.453715 EM: Round [303] log likelihood: -12669.452172 EM: Round [304] log likelihood: -12669.450634 EM: Round [305] log likelihood: -12669.449101 EM: Round [306] log likelihood: -12669.447574 EM: Round [307] log likelihood: -12669.446052 EM: Round [308] log likelihood: -12669.444536 EM: Round [309] log likelihood: -12669.443025 EM: Round [310] log likelihood: -12669.441520 EM: Round [311] log likelihood: -12669.440019 EM: Round [312] log likelihood: -12669.438524 EM: Round [313] log likelihood: -12669.437035 EM: Round [314] log likelihood: -12669.435550 EM: Round [315] log likelihood: -12669.434071 EM: Round [316] log likelihood: -12669.432597 EM: Round [317] log likelihood: -12669.431128 EM: Round [318] log likelihood: -12669.429664 EM: Round [319] log likelihood: -12669.428206 EM: Round [320] log likelihood: -12669.426752 EM: Round [321] log likelihood: -12669.425304 EM: Round [322] log likelihood: -12669.423860 EM: Round [323] log likelihood: -12669.422422 EM: Round [324] log likelihood: -12669.420989 EM: Round [325] log likelihood: -12669.419560 EM: Round [326] log likelihood: -12669.418137 EM: Round [327] log likelihood: -12669.416718 EM: Round [328] log likelihood: -12669.415304 EM: Round [329] log likelihood: -12669.413895 EM: Round [330] log likelihood: -12669.412491 EM: Round [331] log likelihood: -12669.411092 EM: Round [332] log likelihood: -12669.409698 EM: Round [333] log likelihood: -12669.408308 EM: Round [334] log likelihood: -12669.406923 EM: Round [335] log likelihood: -12669.405543 EM: Round [336] log likelihood: -12669.404168 EM: Round [337] log likelihood: -12669.402797 EM: Round [338] log likelihood: -12669.401431 EM: Round [339] log likelihood: -12669.400070 EM: Round [340] log likelihood: -12669.398713 EM: Round [341] log likelihood: -12669.397361 EM: Round [342] log likelihood: -12669.396013 EM: Round [343] log likelihood: -12669.394670 EM: Round [344] log likelihood: -12669.393332 EM: Round [345] log likelihood: -12669.391997 EM: Round [346] log likelihood: -12669.390668 EM: Round [347] log likelihood: -12669.389343 EM: Round [348] log likelihood: -12669.388022 EM: Round [349] log likelihood: -12669.386706 EM: Round [350] log likelihood: -12669.385394 EM: Round [351] log likelihood: -12669.384087 EM: Round [352] log likelihood: -12669.382784 EM: Round [353] log likelihood: -12669.381485 EM: Round [354] log likelihood: -12669.380191 EM: Round [355] log likelihood: -12669.378901 EM: Round [356] log likelihood: -12669.377615 EM: Round [357] log likelihood: -12669.376333 EM: Round [358] log likelihood: -12669.375056 EM: Round [359] log likelihood: -12669.373783 EM: Round [360] log likelihood: -12669.372514 EM: Round [361] log likelihood: -12669.371249 EM: Round [362] log likelihood: -12669.369989 EM: Round [363] log likelihood: -12669.368733 EM: Round [364] log likelihood: -12669.367480 EM: Round [365] log likelihood: -12669.366232 EM: Round [366] log likelihood: -12669.364988 EM: Round [367] log likelihood: -12669.363748 EM: Round [368] log likelihood: -12669.362512 EM: Round [369] log likelihood: -12669.361281 EM: Round [370] log likelihood: -12669.360053 EM: Round [371] log likelihood: -12669.358829 EM: Round [372] log likelihood: -12669.357609 EM: Round [373] log likelihood: -12669.356393 EM: Round [374] log likelihood: -12669.355181 EM: Round [375] log likelihood: -12669.353973 EM: Round [376] log likelihood: -12669.352769 EM: Round [377] log likelihood: -12669.351569 EM: Round [378] log likelihood: -12669.350373 EM: Round [379] log likelihood: -12669.349180 EM: Round [380] log likelihood: -12669.347992 EM: Round [381] log likelihood: -12669.346807 EM: Round [382] log likelihood: -12669.345626 EM: Round [383] log likelihood: -12669.344449 EM: Round [384] log likelihood: -12669.343275 EM: Round [385] log likelihood: -12669.342106 EM: Round [386] log likelihood: -12669.340940 EM: Round [387] log likelihood: -12669.339778 EM: Round [388] log likelihood: -12669.338619 EM: Round [389] log likelihood: -12669.337465 EM: Round [390] log likelihood: -12669.336314 EM: Round [391] log likelihood: -12669.335166 EM: Round [392] log likelihood: -12669.334022 EM: Round [393] log likelihood: -12669.332882 EM: Round [394] log likelihood: -12669.331746 EM: Round [395] log likelihood: -12669.330613 EM: Round [396] log likelihood: 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-12669.041057 EM: Round [852] log likelihood: -12669.040723 EM: Round [853] log likelihood: -12669.040390 EM: Round [854] log likelihood: -12669.040058 EM: Round [855] log likelihood: -12669.039727 EM: Round [856] log likelihood: -12669.039396 EM: Round [857] log likelihood: -12669.039066 EM: Round [858] log likelihood: -12669.038737 EM: Round [859] log likelihood: -12669.038409 EM: Round [860] log likelihood: -12669.038081 EM: Round [861] log likelihood: -12669.037754 EM: Round [862] log likelihood: -12669.037428 EM: Round [863] log likelihood: -12669.037103 EM: Round [864] log likelihood: -12669.036779 EM: Round [865] log likelihood: -12669.036455 EM: Round [866] log likelihood: -12669.036132 EM: Round [867] log likelihood: -12669.035810 EM: Round [868] log likelihood: -12669.035489 EM: Round [869] log likelihood: -12669.035168 EM: Round [870] log likelihood: -12669.034848 EM: Round [871] log likelihood: -12669.034529 EM: Round [872] log likelihood: -12669.034211 EM: Round [873] log likelihood: -12669.033893 EM: Round [874] log likelihood: -12669.033576 EM: Round [875] log likelihood: -12669.033260 EM: Round [876] log likelihood: -12669.032944 EM: Round [877] log likelihood: -12669.032630 EM: Round [878] log likelihood: -12669.032316 EM: Round [879] log likelihood: -12669.032003 EM: Round [880] log likelihood: -12669.031690 EM: Round [881] log likelihood: -12669.031379 EM: Round [882] log likelihood: -12669.031068 EM: Round [883] log likelihood: -12669.030757 EM: Round [884] log likelihood: -12669.030448 EM: Round [885] log likelihood: -12669.030139 EM: Round [886] log likelihood: -12669.029831 EM: Round [887] log likelihood: -12669.029524 EM: Round [888] log likelihood: -12669.029217 EM: Round [889] log likelihood: -12669.028911 EM: Round [890] log likelihood: -12669.028606 EM: Round [891] log likelihood: -12669.028301 EM: Round [892] log likelihood: -12669.027998 EM: Round [893] log likelihood: -12669.027695 EM: Round [894] log likelihood: -12669.027392 EM: Round [895] log likelihood: -12669.027091 EM: Round [896] log likelihood: -12669.026790 EM: Round [897] log likelihood: -12669.026489 EM: Round [898] log likelihood: -12669.026190 EM: Round [899] log likelihood: -12669.025891 EM: Round [900] log likelihood: -12669.025593 EM: Round [901] log likelihood: -12669.025295 EM: Round [902] log likelihood: -12669.024999 EM: Round [903] log likelihood: -12669.024703 EM: Round [904] log likelihood: -12669.024407 EM: Round [905] log likelihood: -12669.024113 EM: Round [906] log likelihood: -12669.023819 EM: Round [907] log likelihood: -12669.023525 EM: Round [908] log likelihood: -12669.023233 EM: Round [909] log likelihood: -12669.022941 EM: Round [910] log likelihood: -12669.022650 EM: Round [911] log likelihood: -12669.022359 EM: Round [912] log likelihood: -12669.022069 EM: Round [913] log likelihood: -12669.021780 EM: Round [914] log likelihood: -12669.021491 EM: Round [915] log likelihood: -12669.021203 EM: Round [916] log likelihood: -12669.020916 EM: Round [917] log likelihood: -12669.020630 EM: Round [918] log likelihood: -12669.020344 EM: Round [919] log likelihood: -12669.020059 EM: Round [920] log likelihood: -12669.019774 EM: Round [921] log likelihood: -12669.019490 EM: Round [922] log likelihood: -12669.019207 EM: Round [923] log likelihood: -12669.018924 EM: Round [924] log likelihood: -12669.018642 EM: Round [925] log likelihood: -12669.018361 EM: Round [926] log likelihood: -12669.018080 EM: Round [927] log likelihood: -12669.017800 EM: Round [928] log likelihood: -12669.017521 EM: Round [929] log likelihood: -12669.017242 EM: Round [930] log likelihood: -12669.016964 EM: Round [931] log likelihood: -12669.016687 EM: Round [932] log likelihood: -12669.016410 EM: Round [933] log likelihood: -12669.016134 EM: Round [934] log likelihood: -12669.015859 EM: Round [935] log likelihood: -12669.015584 EM: Round [936] log likelihood: -12669.015310 EM: Round [937] log likelihood: -12669.015036 EM: Round [938] log likelihood: -12669.014763 EM: Round [939] log likelihood: -12669.014491 EM: Round [940] log likelihood: -12669.014219 EM: Round [941] log likelihood: -12669.013948 EM: Round [942] log likelihood: -12669.013678 EM: Round [943] log likelihood: -12669.013408 EM: Round [944] log likelihood: -12669.013139 EM: Round [945] log likelihood: -12669.012870 EM: Round [946] log likelihood: -12669.012602 EM: Round [947] log likelihood: -12669.012335 EM: Round [948] log likelihood: -12669.012068 EM: Round [949] log likelihood: -12669.011802 EM: Round [950] log likelihood: -12669.011537 EM: Round [951] log likelihood: -12669.011272 EM: Round [952] log likelihood: -12669.011008 EM: Round [953] log likelihood: -12669.010744 EM: Round [954] log likelihood: -12669.010481 EM: Round [955] log likelihood: -12669.010218 EM: Round [956] log likelihood: -12669.009957 EM: Round [957] log likelihood: -12669.009695 EM: Round [958] log likelihood: -12669.009435 EM: Round [959] log likelihood: -12669.009175 EM: Round [960] log likelihood: -12669.008915 EM: Round [961] log likelihood: -12669.008656 EM: Round [962] log likelihood: -12669.008398 EM: Round [963] log likelihood: -12669.008140 EM: Round [964] log likelihood: -12669.007883 EM: Round [965] log likelihood: -12669.007627 EM: Round [966] log likelihood: -12669.007371 EM: Round [967] log likelihood: -12669.007116 EM: Round [968] log likelihood: -12669.006861 EM: Round [969] log likelihood: -12669.006607 EM: Round [970] log likelihood: -12669.006353 EM: Round [971] log likelihood: -12669.006100 EM: Round [972] log likelihood: -12669.005848 EM: Round [973] log likelihood: -12669.005596 EM: Round [974] log likelihood: -12669.005345 EM: Round [975] log likelihood: -12669.005094 EM: Round [976] log likelihood: -12669.004844 EM: Round [977] log likelihood: -12669.004595 EM: Round [978] log likelihood: -12669.004346 EM: Round [979] log likelihood: -12669.004097 EM: Round [980] log likelihood: -12669.003849 EM: Round [981] log likelihood: -12669.003602 EM: Round [982] log likelihood: -12669.003356 EM: Round [983] log likelihood: -12669.003109 EM: Round [984] log likelihood: -12669.002864 EM: Round [985] log likelihood: -12669.002619 EM: Round [986] log likelihood: -12669.002374 EM: Round [987] log likelihood: -12669.002131 EM: Round [988] log likelihood: -12669.001887 EM: Round [989] log likelihood: -12669.001644 EM: Round [990] log likelihood: -12669.001402 EM: Round [991] log likelihood: -12669.001161 EM: Round [992] log likelihood: -12669.000919 EM: Round [993] log likelihood: -12669.000679 EM: Round [994] log likelihood: -12669.000439 EM: Round [995] log likelihood: -12669.000199 EM: Round [996] log likelihood: -12668.999960 EM: Round [997] log likelihood: -12668.999722 EM: Round [998] log likelihood: -12668.999484 EM: Round [999] log likelihood: -12668.999247 EM: Round [1000] log likelihood: -12668.999010 EM: Round [1001] log likelihood: -12668.998774 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.06 minutes. CMD: samtools index /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir -done, see /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -11920.169842 EM: Round [1] log likelihood: -11920.155912 EM: Round [2] log likelihood: -11920.142201 EM: Round [3] log likelihood: -11920.128703 EM: Round [4] log likelihood: -11920.115411 EM: Round [5] log likelihood: -11920.102321 EM: Round [6] log likelihood: -11920.089426 EM: Round [7] log likelihood: -11920.076720 EM: Round [8] log likelihood: -11920.064200 EM: Round [9] log likelihood: -11920.051859 EM: Round [10] log likelihood: -11920.039694 EM: Round [11] log likelihood: -11920.027699 EM: Round [12] log likelihood: -11920.015870 EM: Round [13] log likelihood: -11920.004203 EM: Round [14] log likelihood: -11919.992694 EM: Round [15] log likelihood: -11919.981339 EM: Round [16] log likelihood: -11919.970134 EM: Round [17] log likelihood: -11919.959076 EM: Round [18] log likelihood: -11919.948161 EM: Round [19] log likelihood: -11919.937386 EM: Round [20] log likelihood: -11919.926747 EM: Round [21] log likelihood: -11919.916242 EM: Round [22] log likelihood: -11919.905866 EM: Round [23] log likelihood: -11919.895619 EM: Round [24] log likelihood: -11919.885495 EM: Round [25] log likelihood: -11919.875494 EM: Round [26] log likelihood: -11919.865611 EM: Round [27] log likelihood: -11919.855845 EM: Round [28] log likelihood: -11919.846193 EM: Round [29] log likelihood: -11919.836653 EM: Round [30] log likelihood: -11919.827222 EM: Round [31] log likelihood: -11919.817898 EM: Round [32] log likelihood: -11919.808679 EM: Round [33] log likelihood: -11919.799563 EM: Round [34] log likelihood: -11919.790547 EM: Round [35] log likelihood: -11919.781630 EM: Round [36] log likelihood: -11919.772810 EM: Round [37] log likelihood: -11919.764085 EM: Round [38] log likelihood: -11919.755452 EM: Round [39] log likelihood: -11919.746911 EM: Round [40] log likelihood: -11919.738460 EM: Round [41] log likelihood: -11919.730096 EM: Round [42] log likelihood: -11919.721818 EM: Round [43] log likelihood: -11919.713625 EM: Round [44] log likelihood: -11919.705515 EM: Round [45] log likelihood: -11919.697487 EM: Round [46] log likelihood: -11919.689539 EM: Round [47] log likelihood: -11919.681669 EM: Round [48] log likelihood: -11919.673877 EM: Round [49] log likelihood: -11919.666161 EM: Round [50] log likelihood: -11919.658519 EM: Round [51] log likelihood: -11919.650951 EM: Round [52] log likelihood: -11919.643454 EM: Round [53] log likelihood: -11919.636029 EM: Round [54] log likelihood: -11919.628673 EM: Round [55] log likelihood: -11919.621386 EM: Round [56] log likelihood: -11919.614166 EM: Round [57] log likelihood: -11919.607013 EM: Round [58] log likelihood: -11919.599924 EM: Round [59] log likelihood: -11919.592900 EM: Round [60] log likelihood: -11919.585939 EM: Round [61] log likelihood: -11919.579040 EM: Round [62] log likelihood: -11919.572203 EM: Round [63] log likelihood: -11919.565425 EM: Round [64] log likelihood: -11919.558707 EM: Round [65] log likelihood: -11919.552048 EM: Round [66] log likelihood: -11919.545445 EM: Round [67] log likelihood: -11919.538900 EM: Round [68] log likelihood: -11919.532410 EM: Round [69] log likelihood: -11919.525975 EM: Round [70] log likelihood: -11919.519594 EM: Round [71] log likelihood: -11919.513267 EM: Round [72] log likelihood: -11919.506992 EM: Round [73] log likelihood: -11919.500768 EM: Round [74] log likelihood: -11919.494596 EM: Round [75] log likelihood: -11919.488475 EM: Round [76] log likelihood: -11919.482402 EM: Round [77] log likelihood: -11919.476379 EM: Round [78] log likelihood: -11919.470404 EM: Round [79] log likelihood: -11919.464477 EM: Round [80] log likelihood: -11919.458596 EM: Round [81] log likelihood: -11919.452762 EM: Round [82] log likelihood: -11919.446973 EM: Round [83] log likelihood: -11919.441229 EM: Round [84] log likelihood: -11919.435530 EM: Round [85] log likelihood: -11919.429874 EM: Round [86] log likelihood: -11919.424262 EM: Round [87] log likelihood: -11919.418692 EM: Round [88] log likelihood: -11919.413165 EM: Round [89] log likelihood: -11919.407679 EM: Round [90] log likelihood: -11919.402234 EM: Round [91] log likelihood: -11919.396829 EM: Round [92] log likelihood: -11919.391465 EM: Round [93] log likelihood: -11919.386140 EM: Round [94] log likelihood: -11919.380854 EM: Round [95] log likelihood: -11919.375606 EM: Round [96] log likelihood: -11919.370397 EM: Round [97] log likelihood: -11919.365225 EM: Round [98] log likelihood: -11919.360090 EM: Round [99] log likelihood: -11919.354991 EM: Round [100] log likelihood: -11919.349929 EM: Round [101] log likelihood: -11919.344902 EM: Round [102] log likelihood: -11919.339911 EM: Round [103] log likelihood: -11919.334955 EM: Round [104] log likelihood: -11919.330033 EM: Round [105] log likelihood: -11919.325145 EM: Round [106] log likelihood: -11919.320291 EM: Round [107] log likelihood: -11919.315470 EM: Round [108] log likelihood: -11919.310682 EM: Round [109] log likelihood: -11919.305927 EM: Round [110] log likelihood: -11919.301203 EM: Round [111] log likelihood: -11919.296512 EM: Round [112] log likelihood: -11919.291851 EM: Round [113] log likelihood: -11919.287222 EM: Round [114] log likelihood: -11919.282624 EM: Round [115] log likelihood: -11919.278056 EM: Round [116] log likelihood: -11919.273517 EM: Round [117] log likelihood: -11919.269009 EM: Round [118] log likelihood: -11919.264530 EM: Round [119] log likelihood: -11919.260080 EM: Round [120] log likelihood: -11919.255658 EM: Round [121] log likelihood: -11919.251266 EM: Round [122] log likelihood: -11919.246901 EM: Round [123] log likelihood: -11919.242564 EM: Round [124] log likelihood: -11919.238254 EM: Round [125] log likelihood: -11919.233972 EM: Round [126] log likelihood: -11919.229716 EM: Round [127] log likelihood: -11919.225488 EM: Round [128] log likelihood: -11919.221285 EM: Round [129] log likelihood: -11919.217109 EM: Round [130] log likelihood: -11919.212959 EM: Round [131] log likelihood: -11919.208834 EM: Round [132] log likelihood: -11919.204734 EM: Round [133] log likelihood: -11919.200659 EM: Round [134] log likelihood: -11919.196610 EM: Round [135] log likelihood: -11919.192584 EM: Round [136] log likelihood: -11919.188583 EM: Round [137] log likelihood: -11919.184606 EM: Round [138] log likelihood: -11919.180653 EM: Round [139] log likelihood: -11919.176724 EM: Round [140] log likelihood: -11919.172818 EM: Round [141] log likelihood: -11919.168934 EM: Round [142] log likelihood: -11919.165074 EM: Round [143] log likelihood: -11919.161237 EM: Round [144] log likelihood: -11919.157422 EM: Round [145] log likelihood: -11919.153629 EM: Round [146] log likelihood: -11919.149858 EM: Round [147] log likelihood: -11919.146109 EM: Round [148] log likelihood: -11919.142381 EM: Round [149] log likelihood: -11919.138675 EM: Round [150] log likelihood: -11919.134990 EM: Round [151] log likelihood: -11919.131326 EM: Round [152] log likelihood: -11919.127683 EM: Round [153] log likelihood: -11919.124061 EM: Round [154] log likelihood: -11919.120459 EM: Round [155] log likelihood: -11919.116877 EM: Round [156] log likelihood: -11919.113315 EM: Round [157] log likelihood: -11919.109773 EM: Round [158] log likelihood: -11919.106251 EM: Round [159] log likelihood: -11919.102748 EM: Round [160] log likelihood: -11919.099264 EM: Round [161] log likelihood: -11919.095800 EM: Round [162] log likelihood: -11919.092355 EM: Round [163] log likelihood: -11919.088928 EM: Round [164] log likelihood: -11919.085520 EM: Round [165] log likelihood: -11919.082131 EM: Round [166] log likelihood: -11919.078760 EM: Round [167] log likelihood: -11919.075407 EM: Round [168] log likelihood: -11919.072072 EM: Round [169] log likelihood: -11919.068755 EM: Round [170] log likelihood: -11919.065455 EM: Round [171] log likelihood: -11919.062173 EM: Round [172] log likelihood: -11919.058909 EM: Round [173] log likelihood: -11919.055662 EM: Round [174] log likelihood: -11919.052432 EM: Round [175] log likelihood: -11919.049218 EM: Round [176] log likelihood: -11919.046022 EM: Round [177] log likelihood: -11919.042842 EM: Round [178] log likelihood: -11919.039679 EM: Round [179] log likelihood: -11919.036532 EM: Round [180] log likelihood: -11919.033402 EM: Round [181] log likelihood: -11919.030287 EM: Round [182] log likelihood: -11919.027189 EM: Round [183] log likelihood: -11919.024106 EM: Round [184] log likelihood: -11919.021039 EM: Round [185] log likelihood: -11919.017988 EM: Round [186] log likelihood: -11919.014952 EM: Round [187] log likelihood: -11919.011931 EM: Round [188] log likelihood: -11919.008926 EM: Round [189] log likelihood: -11919.005936 EM: Round [190] log likelihood: -11919.002961 EM: Round [191] log likelihood: -11919.000000 EM: Round [192] log likelihood: -11918.997055 EM: Round [193] log likelihood: -11918.994124 EM: Round [194] log likelihood: -11918.991207 EM: Round [195] log likelihood: -11918.988305 EM: Round [196] log likelihood: -11918.985418 EM: Round [197] log likelihood: -11918.982544 EM: Round [198] log likelihood: -11918.979684 EM: Round [199] log likelihood: -11918.976839 EM: Round [200] log likelihood: -11918.974007 EM: Round [201] log likelihood: -11918.971189 EM: Round [202] log likelihood: -11918.968385 EM: Round [203] log likelihood: -11918.965594 EM: Round [204] log likelihood: -11918.962816 EM: Round [205] log likelihood: -11918.960052 EM: Round [206] log likelihood: -11918.957301 EM: Round [207] log likelihood: -11918.954564 EM: Round [208] log likelihood: -11918.951839 EM: Round [209] log likelihood: -11918.949127 EM: Round [210] log likelihood: -11918.946428 EM: Round [211] log likelihood: -11918.943742 EM: Round [212] log likelihood: -11918.941068 EM: Round [213] log likelihood: -11918.938407 EM: Round [214] log likelihood: -11918.935759 EM: Round [215] log likelihood: -11918.933123 EM: Round [216] log likelihood: -11918.930499 EM: Round [217] log likelihood: -11918.927887 EM: Round [218] log likelihood: -11918.925287 EM: Round [219] log likelihood: -11918.922700 EM: Round [220] log likelihood: -11918.920124 EM: Round [221] log likelihood: -11918.917560 EM: Round [222] log likelihood: -11918.915008 EM: Round [223] log likelihood: -11918.912468 EM: Round [224] log likelihood: -11918.909939 EM: Round [225] log likelihood: -11918.907422 EM: Round [226] log likelihood: 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likelihood: -11918.852524 EM: Round [249] log likelihood: -11918.850260 EM: Round [250] log likelihood: -11918.848006 EM: Round [251] log likelihood: -11918.845762 EM: Round [252] log likelihood: -11918.843527 EM: Round [253] log likelihood: -11918.841302 EM: Round [254] log likelihood: -11918.839086 EM: Round [255] log likelihood: -11918.836880 EM: Round [256] log likelihood: -11918.834683 EM: Round [257] log likelihood: -11918.832495 EM: Round [258] log likelihood: -11918.830317 EM: Round [259] log likelihood: -11918.828147 EM: Round [260] log likelihood: -11918.825987 EM: Round [261] log likelihood: -11918.823836 EM: Round [262] log likelihood: -11918.821694 EM: Round [263] log likelihood: -11918.819560 EM: Round [264] log likelihood: -11918.817436 EM: Round [265] log likelihood: -11918.815320 EM: Round [266] log likelihood: -11918.813214 EM: Round [267] log likelihood: -11918.811115 EM: Round [268] log likelihood: -11918.809026 EM: Round [269] log likelihood: -11918.806945 EM: Round [270] log likelihood: -11918.804873 EM: Round [271] log likelihood: -11918.802809 EM: Round [272] log likelihood: -11918.800754 EM: Round [273] log likelihood: -11918.798707 EM: Round [274] log likelihood: -11918.796668 EM: Round [275] log likelihood: -11918.794637 EM: Round [276] log likelihood: -11918.792615 EM: Round [277] log likelihood: -11918.790601 EM: Round [278] log likelihood: -11918.788596 EM: Round [279] log likelihood: -11918.786598 EM: Round [280] log likelihood: -11918.784608 EM: Round [281] log likelihood: -11918.782626 EM: Round [282] log likelihood: -11918.780653 EM: Round [283] log likelihood: -11918.778687 EM: Round [284] log likelihood: -11918.776729 EM: Round [285] log likelihood: -11918.774779 EM: Round [286] log likelihood: -11918.772836 EM: Round [287] log likelihood: -11918.770901 EM: Round [288] log likelihood: -11918.768974 EM: Round [289] log likelihood: -11918.767055 EM: Round [290] log likelihood: -11918.765143 EM: Round [291] log likelihood: 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likelihood: -11918.723163 EM: Round [314] log likelihood: -11918.721421 EM: Round [315] log likelihood: -11918.719685 EM: Round [316] log likelihood: -11918.717955 EM: Round [317] log likelihood: -11918.716232 EM: Round [318] log likelihood: -11918.714516 EM: Round [319] log likelihood: -11918.712806 EM: Round [320] log likelihood: -11918.711102 EM: Round [321] log likelihood: -11918.709405 EM: Round [322] log likelihood: -11918.707714 EM: Round [323] log likelihood: -11918.706029 EM: Round [324] log likelihood: -11918.704351 EM: Round [325] log likelihood: -11918.702678 EM: Round [326] log likelihood: -11918.701012 EM: Round [327] log likelihood: -11918.699352 EM: Round [328] log likelihood: -11918.697699 EM: Round [329] log likelihood: -11918.696051 EM: Round [330] log likelihood: -11918.694409 EM: Round [331] log likelihood: -11918.692774 EM: Round [332] log likelihood: -11918.691144 EM: Round [333] log likelihood: -11918.689521 EM: Round [334] log likelihood: -11918.687903 EM: Round [335] log likelihood: -11918.686291 EM: Round [336] log likelihood: -11918.684685 EM: Round [337] log likelihood: -11918.683085 EM: Round [338] log likelihood: -11918.681491 EM: Round [339] log likelihood: -11918.679902 EM: Round [340] log likelihood: -11918.678320 EM: Round [341] log likelihood: -11918.676743 EM: Round [342] log likelihood: -11918.675171 EM: Round [343] log likelihood: -11918.673606 EM: Round [344] log likelihood: -11918.672046 EM: Round [345] log likelihood: -11918.670491 EM: Round [346] log likelihood: -11918.668942 EM: Round [347] log likelihood: -11918.667399 EM: Round [348] log likelihood: -11918.665861 EM: Round [349] log likelihood: -11918.664329 EM: Round [350] log likelihood: -11918.662802 EM: Round [351] log likelihood: -11918.661280 EM: Round [352] log likelihood: -11918.659764 EM: Round [353] log likelihood: -11918.658254 EM: Round [354] log likelihood: -11918.656748 EM: Round [355] log likelihood: -11918.655248 EM: Round [356] log likelihood: -11918.653754 EM: Round [357] log likelihood: -11918.652264 EM: Round [358] log likelihood: -11918.650780 EM: Round [359] log likelihood: -11918.649301 EM: Round [360] log likelihood: -11918.647827 EM: Round [361] log likelihood: -11918.646359 EM: Round [362] log likelihood: -11918.644895 EM: Round [363] log likelihood: -11918.643437 EM: Round [364] log likelihood: -11918.641983 EM: Round [365] log likelihood: -11918.640535 EM: Round [366] log likelihood: -11918.639092 EM: Round [367] log likelihood: -11918.637654 EM: Round [368] log likelihood: -11918.636221 EM: Round [369] log likelihood: -11918.634792 EM: Round [370] log likelihood: -11918.633369 EM: Round [371] log likelihood: -11918.631951 EM: Round [372] log likelihood: -11918.630537 EM: Round [373] log likelihood: -11918.629129 EM: Round [374] log likelihood: -11918.627725 EM: Round [375] log likelihood: -11918.626326 EM: Round [376] log likelihood: -11918.624932 EM: Round [377] log likelihood: -11918.623542 EM: Round [378] log likelihood: -11918.622158 EM: Round [379] log likelihood: -11918.620778 EM: Round [380] log likelihood: -11918.619403 EM: Round [381] log likelihood: -11918.618032 EM: Round [382] log likelihood: -11918.616666 EM: Round [383] log likelihood: -11918.615305 EM: Round [384] log likelihood: -11918.613948 EM: Round [385] log likelihood: -11918.612596 EM: Round [386] log likelihood: -11918.611249 EM: Round [387] log likelihood: -11918.609906 EM: Round [388] log likelihood: -11918.608568 EM: Round [389] log likelihood: -11918.607234 EM: Round [390] log likelihood: -11918.605905 EM: Round [391] log likelihood: -11918.604580 EM: Round [392] log likelihood: -11918.603259 EM: Round [393] log likelihood: -11918.601943 EM: Round [394] log likelihood: -11918.600632 EM: Round [395] log likelihood: -11918.599324 EM: Round [396] log likelihood: -11918.598022 EM: Round [397] log likelihood: -11918.596723 EM: Round [398] log likelihood: -11918.595429 EM: Round [399] log likelihood: -11918.594139 EM: Round [400] log likelihood: -11918.592853 EM: Round [401] log likelihood: -11918.591572 EM: Round [402] log likelihood: -11918.590295 EM: Round [403] log likelihood: -11918.589022 EM: Round [404] log likelihood: -11918.587753 EM: Round [405] log likelihood: -11918.586489 EM: Round [406] log likelihood: -11918.585229 EM: Round [407] log likelihood: -11918.583973 EM: Round [408] log likelihood: -11918.582721 EM: Round [409] log likelihood: -11918.581473 EM: Round [410] log likelihood: -11918.580229 EM: Round [411] log likelihood: -11918.578989 EM: Round [412] log likelihood: -11918.577753 EM: Round [413] log likelihood: -11918.576522 EM: Round [414] log likelihood: -11918.575294 EM: Round [415] log likelihood: -11918.574070 EM: Round [416] log likelihood: -11918.572851 EM: Round [417] log likelihood: -11918.571635 EM: Round [418] log likelihood: -11918.570423 EM: Round [419] log likelihood: -11918.569215 EM: Round [420] log likelihood: -11918.568012 EM: Round [421] log likelihood: -11918.566812 EM: Round [422] log likelihood: -11918.565615 EM: Round [423] log likelihood: -11918.564423 EM: Round [424] log likelihood: -11918.563235 EM: Round [425] log likelihood: -11918.562050 EM: Round [426] log likelihood: -11918.560869 EM: Round [427] log likelihood: -11918.559692 EM: Round [428] log likelihood: -11918.558519 EM: Round [429] log likelihood: -11918.557350 EM: Round [430] log likelihood: -11918.556184 EM: Round [431] log likelihood: -11918.555022 EM: Round [432] log likelihood: -11918.553864 EM: Round [433] log likelihood: -11918.552709 EM: Round [434] log likelihood: -11918.551558 EM: Round [435] log likelihood: -11918.550411 EM: Round [436] log likelihood: -11918.549267 EM: Round [437] log likelihood: -11918.548127 EM: Round [438] log likelihood: -11918.546991 EM: Round [439] log likelihood: -11918.545858 EM: Round [440] log likelihood: -11918.544729 EM: Round [441] log likelihood: -11918.543604 EM: Round [442] log likelihood: -11918.542482 EM: Round [443] log likelihood: -11918.541363 EM: Round [444] log likelihood: -11918.540248 EM: Round [445] log likelihood: -11918.539137 EM: Round [446] log likelihood: -11918.538029 EM: Round [447] log likelihood: -11918.536924 EM: Round [448] log likelihood: -11918.535823 EM: Round [449] log likelihood: -11918.534726 EM: Round [450] log likelihood: -11918.533631 EM: Round [451] log likelihood: -11918.532541 EM: Round [452] log likelihood: -11918.531453 EM: Round [453] log likelihood: -11918.530369 EM: Round [454] log likelihood: -11918.529289 EM: Round [455] log likelihood: -11918.528212 EM: Round [456] log likelihood: -11918.527138 EM: Round [457] log likelihood: -11918.526067 EM: Round [458] log likelihood: -11918.525000 EM: Round [459] log likelihood: -11918.523936 EM: Round [460] log likelihood: -11918.522876 EM: Round [461] log likelihood: -11918.521819 EM: Round [462] log likelihood: -11918.520765 EM: Round [463] log likelihood: -11918.519714 EM: Round [464] log likelihood: -11918.518666 EM: Round [465] log likelihood: -11918.517622 EM: Round [466] log likelihood: -11918.516581 EM: Round [467] log likelihood: -11918.515543 EM: Round [468] log likelihood: -11918.514508 EM: Round [469] log likelihood: -11918.513477 EM: Round [470] log likelihood: -11918.512448 EM: Round [471] log likelihood: -11918.511423 EM: Round [472] log likelihood: -11918.510401 EM: Round [473] log likelihood: -11918.509382 EM: Round [474] log likelihood: -11918.508366 EM: Round [475] log likelihood: -11918.507353 EM: Round [476] log likelihood: -11918.506344 EM: Round [477] log likelihood: -11918.505337 EM: Round [478] log likelihood: -11918.504334 EM: Round [479] log likelihood: -11918.503333 EM: Round [480] log likelihood: -11918.502336 EM: Round [481] log likelihood: -11918.501341 EM: Round [482] log likelihood: -11918.500350 EM: Round [483] log likelihood: -11918.499361 EM: Round [484] log likelihood: -11918.498376 EM: Round [485] log likelihood: -11918.497393 EM: Round [486] log likelihood: -11918.496414 EM: Round [487] log likelihood: -11918.495437 EM: Round [488] log likelihood: -11918.494464 EM: Round [489] log likelihood: -11918.493493 EM: Round [490] log likelihood: -11918.492525 EM: Round [491] log likelihood: -11918.491560 EM: Round [492] log likelihood: -11918.490598 EM: Round [493] log likelihood: -11918.489639 EM: Round [494] log likelihood: -11918.488683 EM: Round [495] log likelihood: -11918.487730 EM: Round [496] log likelihood: -11918.486779 EM: Round [497] log likelihood: -11918.485831 EM: Round [498] log likelihood: -11918.484886 EM: Round [499] log likelihood: -11918.483944 EM: Round [500] log likelihood: -11918.483005 EM: Round [501] log likelihood: -11918.482069 EM: Round [502] log likelihood: -11918.481135 EM: Round [503] log likelihood: -11918.480204 EM: Round [504] log likelihood: -11918.479276 EM: Round [505] log likelihood: -11918.478351 EM: Round [506] log likelihood: -11918.477428 EM: Round [507] log likelihood: -11918.476508 EM: Round [508] log likelihood: -11918.475591 EM: Round [509] log likelihood: -11918.474676 EM: Round [510] log likelihood: -11918.473764 EM: Round [511] log likelihood: -11918.472855 EM: Round [512] log likelihood: -11918.471949 EM: Round [513] log likelihood: -11918.471045 EM: Round [514] log likelihood: -11918.470144 EM: Round [515] log likelihood: -11918.469245 EM: Round [516] log likelihood: -11918.468349 EM: Round [517] log likelihood: -11918.467456 EM: Round [518] log likelihood: -11918.466566 EM: Round [519] log likelihood: -11918.465678 EM: Round [520] log likelihood: -11918.464792 EM: Round [521] log likelihood: -11918.463909 EM: Round [522] log likelihood: -11918.463029 EM: Round [523] log likelihood: -11918.462151 EM: Round [524] log likelihood: -11918.461276 EM: Round [525] log likelihood: -11918.460404 EM: Round [526] log likelihood: -11918.459534 EM: Round [527] log likelihood: -11918.458666 EM: Round [528] log likelihood: -11918.457801 EM: Round [529] log likelihood: -11918.456938 EM: Round [530] log likelihood: -11918.456078 EM: Round [531] log likelihood: -11918.455221 EM: Round [532] log likelihood: -11918.454366 EM: Round [533] log likelihood: -11918.453513 EM: Round [534] log likelihood: -11918.452663 EM: Round [535] log likelihood: -11918.451815 EM: Round [536] log likelihood: -11918.450970 EM: Round [537] log likelihood: -11918.450127 EM: Round [538] log likelihood: -11918.449287 EM: Round [539] log likelihood: -11918.448449 EM: Round [540] log likelihood: -11918.447614 EM: Round [541] log likelihood: -11918.446780 EM: Round [542] log likelihood: -11918.445950 EM: Round [543] log likelihood: -11918.445121 EM: Round [544] log likelihood: -11918.444295 EM: Round [545] log likelihood: -11918.443472 EM: Round [546] log likelihood: -11918.442650 EM: Round [547] log likelihood: -11918.441831 EM: Round [548] log likelihood: -11918.441015 EM: Round [549] log likelihood: -11918.440200 EM: Round [550] log likelihood: -11918.439388 EM: Round [551] log likelihood: -11918.438579 EM: Round [552] log likelihood: -11918.437771 EM: Round [553] log likelihood: -11918.436966 EM: Round [554] log likelihood: -11918.436164 EM: Round [555] log likelihood: -11918.435363 EM: Round [556] log likelihood: -11918.434565 EM: Round [557] log likelihood: -11918.433769 EM: Round [558] log likelihood: -11918.432975 EM: Round [559] log likelihood: -11918.432184 EM: Round [560] log likelihood: -11918.431394 EM: Round [561] log likelihood: -11918.430607 EM: Round [562] log likelihood: -11918.429823 EM: Round [563] log likelihood: -11918.429040 EM: Round [564] log likelihood: -11918.428260 EM: Round [565] log likelihood: -11918.427481 EM: Round [566] log likelihood: -11918.426705 EM: Round [567] log likelihood: -11918.425932 EM: Round [568] log likelihood: -11918.425160 EM: Round [569] log likelihood: -11918.424391 EM: Round [570] log likelihood: -11918.423623 EM: Round [571] log likelihood: -11918.422858 EM: Round [572] log likelihood: -11918.422095 EM: Round [573] log likelihood: -11918.421334 EM: Round [574] log likelihood: -11918.420575 EM: Round [575] log likelihood: -11918.419819 EM: Round [576] log likelihood: -11918.419064 EM: Round [577] log likelihood: -11918.418312 EM: Round [578] log likelihood: -11918.417561 EM: Round [579] log likelihood: -11918.416813 EM: Round [580] log likelihood: -11918.416067 EM: Round [581] log likelihood: -11918.415323 EM: Round [582] log likelihood: -11918.414581 EM: Round [583] log likelihood: -11918.413841 EM: Round [584] log likelihood: -11918.413103 EM: Round [585] log likelihood: -11918.412367 EM: Round [586] log likelihood: -11918.411633 EM: Round [587] log likelihood: -11918.410901 EM: Round [588] log likelihood: -11918.410172 EM: Round [589] log likelihood: -11918.409444 EM: Round [590] log likelihood: -11918.408718 EM: Round [591] log likelihood: -11918.407994 EM: Round [592] log likelihood: -11918.407273 EM: Round [593] log likelihood: -11918.406553 EM: Round [594] log likelihood: -11918.405835 EM: Round [595] log likelihood: -11918.405119 EM: Round [596] log likelihood: -11918.404405 EM: Round [597] log likelihood: -11918.403694 EM: Round [598] log likelihood: -11918.402984 EM: Round [599] log likelihood: -11918.402276 EM: Round [600] log likelihood: -11918.401570 EM: Round [601] log likelihood: -11918.400866 EM: Round [602] log likelihood: -11918.400163 EM: Round [603] log likelihood: -11918.399463 EM: Round [604] log likelihood: -11918.398765 EM: Round [605] log likelihood: -11918.398068 EM: Round [606] log likelihood: -11918.397374 EM: Round [607] log likelihood: -11918.396681 EM: Round [608] log likelihood: -11918.395991 EM: Round [609] log likelihood: -11918.395302 EM: Round [610] log likelihood: -11918.394615 EM: Round [611] log likelihood: -11918.393930 EM: Round [612] log likelihood: -11918.393246 EM: Round [613] log likelihood: -11918.392565 EM: Round [614] log likelihood: -11918.391885 EM: Round [615] log likelihood: -11918.391208 EM: Round [616] log likelihood: -11918.390532 EM: Round [617] log likelihood: -11918.389858 EM: Round [618] log likelihood: -11918.389186 EM: Round [619] log likelihood: -11918.388515 EM: Round [620] log likelihood: -11918.387847 EM: Round [621] log likelihood: -11918.387180 EM: Round [622] log likelihood: -11918.386515 EM: Round [623] log likelihood: -11918.385852 EM: Round [624] log likelihood: -11918.385190 EM: Round [625] log likelihood: -11918.384531 EM: Round [626] log likelihood: -11918.383873 EM: Round [627] log likelihood: -11918.383217 EM: Round [628] log likelihood: -11918.382563 EM: Round [629] log likelihood: -11918.381910 EM: Round [630] log likelihood: -11918.381259 EM: Round [631] log likelihood: -11918.380610 EM: Round [632] log likelihood: -11918.379963 EM: Round [633] log likelihood: -11918.379317 EM: Round [634] log likelihood: -11918.378674 EM: Round [635] log likelihood: -11918.378032 EM: Round [636] log likelihood: -11918.377391 EM: Round [637] log likelihood: -11918.376752 EM: Round [638] log likelihood: -11918.376116 EM: Round [639] log likelihood: -11918.375480 EM: Round [640] log likelihood: -11918.374847 EM: Round [641] log likelihood: -11918.374215 EM: Round [642] log likelihood: -11918.373585 EM: Round [643] log likelihood: -11918.372956 EM: Round [644] log likelihood: -11918.372329 EM: Round [645] log likelihood: -11918.371704 EM: Round [646] log likelihood: -11918.371081 EM: Round [647] log likelihood: -11918.370459 EM: Round [648] log likelihood: -11918.369839 EM: Round [649] log likelihood: -11918.369220 EM: Round [650] log likelihood: -11918.368603 EM: Round [651] log likelihood: -11918.367988 EM: Round [652] log likelihood: -11918.367374 EM: Round [653] log likelihood: -11918.366762 EM: Round [654] log likelihood: -11918.366152 EM: Round [655] log likelihood: -11918.365543 EM: Round [656] log likelihood: -11918.364936 EM: Round [657] log likelihood: -11918.364330 EM: Round [658] log likelihood: -11918.363726 EM: Round [659] log likelihood: -11918.363124 EM: Round [660] log likelihood: -11918.362523 EM: Round [661] log likelihood: -11918.361924 EM: Round [662] log likelihood: -11918.361326 EM: Round [663] log likelihood: -11918.360730 EM: Round [664] log likelihood: -11918.360136 EM: Round [665] log likelihood: -11918.359543 EM: Round [666] log likelihood: -11918.358952 EM: Round [667] log likelihood: -11918.358362 EM: Round [668] log likelihood: -11918.357774 EM: Round [669] log likelihood: -11918.357187 EM: Round [670] log likelihood: -11918.356602 EM: Round [671] log likelihood: -11918.356018 EM: Round [672] log likelihood: -11918.355436 EM: Round [673] log likelihood: -11918.354855 EM: Round [674] log likelihood: -11918.354276 EM: Round [675] log likelihood: -11918.353699 EM: Round [676] log likelihood: -11918.353123 EM: Round [677] log likelihood: -11918.352548 EM: Round [678] log likelihood: -11918.351975 EM: Round [679] log likelihood: -11918.351403 EM: Round [680] log likelihood: -11918.350833 EM: Round [681] log likelihood: -11918.350265 EM: Round [682] log likelihood: -11918.349698 EM: Round [683] log likelihood: -11918.349132 EM: Round [684] log likelihood: -11918.348568 EM: Round [685] log likelihood: -11918.348005 EM: Round [686] log likelihood: -11918.347444 EM: Round [687] log likelihood: -11918.346884 EM: Round [688] log likelihood: -11918.346326 EM: Round [689] log likelihood: -11918.345769 EM: Round [690] log likelihood: -11918.345214 EM: Round [691] log likelihood: -11918.344660 EM: Round [692] log likelihood: -11918.344107 EM: Round [693] log likelihood: -11918.343556 EM: Round [694] log likelihood: -11918.343006 EM: Round [695] log likelihood: -11918.342458 EM: Round [696] log likelihood: -11918.341911 EM: Round [697] log likelihood: -11918.341366 EM: Round [698] log likelihood: -11918.340822 EM: Round [699] log likelihood: -11918.340279 EM: Round [700] log likelihood: -11918.339738 EM: Round [701] log likelihood: -11918.339198 EM: Round [702] log likelihood: -11918.338659 EM: Round [703] log likelihood: -11918.338122 EM: Round [704] log likelihood: -11918.337587 EM: Round [705] log likelihood: -11918.337052 EM: Round [706] log likelihood: -11918.336519 EM: Round [707] log likelihood: -11918.335988 EM: Round [708] log likelihood: -11918.335458 EM: Round [709] log likelihood: -11918.334929 EM: Round [710] log likelihood: -11918.334401 EM: Round [711] log likelihood: -11918.333875 EM: Round [712] log likelihood: -11918.333350 EM: Round [713] log likelihood: -11918.332827 EM: Round [714] log likelihood: -11918.332305 EM: Round [715] log likelihood: -11918.331784 EM: Round [716] log likelihood: -11918.331264 EM: Round [717] log likelihood: -11918.330746 EM: Round [718] log likelihood: -11918.330230 EM: Round [719] log likelihood: -11918.329714 EM: Round [720] log likelihood: -11918.329200 EM: Round [721] log likelihood: -11918.328687 EM: Round [722] log likelihood: -11918.328175 EM: Round [723] log likelihood: -11918.327665 EM: Round [724] log likelihood: -11918.327156 EM: Round [725] log likelihood: -11918.326649 EM: Round [726] log likelihood: -11918.326142 EM: Round [727] log likelihood: -11918.325637 EM: Round [728] log likelihood: -11918.325133 EM: Round [729] log likelihood: -11918.324631 EM: Round [730] log likelihood: -11918.324130 EM: Round [731] log likelihood: -11918.323630 EM: Round [732] log likelihood: -11918.323131 EM: Round [733] log likelihood: -11918.322634 EM: Round [734] log likelihood: -11918.322137 EM: Round [735] log likelihood: -11918.321642 EM: Round [736] log likelihood: -11918.321149 EM: Round [737] log likelihood: -11918.320656 EM: Round [738] log likelihood: -11918.320165 EM: Round [739] log likelihood: -11918.319675 EM: Round [740] log likelihood: -11918.319187 EM: Round [741] log likelihood: -11918.318699 EM: Round [742] log likelihood: -11918.318213 EM: Round [743] log likelihood: -11918.317728 EM: Round [744] log likelihood: -11918.317244 EM: Round [745] log likelihood: -11918.316762 EM: Round [746] log likelihood: -11918.316280 EM: Round [747] log likelihood: -11918.315800 EM: Round [748] log likelihood: -11918.315321 EM: Round [749] log likelihood: -11918.314843 EM: Round [750] log likelihood: -11918.314367 EM: Round [751] log likelihood: -11918.313891 EM: Round [752] log likelihood: -11918.313417 EM: Round [753] log likelihood: -11918.312944 EM: Round [754] log likelihood: -11918.312473 EM: Round [755] log likelihood: -11918.312002 EM: Round [756] log likelihood: -11918.311533 EM: Round [757] log likelihood: -11918.311064 EM: Round [758] log likelihood: -11918.310597 EM: Round [759] log likelihood: -11918.310131 EM: Round [760] log likelihood: -11918.309667 EM: Round [761] log likelihood: -11918.309203 EM: Round [762] log likelihood: -11918.308741 EM: Round [763] log likelihood: -11918.308280 EM: Round [764] log likelihood: -11918.307819 EM: Round [765] log likelihood: -11918.307361 EM: Round [766] log likelihood: -11918.306903 EM: Round [767] log likelihood: -11918.306446 EM: Round [768] log likelihood: -11918.305991 EM: Round [769] log likelihood: -11918.305536 EM: Round [770] log likelihood: -11918.305083 EM: Round [771] log likelihood: -11918.304631 EM: Round [772] log likelihood: -11918.304180 EM: Round [773] log likelihood: -11918.303730 EM: Round [774] log likelihood: -11918.303281 EM: Round [775] log likelihood: -11918.302833 EM: Round [776] log likelihood: -11918.302387 EM: Round [777] log likelihood: -11918.301941 EM: Round [778] log likelihood: -11918.301497 EM: Round [779] log likelihood: -11918.301054 EM: Round [780] log likelihood: -11918.300612 EM: Round [781] log likelihood: -11918.300171 EM: Round [782] log likelihood: -11918.299731 EM: Round [783] log likelihood: -11918.299292 EM: Round [784] log likelihood: -11918.298854 EM: Round [785] log likelihood: -11918.298418 EM: Round [786] log likelihood: -11918.297982 EM: Round [787] log likelihood: -11918.297547 EM: Round [788] log likelihood: -11918.297114 EM: Round [789] log likelihood: -11918.296682 EM: Round [790] log likelihood: -11918.296250 EM: Round [791] log likelihood: -11918.295820 EM: Round [792] log likelihood: -11918.295391 EM: Round [793] log likelihood: -11918.294963 EM: Round [794] log likelihood: -11918.294536 EM: Round [795] log likelihood: -11918.294110 EM: Round [796] log likelihood: -11918.293685 EM: Round [797] log likelihood: -11918.293261 EM: Round [798] log likelihood: -11918.292838 EM: Round [799] log likelihood: -11918.292416 EM: Round [800] log likelihood: -11918.291995 EM: Round [801] log likelihood: -11918.291575 EM: Round [802] log likelihood: -11918.291157 EM: Round [803] log likelihood: -11918.290739 EM: Round [804] log likelihood: -11918.290322 EM: Round [805] log likelihood: -11918.289906 EM: Round [806] log likelihood: -11918.289492 EM: Round [807] log likelihood: -11918.289078 EM: Round [808] log likelihood: -11918.288666 EM: Round [809] log likelihood: -11918.288254 EM: Round [810] log likelihood: -11918.287843 EM: Round [811] log likelihood: -11918.287434 EM: Round [812] log likelihood: -11918.287025 EM: Round [813] log likelihood: -11918.286617 EM: Round [814] log likelihood: -11918.286211 EM: Round [815] log likelihood: -11918.285805 EM: Round [816] log likelihood: -11918.285401 EM: Round [817] log likelihood: -11918.284997 EM: Round [818] log likelihood: -11918.284594 EM: Round [819] log likelihood: -11918.284193 EM: Round [820] log likelihood: -11918.283792 EM: Round [821] log likelihood: -11918.283392 EM: Round [822] log likelihood: -11918.282993 EM: Round [823] log likelihood: -11918.282596 EM: Round [824] log likelihood: -11918.282199 EM: Round [825] log likelihood: -11918.281803 EM: Round [826] log likelihood: -11918.281408 EM: Round [827] log likelihood: -11918.281014 EM: Round [828] log likelihood: -11918.280621 EM: Round [829] log likelihood: -11918.280229 EM: Round [830] log likelihood: -11918.279838 EM: Round [831] log likelihood: -11918.279448 EM: Round [832] log likelihood: -11918.279059 EM: Round [833] log likelihood: -11918.278671 EM: Round [834] log likelihood: -11918.278283 EM: Round [835] log likelihood: -11918.277897 EM: Round [836] log likelihood: -11918.277512 EM: Round [837] log likelihood: -11918.277127 EM: Round [838] log likelihood: -11918.276744 EM: Round [839] log likelihood: -11918.276361 EM: Round [840] log likelihood: -11918.275979 EM: Round [841] log likelihood: -11918.275599 EM: Round [842] log likelihood: -11918.275219 EM: Round [843] log likelihood: -11918.274840 EM: Round [844] log likelihood: -11918.274462 EM: Round [845] log likelihood: -11918.274085 EM: Round [846] log likelihood: -11918.273708 EM: Round [847] log likelihood: -11918.273333 EM: Round [848] log likelihood: -11918.272959 EM: Round [849] log likelihood: -11918.272585 EM: Round [850] log likelihood: -11918.272213 EM: Round [851] log likelihood: -11918.271841 EM: Round [852] log likelihood: -11918.271470 EM: Round [853] log likelihood: -11918.271100 EM: Round [854] log likelihood: -11918.270731 EM: Round [855] log likelihood: -11918.270363 EM: Round [856] log likelihood: -11918.269996 EM: Round [857] log likelihood: -11918.269630 EM: Round [858] log likelihood: -11918.269264 EM: Round [859] log likelihood: -11918.268900 EM: Round [860] log likelihood: -11918.268536 EM: Round [861] log likelihood: -11918.268173 EM: Round [862] log likelihood: -11918.267811 EM: Round [863] log likelihood: -11918.267450 EM: Round [864] log likelihood: -11918.267090 EM: Round [865] log likelihood: -11918.266730 EM: Round [866] log likelihood: -11918.266372 EM: Round [867] log likelihood: -11918.266014 EM: Round [868] log likelihood: -11918.265657 EM: Round [869] log likelihood: -11918.265301 EM: Round [870] log likelihood: -11918.264946 EM: Round [871] log likelihood: -11918.264592 EM: Round [872] log likelihood: -11918.264239 EM: Round [873] log likelihood: -11918.263886 EM: Round [874] log likelihood: -11918.263534 EM: Round [875] log likelihood: -11918.263183 EM: Round [876] log likelihood: -11918.262833 EM: Round [877] log likelihood: -11918.262484 EM: Round [878] log likelihood: -11918.262136 EM: Round [879] log likelihood: -11918.261788 EM: Round [880] log likelihood: -11918.261442 EM: Round [881] log likelihood: -11918.261096 EM: Round [882] log likelihood: -11918.260751 EM: Round [883] log likelihood: -11918.260406 EM: Round [884] log likelihood: -11918.260063 EM: Round [885] log likelihood: -11918.259720 EM: Round [886] log likelihood: -11918.259379 EM: Round [887] log likelihood: -11918.259038 EM: Round [888] log likelihood: -11918.258697 EM: Round [889] log likelihood: -11918.258358 EM: Round [890] log likelihood: -11918.258019 EM: Round [891] log likelihood: -11918.257682 EM: Round [892] log likelihood: -11918.257345 EM: Round [893] log likelihood: -11918.257009 EM: Round [894] log likelihood: -11918.256673 EM: Round [895] log likelihood: -11918.256339 EM: Round [896] log likelihood: -11918.256005 EM: Round [897] log likelihood: -11918.255672 EM: Round [898] log likelihood: -11918.255340 EM: Round [899] log likelihood: -11918.255008 EM: Round [900] log likelihood: -11918.254678 EM: Round [901] log likelihood: -11918.254348 EM: Round [902] log likelihood: -11918.254019 EM: Round [903] log likelihood: -11918.253691 EM: Round [904] log likelihood: -11918.253363 EM: Round [905] log likelihood: -11918.253036 EM: Round [906] log likelihood: -11918.252710 EM: Round [907] log likelihood: -11918.252385 EM: Round [908] log likelihood: -11918.252061 EM: Round [909] log likelihood: -11918.251737 EM: Round [910] log likelihood: -11918.251414 EM: Round [911] log likelihood: -11918.251092 EM: Round [912] log likelihood: -11918.250771 EM: Round [913] log likelihood: -11918.250450 EM: Round [914] log likelihood: -11918.250130 EM: Round [915] log likelihood: -11918.249811 EM: Round [916] log likelihood: -11918.249493 EM: Round [917] log likelihood: -11918.249175 EM: Round [918] log likelihood: -11918.248858 EM: Round [919] log likelihood: -11918.248542 EM: Round [920] log likelihood: -11918.248227 EM: Round [921] log likelihood: -11918.247912 EM: Round [922] log likelihood: -11918.247598 EM: Round [923] log likelihood: -11918.247285 EM: Round [924] log likelihood: -11918.246973 EM: Round [925] log likelihood: -11918.246661 EM: Round [926] log likelihood: -11918.246350 EM: Round [927] log likelihood: -11918.246040 EM: Round [928] log likelihood: -11918.245731 EM: Round [929] log likelihood: -11918.245422 EM: Round [930] log likelihood: -11918.245114 EM: Round [931] log likelihood: -11918.244806 EM: Round [932] log likelihood: -11918.244500 EM: Round [933] log likelihood: -11918.244194 EM: Round [934] log likelihood: -11918.243889 EM: Round [935] log likelihood: -11918.243584 EM: Round [936] log likelihood: -11918.243281 EM: Round [937] log likelihood: -11918.242978 EM: Round [938] log likelihood: -11918.242675 EM: Round [939] log likelihood: -11918.242374 EM: Round [940] log likelihood: -11918.242073 EM: Round [941] log likelihood: -11918.241773 EM: Round [942] log likelihood: -11918.241473 EM: Round [943] log likelihood: -11918.241174 EM: Round [944] log likelihood: -11918.240876 EM: Round [945] log likelihood: -11918.240579 EM: Round [946] log likelihood: -11918.240282 EM: Round [947] log likelihood: -11918.239986 EM: Round [948] log likelihood: -11918.239691 EM: Round [949] log likelihood: -11918.239396 EM: Round [950] log likelihood: -11918.239102 EM: Round [951] log likelihood: -11918.238809 EM: Round [952] log likelihood: -11918.238516 EM: Round [953] log likelihood: -11918.238224 EM: Round [954] log likelihood: -11918.237933 EM: Round [955] log likelihood: -11918.237643 EM: Round [956] log likelihood: -11918.237353 EM: Round [957] log likelihood: -11918.237064 EM: Round [958] log likelihood: -11918.236775 EM: Round [959] log likelihood: -11918.236487 EM: Round [960] log likelihood: -11918.236200 EM: Round [961] log likelihood: -11918.235913 EM: Round [962] log likelihood: -11918.235628 EM: Round [963] log likelihood: -11918.235342 EM: Round [964] log likelihood: -11918.235058 EM: Round [965] log likelihood: -11918.234774 EM: Round [966] log likelihood: -11918.234491 EM: Round [967] log likelihood: -11918.234208 EM: Round [968] log likelihood: -11918.233926 EM: Round [969] log likelihood: -11918.233645 EM: Round [970] log likelihood: -11918.233364 EM: Round [971] log likelihood: -11918.233085 EM: Round [972] log likelihood: -11918.232805 EM: Round [973] log likelihood: -11918.232527 EM: Round [974] log likelihood: -11918.232249 EM: Round [975] log likelihood: -11918.231971 EM: Round [976] log likelihood: -11918.231694 EM: Round [977] log likelihood: -11918.231418 EM: Round [978] log likelihood: -11918.231143 EM: Round [979] log likelihood: -11918.230868 EM: Round [980] log likelihood: -11918.230594 EM: Round [981] log likelihood: -11918.230320 EM: Round [982] log likelihood: -11918.230048 EM: Round [983] log likelihood: -11918.229775 EM: Round [984] log likelihood: -11918.229504 EM: Round [985] log likelihood: -11918.229233 EM: Round [986] log likelihood: -11918.228962 EM: Round [987] log likelihood: -11918.228692 EM: Round [988] log likelihood: -11918.228423 EM: Round [989] log likelihood: -11918.228155 EM: Round [990] log likelihood: -11918.227887 EM: Round [991] log likelihood: -11918.227620 EM: Round [992] log likelihood: -11918.227353 EM: Round [993] log likelihood: -11918.227087 EM: Round [994] log likelihood: -11918.226821 EM: Round [995] log likelihood: -11918.226557 EM: Round [996] log likelihood: -11918.226292 EM: Round [997] log likelihood: -11918.226029 EM: Round [998] log likelihood: -11918.225766 EM: Round [999] log likelihood: -11918.225503 EM: Round [1000] log likelihood: -11918.225241 EM: Round [1001] log likelihood: -11918.224980 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 295315142 Execution Time = 5.29 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n5ewjTXfr6/fi_workdir/microH.dat Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.n5ewjTXfr6/fi_workdir/microH.dat Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.n5ewjTXfr6/fi_workdir/microH.dat /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_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.n5ewjTXfr6/fi_workdir/microH.dat /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.n5ewjTXfr6 --json_outfile /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.n5ewjTXfr6 --json_outfile /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1 Running: touch /tmp/nxf.n5ewjTXfr6/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.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_T46_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000135477.11] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000257259.3] WARNING, no entry stored in dbm for [ENSG00000257259.3] WARNING, no entry stored in dbm for [ENSG00000257259.3] WARNING, no entry stored in dbm for [ENSG00000257259.3] WARNING, no entry stored in dbm for [ENSG00000257259.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.n5ewjTXfr6/ctat_genome_lib_build_dir > /tmp/nxf.n5ewjTXfr6/1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.n5ewjTXfr6/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory