Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/2f1ab7db80a50194505cda6a54a440/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/7dbee5c6f334ab661e3c02c0267dc0/.command.sh 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/f4/7dbee5c6f334ab661e3c02c0267dc0/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/2f1ab7db80a50194505cda6a54a440/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/bb1e2d64c50b7674419b4fcdbad69a/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/cytoBand.txt Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed -parsing GTF file: /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --CPU 8 --out_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star --out_dir /tmp/nxf.b9RdbAI3hE/fi_workdir --reads "/tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:30:49 ..... started STAR run Jun 08 10:30:49 ..... loading genome Jun 08 10:32:32 ... generating Suffix Array index Jun 08 10:36:12 ... completed Suffix Array index Jun 08 10:36:12 ..... processing annotations GTF Jun 08 10:36:12 ..... inserting junctions into the genome indices Jun 08 10:37:13 ..... started mapping Jun 08 11:28:13 ..... finished mapping Jun 08 11:28:14 ..... started sorting BAM Jun 08 11:28:16 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.sortedByCoord.out.bam Execution Time = 57.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --CPU 8 --out_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star --out_dir /tmp/nxf.b9RdbAI3hE/fi_workdir --reads "/tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:28:38 : INFO : Done. Execution Time = 0.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf -parsing /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] [1300000] [1310000] [1320000] [1330000] [1340000] [1350000] [1360000] [1370000] [1380000] [1390000] [1400000] [1410000] [1420000] [1430000] [1440000] [1450000] [1460000] [1470000] [1480000] [1490000] [1500000] [1510000] [1520000] [1530000] [1540000] [1550000] [1560000] [1570000] [1580000] [1590000] [1600000] [1610000] [1620000] [1630000] [1640000] [1650000] [1660000] [1670000] [1680000] [1690000] [1700000] [1710000] [1720000] [1730000] [1740000] [1750000] [1760000] [1770000] [1780000] [1790000] [1800000] [1810000] [1820000] [1830000] [1840000] [1850000] [1860000] [1870000] [1880000] [1890000] [1900000] [1910000] [1920000] [1930000] [1940000] [1950000] [1960000] [1970000] [1980000] [1990000] [2000000] [2010000] [2020000] [2030000] [2040000] [2050000] [2060000] [2070000] [2080000] [2090000] [2100000] [2110000] [2120000] [2130000] [2140000] [2150000] [2160000] [2170000] [2180000] [2190000] [2200000] [2210000] [2220000] [2230000] [2240000] [2250000] [2260000] [2270000] [2280000] [2290000] [2300000] [2310000] [2320000] [2330000] [2340000] [2350000] [2360000] [2370000] [2380000] [2390000] [2400000] [2410000] [2420000] [2430000] [2440000] [2450000] [2460000] [2470000] [2480000] [2490000] [2500000] [2510000] [2520000] [2530000] [2540000] [2550000] [2560000] [2570000] [2580000] [2590000] [2600000] [2610000] [2620000] [2630000] [2640000] [2650000] [2660000] [2670000] [2680000] [2690000] [2700000] [2710000] [2720000] [2730000] [2740000] [2750000] [2760000] [2770000] [2780000] [2790000] [2800000] [2810000] [2820000] [2830000] [2840000] [2850000] [2860000] [2870000] [2880000] [2890000] [2900000] [2910000] [2920000] [2930000] [2940000] [2950000] [2960000] [2970000] [2980000] [2990000] [3000000] [3010000] [3020000] [3030000] [3040000] [3050000] [3060000] [3070000] [3080000] [3090000] [3100000] [3110000] [3120000] [3130000] [3140000] [3150000] [3160000] [3170000] [3180000] [3190000] [3200000] [3210000] [3220000] [3230000] [3240000] [3250000] [3260000] [3270000] [3280000] [3290000] [3300000] [3310000] [3320000] [3330000] [3340000] [3350000] [3360000] [3370000] [3380000] [3390000] [3400000] [3410000] [3420000] -done parsing /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 21, 'per_id < 96' => 23149, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 60, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 10, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 272, 'seq-similar region overlap' => 214, 'exons hit < 2' => 6, 'num genes matched < 2' => 33, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 12, 'excessive soft clipping' => 26406, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 26, 'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 20, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 46, 'low complexity anchor region' => 20, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4, ' ** passed ** ' => 45164, 'small anchor length' => 315 }; -writing fusion junction support info. Execution Time = 1.92 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] -fusion SPANNING read extraction for scaff: AC002066.1--SYK [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: AC004917.1--SLC26A3 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: AC005050.1--SLC26A3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: AC092142.1--ELAPOR2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] -fusion SPANNING read extraction for scaff: AL033504.1--SASH1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [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] -fusion SPANNING read extraction for scaff: BIRC6--ITGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: CENPP--ASZ1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: CHST11--SYK [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: CHST11--DIRAS2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: CHST11--OR7E109P [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [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: CLASP1--NRCAM [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: COBL--LINC01866 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: COBL--RN7SKP168 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] -fusion SPANNING read extraction for scaff: COL13A1--SPON1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] -fusion SPANNING read extraction for scaff: DGCR2--WARS2-AS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] -fusion SPANNING read extraction for scaff: EPHB2--TMEM39B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] -fusion SPANNING read extraction for scaff: FAF1--CDKN2C [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: FAF1--MIR4421 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] -fusion SPANNING read extraction for scaff: GLIS3--FGF7P4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] -fusion SPANNING read extraction for scaff: GLIS3--FGF7P6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] -fusion SPANNING read extraction for scaff: GTF2H2--FAM114A1 [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] -fusion SPANNING read extraction for scaff: HMGA2--CHMP1A [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: LPAR1--SUSD1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] -fusion SPANNING read extraction for scaff: MFSD14B--LINC01591 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] -fusion SPANNING read extraction for scaff: MMP24OS--PTPRT -fusion SPANNING read extraction for scaff: NTM-AS1--OPCML [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [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] -fusion SPANNING read extraction for scaff: NUP98--PRMT3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] -fusion SPANNING read extraction for scaff: PARD3--AL392046.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [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] -fusion SPANNING read extraction for scaff: POLR2J3--KIF16B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] -fusion SPANNING read extraction for scaff: PSMB2--CELF4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] -fusion SPANNING read extraction for scaff: PXN--PLA2G1B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: SDHAF3--AC025614.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: SDHAF3--LINC01985 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: SLC30A7--UROC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] -fusion SPANNING read extraction for scaff: SLC34A2--ROS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] -fusion SPANNING read extraction for scaff: SMARCA2--TRIM72 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] -fusion SPANNING read extraction for scaff: ST7--AC006001.3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: TENT4B--AF254982.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: TENT4B--AP001464.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] -fusion SPANNING read extraction for scaff: UHRF2--SLC1A1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] -fusion SPANNING read extraction for scaff: XYLB--GOLGA4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] -fusion SPANNING read extraction for scaff: ZBTB40--ZMYM4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: ZFP62--SIMC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: ZNF559--ZNF177 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 27491, 'lacks exon overlap' => 174764 }; Execution Time = 4.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -20978.211364 EM: Round [1] log likelihood: -20970.110148 EM: Round [2] log likelihood: -20968.416238 EM: Round [3] log likelihood: -20967.049984 EM: Round [4] log likelihood: -20965.936952 EM: Round [5] log likelihood: -20965.024101 EM: Round [6] log likelihood: -20964.270527 EM: Round [7] log likelihood: -20963.644411 EM: Round [8] log likelihood: -20963.120815 EM: Round [9] log likelihood: -20962.680076 EM: Round [10] log likelihood: -20962.306607 EM: Round [11] log likelihood: -20961.987992 EM: Round [12] log likelihood: -20961.714298 EM: Round [13] log likelihood: -20961.477545 EM: Round [14] log likelihood: -20961.271301 EM: Round [15] log likelihood: -20961.090358 EM: Round [16] log likelihood: -20960.930485 EM: Round [17] log likelihood: -20960.788233 EM: Round [18] log likelihood: -20960.660780 EM: Round [19] log likelihood: -20960.545808 EM: Round [20] log likelihood: -20960.441407 EM: Round [21] log likelihood: -20960.345996 EM: Round [22] log likelihood: -20960.258264 EM: Round [23] log likelihood: -20960.177116 EM: Round [24] log likelihood: -20960.101639 EM: Round [25] log likelihood: -20960.031066 EM: Round [26] log likelihood: -20959.964750 EM: Round [27] log likelihood: -20959.902145 EM: Round [28] log likelihood: -20959.842788 EM: Round [29] log likelihood: -20959.786285 EM: Round [30] log likelihood: -20959.732301 EM: Round [31] log likelihood: -20959.680547 EM: Round [32] log likelihood: -20959.630777 EM: Round [33] log likelihood: -20959.582778 EM: Round [34] log likelihood: -20959.536366 EM: Round [35] log likelihood: -20959.491383 EM: Round [36] log likelihood: -20959.447691 EM: Round [37] log likelihood: -20959.405169 EM: Round [38] log likelihood: -20959.363712 EM: Round [39] log likelihood: -20959.323231 EM: Round [40] log likelihood: -20959.283643 EM: Round [41] log likelihood: -20959.244880 EM: Round [42] log likelihood: -20959.206878 EM: Round [43] log likelihood: -20959.169583 EM: Round [44] log likelihood: -20959.132948 EM: Round [45] log likelihood: -20959.096928 EM: Round [46] log likelihood: -20959.061487 EM: Round [47] log likelihood: -20959.026589 EM: Round [48] log likelihood: -20958.992206 EM: Round [49] log likelihood: -20958.958309 EM: Round [50] log likelihood: -20958.924875 EM: Round [51] log likelihood: -20958.891882 EM: Round [52] log likelihood: -20958.859310 EM: Round [53] log likelihood: -20958.827141 EM: Round [54] log likelihood: -20958.795360 EM: Round [55] log likelihood: -20958.763951 EM: Round [56] log likelihood: -20958.732901 EM: Round [57] log likelihood: -20958.702198 EM: Round [58] log likelihood: -20958.671831 EM: Round [59] log likelihood: -20958.641790 EM: Round [60] log likelihood: -20958.612064 EM: Round [61] log likelihood: -20958.582646 EM: Round [62] log likelihood: -20958.553526 EM: Round [63] log likelihood: -20958.524698 EM: Round [64] log likelihood: -20958.496154 EM: Round [65] log likelihood: -20958.467887 EM: Round [66] log likelihood: -20958.439892 EM: Round [67] log likelihood: -20958.412162 EM: Round [68] log likelihood: -20958.384691 EM: Round [69] log likelihood: -20958.357475 EM: Round [70] log likelihood: -20958.330508 EM: Round [71] log likelihood: -20958.303786 EM: Round [72] log likelihood: -20958.277304 EM: Round [73] log likelihood: -20958.251058 EM: Round [74] log likelihood: -20958.225043 EM: Round [75] log likelihood: -20958.199255 EM: Round [76] log likelihood: -20958.173691 EM: Round [77] log likelihood: -20958.148347 EM: Round [78] log likelihood: -20958.123219 EM: Round [79] log likelihood: -20958.098303 EM: Round [80] log likelihood: -20958.073597 EM: Round [81] log likelihood: -20958.049098 EM: Round [82] log likelihood: -20958.024801 EM: Round [83] log likelihood: -20958.000704 EM: Round [84] log likelihood: -20957.976804 EM: Round [85] log likelihood: -20957.953098 EM: Round [86] log likelihood: -20957.929583 EM: Round [87] log likelihood: -20957.906257 EM: Round [88] log likelihood: -20957.883116 EM: Round [89] log likelihood: -20957.860159 EM: Round [90] log likelihood: -20957.837382 EM: Round [91] log likelihood: -20957.814784 EM: Round [92] log likelihood: -20957.792361 EM: Round [93] log likelihood: -20957.770112 EM: Round [94] log likelihood: -20957.748033 EM: Round [95] log likelihood: -20957.726123 EM: Round [96] log likelihood: -20957.704380 EM: Round [97] log likelihood: -20957.682801 EM: Round [98] log likelihood: -20957.661384 EM: Round [99] log likelihood: -20957.640128 EM: Round [100] log likelihood: -20957.619029 EM: Round [101] log likelihood: -20957.598086 EM: Round [102] log likelihood: -20957.577298 EM: Round [103] log likelihood: -20957.556661 EM: Round [104] log likelihood: -20957.536175 EM: Round [105] log likelihood: -20957.515838 EM: Round [106] log likelihood: -20957.495646 EM: Round [107] log likelihood: -20957.475600 EM: Round [108] log likelihood: -20957.455697 EM: Round [109] log likelihood: -20957.435935 EM: Round [110] log likelihood: -20957.416312 EM: Round [111] log likelihood: -20957.396828 EM: Round [112] log likelihood: -20957.377480 EM: Round [113] log likelihood: -20957.358266 EM: Round [114] log likelihood: -20957.339186 EM: Round [115] log likelihood: -20957.320237 EM: Round [116] log likelihood: -20957.301419 EM: Round [117] log likelihood: -20957.282729 EM: Round [118] log likelihood: -20957.264166 EM: Round [119] log likelihood: -20957.245729 EM: Round [120] log likelihood: -20957.227416 EM: Round [121] log likelihood: -20957.209226 EM: Round [122] log likelihood: -20957.191157 EM: Round [123] log likelihood: -20957.173209 EM: Round [124] log likelihood: -20957.155379 EM: Round [125] log likelihood: -20957.137667 EM: Round [126] log likelihood: -20957.120071 EM: Round [127] log likelihood: -20957.102591 EM: Round [128] log likelihood: -20957.085223 EM: Round [129] log likelihood: -20957.067969 EM: Round [130] log likelihood: -20957.050825 EM: Round [131] log likelihood: -20957.033792 EM: Round [132] log likelihood: -20957.016868 EM: Round [133] log likelihood: -20957.000052 EM: Round [134] log likelihood: -20956.983342 EM: Round [135] log likelihood: -20956.966738 EM: Round [136] log likelihood: -20956.950238 EM: Round [137] log likelihood: -20956.933842 EM: Round [138] log likelihood: -20956.917548 EM: Round [139] log likelihood: -20956.901355 EM: Round [140] log likelihood: -20956.885262 EM: Round [141] log likelihood: -20956.869269 EM: Round [142] log likelihood: -20956.853374 EM: Round [143] log likelihood: -20956.837577 EM: Round [144] log likelihood: -20956.821875 EM: Round [145] log likelihood: -20956.806269 EM: Round [146] log likelihood: -20956.790757 EM: Round [147] log likelihood: -20956.775339 EM: Round [148] log likelihood: -20956.760014 EM: Round [149] log likelihood: -20956.744780 EM: Round [150] log likelihood: -20956.729636 EM: Round [151] log likelihood: -20956.714583 EM: Round [152] log likelihood: -20956.699619 EM: Round [153] log likelihood: -20956.684743 EM: Round [154] log likelihood: -20956.669954 EM: Round [155] log likelihood: -20956.655252 EM: Round [156] log likelihood: -20956.640635 EM: Round [157] log likelihood: -20956.626103 EM: Round [158] log likelihood: -20956.611656 EM: Round [159] log likelihood: -20956.597291 EM: Round [160] log likelihood: -20956.583010 EM: Round [161] log likelihood: -20956.568810 EM: Round [162] log likelihood: -20956.554691 EM: Round [163] log likelihood: -20956.540652 EM: Round [164] log likelihood: -20956.526693 EM: Round [165] log likelihood: -20956.512813 EM: Round [166] log likelihood: -20956.499011 EM: Round [167] log likelihood: -20956.485286 EM: Round [168] log likelihood: -20956.471638 EM: Round [169] log likelihood: -20956.458067 EM: Round [170] log likelihood: -20956.444570 EM: Round [171] log likelihood: -20956.431148 EM: Round [172] log likelihood: -20956.417801 EM: Round [173] log likelihood: -20956.404526 EM: Round [174] log likelihood: -20956.391325 EM: Round [175] log likelihood: -20956.378195 EM: Round [176] log likelihood: -20956.365138 EM: Round [177] log likelihood: -20956.352151 EM: Round [178] log likelihood: -20956.339234 EM: Round [179] log likelihood: -20956.326387 EM: Round [180] log likelihood: -20956.313609 EM: Round [181] log likelihood: -20956.300900 EM: Round [182] log likelihood: -20956.288258 EM: Round [183] log likelihood: -20956.275684 EM: Round [184] log likelihood: -20956.263177 EM: Round [185] log likelihood: -20956.250736 EM: Round [186] log likelihood: -20956.238360 EM: Round [187] log likelihood: -20956.226050 EM: Round [188] log likelihood: -20956.213805 EM: Round [189] log likelihood: -20956.201623 EM: Round [190] log likelihood: -20956.189505 EM: Round [191] log likelihood: -20956.177450 EM: Round [192] log likelihood: -20956.165458 EM: Round [193] log likelihood: -20956.153527 EM: Round [194] log likelihood: -20956.141658 EM: Round [195] log likelihood: -20956.129851 EM: Round [196] log likelihood: -20956.118103 EM: Round [197] log likelihood: -20956.106416 EM: Round [198] log likelihood: -20956.094788 EM: Round [199] log likelihood: -20956.083220 EM: Round [200] log likelihood: -20956.071710 EM: Round [201] log likelihood: -20956.060258 EM: Round [202] log likelihood: -20956.048864 EM: Round [203] log likelihood: -20956.037527 EM: Round [204] log likelihood: -20956.026247 EM: Round [205] log likelihood: -20956.015024 EM: Round [206] log likelihood: -20956.003856 EM: Round [207] log likelihood: -20955.992744 EM: Round [208] log likelihood: -20955.981687 EM: Round [209] log likelihood: -20955.970685 EM: Round [210] log likelihood: -20955.959737 EM: Round [211] log likelihood: -20955.948843 EM: Round [212] log likelihood: -20955.938002 EM: Round [213] log likelihood: -20955.927214 EM: Round [214] log likelihood: -20955.916479 EM: Round [215] log likelihood: -20955.905796 EM: Round [216] log likelihood: -20955.895166 EM: Round [217] log likelihood: -20955.884586 EM: Round [218] log likelihood: -20955.874058 EM: Round [219] log likelihood: -20955.863580 EM: Round [220] log likelihood: -20955.853153 EM: Round [221] log likelihood: -20955.842776 EM: Round [222] log likelihood: -20955.832448 EM: Round [223] log likelihood: -20955.822169 EM: Round [224] log likelihood: -20955.811940 EM: Round [225] log likelihood: -20955.801759 EM: Round [226] log likelihood: -20955.791626 EM: Round [227] log likelihood: -20955.781541 EM: Round [228] log likelihood: -20955.771504 EM: Round [229] log likelihood: -20955.761514 EM: Round [230] log likelihood: -20955.751570 EM: Round [231] log likelihood: -20955.741673 EM: Round [232] log likelihood: -20955.731823 EM: Round [233] log likelihood: -20955.722018 EM: Round [234] log likelihood: -20955.712258 EM: Round [235] log likelihood: -20955.702544 EM: Round [236] log likelihood: -20955.692875 EM: Round [237] log likelihood: -20955.683250 EM: Round [238] log likelihood: -20955.673670 EM: Round [239] log likelihood: -20955.664133 EM: Round [240] log likelihood: -20955.654641 EM: Round [241] log likelihood: -20955.645191 EM: Round [242] log likelihood: -20955.635785 EM: Round [243] log likelihood: -20955.626421 EM: Round [244] log likelihood: -20955.617100 EM: Round [245] log likelihood: -20955.607821 EM: Round [246] log likelihood: -20955.598584 EM: Round [247] log likelihood: -20955.589389 EM: Round [248] log likelihood: -20955.580235 EM: Round [249] log likelihood: -20955.571122 EM: Round [250] log likelihood: -20955.562050 EM: Round [251] log likelihood: -20955.553018 EM: Round [252] log likelihood: -20955.544027 EM: Round [253] log likelihood: -20955.535076 EM: Round [254] log likelihood: -20955.526164 EM: Round [255] log likelihood: -20955.517292 EM: Round [256] log likelihood: -20955.508459 EM: Round [257] log likelihood: -20955.499665 EM: Round [258] log likelihood: -20955.490909 EM: Round [259] log likelihood: -20955.482193 EM: Round [260] log likelihood: -20955.473514 EM: Round [261] log likelihood: -20955.464873 EM: Round [262] log likelihood: -20955.456270 EM: Round [263] log likelihood: -20955.447705 EM: Round [264] log likelihood: -20955.439176 EM: Round [265] log likelihood: -20955.430685 EM: Round [266] log likelihood: -20955.422230 EM: Round [267] log likelihood: -20955.413812 EM: Round [268] log likelihood: -20955.405430 EM: Round [269] log likelihood: -20955.397085 EM: Round [270] log likelihood: -20955.388775 EM: Round [271] log likelihood: -20955.380500 EM: Round [272] log likelihood: -20955.372261 EM: Round [273] log likelihood: -20955.364057 EM: Round [274] log likelihood: -20955.355889 EM: Round [275] log likelihood: -20955.347754 EM: Round [276] log likelihood: -20955.339655 EM: Round [277] log likelihood: -20955.331589 EM: Round [278] log likelihood: -20955.323558 EM: Round [279] log likelihood: -20955.315561 EM: Round [280] log likelihood: -20955.307597 EM: Round [281] log likelihood: -20955.299667 EM: Round [282] log likelihood: -20955.291770 EM: Round [283] log likelihood: -20955.283906 EM: Round [284] log likelihood: -20955.276074 EM: Round [285] log likelihood: -20955.268276 EM: Round [286] log likelihood: -20955.260510 EM: Round [287] log likelihood: -20955.252776 EM: Round [288] log likelihood: -20955.245074 EM: Round [289] log likelihood: -20955.237405 EM: Round [290] log likelihood: -20955.229766 EM: Round [291] log likelihood: -20955.222160 EM: Round [292] log likelihood: -20955.214584 EM: Round [293] log likelihood: -20955.207040 EM: Round [294] log likelihood: -20955.199527 EM: Round [295] log likelihood: -20955.192044 EM: Round [296] log likelihood: -20955.184592 EM: Round [297] log likelihood: -20955.177171 EM: Round [298] log likelihood: -20955.169779 EM: Round [299] log likelihood: -20955.162418 EM: Round [300] log likelihood: -20955.155086 EM: Round [301] log likelihood: -20955.147785 EM: Round [302] log likelihood: -20955.140512 EM: Round [303] log likelihood: -20955.133270 EM: Round [304] log likelihood: -20955.126056 EM: Round [305] log likelihood: -20955.118871 EM: Round [306] log likelihood: -20955.111715 EM: Round [307] log likelihood: -20955.104588 EM: Round [308] log likelihood: -20955.097489 EM: Round [309] log likelihood: -20955.090419 EM: Round [310] log likelihood: -20955.083377 EM: Round [311] log likelihood: -20955.076363 EM: Round [312] log likelihood: -20955.069376 EM: Round [313] log likelihood: -20955.062418 EM: Round [314] log likelihood: -20955.055487 EM: Round [315] log likelihood: -20955.048583 EM: Round [316] log likelihood: -20955.041707 EM: Round [317] log likelihood: -20955.034858 EM: Round [318] log likelihood: -20955.028036 EM: Round [319] log likelihood: -20955.021240 EM: Round [320] log likelihood: -20955.014471 EM: Round [321] log likelihood: -20955.007729 EM: Round [322] log likelihood: -20955.001013 EM: Round [323] log likelihood: -20954.994323 EM: Round [324] log likelihood: -20954.987660 EM: Round [325] log likelihood: -20954.981022 EM: Round [326] log likelihood: -20954.974410 EM: Round [327] log likelihood: -20954.967824 EM: Round [328] log likelihood: -20954.961263 EM: Round [329] log likelihood: -20954.954727 EM: Round [330] log likelihood: -20954.948217 EM: Round [331] log likelihood: -20954.941732 EM: Round [332] log likelihood: -20954.935272 EM: Round [333] log likelihood: -20954.928836 EM: Round [334] log likelihood: -20954.922426 EM: Round [335] log likelihood: -20954.916040 EM: Round [336] log likelihood: -20954.909678 EM: Round [337] log likelihood: -20954.903340 EM: Round [338] log likelihood: -20954.897027 EM: Round [339] log likelihood: -20954.890738 EM: Round [340] log likelihood: -20954.884473 EM: Round [341] log likelihood: -20954.878231 EM: Round [342] log likelihood: -20954.872013 EM: Round [343] log likelihood: -20954.865819 EM: Round [344] log likelihood: -20954.859648 EM: Round [345] log likelihood: -20954.853500 EM: Round [346] log likelihood: -20954.847376 EM: Round [347] log likelihood: -20954.841274 EM: Round [348] log likelihood: -20954.835195 EM: Round [349] log likelihood: -20954.829140 EM: Round [350] log likelihood: -20954.823107 EM: Round [351] log likelihood: -20954.817096 EM: Round [352] log likelihood: -20954.811108 EM: Round [353] log likelihood: -20954.805142 EM: Round [354] log likelihood: -20954.799199 EM: Round [355] log likelihood: -20954.793277 EM: Round [356] log likelihood: -20954.787378 EM: Round [357] log likelihood: -20954.781500 EM: Round [358] log likelihood: -20954.775645 EM: Round [359] log likelihood: -20954.769810 EM: Round [360] log likelihood: -20954.763998 EM: Round [361] log likelihood: -20954.758207 EM: Round [362] log likelihood: -20954.752437 EM: Round [363] log likelihood: -20954.746688 EM: Round [364] log likelihood: -20954.740961 EM: Round [365] log likelihood: -20954.735254 EM: Round [366] log likelihood: -20954.729569 EM: Round [367] log likelihood: -20954.723904 EM: Round [368] log likelihood: -20954.718260 EM: Round [369] log likelihood: -20954.712636 EM: Round [370] log likelihood: -20954.707033 EM: Round [371] log likelihood: -20954.701450 EM: Round [372] log likelihood: -20954.695888 EM: Round [373] log likelihood: -20954.690346 EM: Round [374] log likelihood: -20954.684824 EM: Round [375] log likelihood: -20954.679322 EM: Round [376] log likelihood: -20954.673839 EM: Round [377] log likelihood: -20954.668377 EM: Round [378] log likelihood: -20954.662934 EM: Round [379] log likelihood: -20954.657511 EM: Round [380] log likelihood: -20954.652107 EM: Round [381] log likelihood: -20954.646723 EM: Round [382] log likelihood: -20954.641358 EM: Round [383] log likelihood: -20954.636012 EM: Round [384] log likelihood: -20954.630685 EM: Round [385] log likelihood: -20954.625378 EM: Round [386] log likelihood: -20954.620089 EM: Round [387] log likelihood: -20954.614819 EM: Round [388] log likelihood: -20954.609568 EM: Round [389] log likelihood: -20954.604336 EM: Round [390] log likelihood: -20954.599122 EM: Round [391] log likelihood: -20954.593927 EM: Round [392] log likelihood: -20954.588750 EM: Round [393] log likelihood: -20954.583591 EM: Round [394] log likelihood: -20954.578450 EM: Round [395] log likelihood: -20954.573328 EM: Round [396] log likelihood: -20954.568224 EM: Round [397] log likelihood: -20954.563138 EM: Round [398] log likelihood: -20954.558069 EM: Round [399] log likelihood: -20954.553019 EM: Round [400] log likelihood: -20954.547986 EM: Round [401] log likelihood: -20954.542970 EM: Round [402] log likelihood: -20954.537973 EM: Round [403] log likelihood: -20954.532992 EM: Round [404] log likelihood: -20954.528029 EM: Round [405] log likelihood: -20954.523084 EM: Round [406] log likelihood: -20954.518155 EM: Round [407] log likelihood: -20954.513244 EM: Round [408] log likelihood: -20954.508350 EM: Round [409] log likelihood: -20954.503473 EM: Round [410] log likelihood: -20954.498613 EM: Round [411] log likelihood: -20954.493769 EM: Round [412] log likelihood: -20954.488942 EM: Round [413] log likelihood: -20954.484132 EM: Round [414] log likelihood: -20954.479339 EM: Round [415] log likelihood: -20954.474562 EM: Round [416] log likelihood: -20954.469801 EM: Round [417] log likelihood: -20954.465057 EM: Round [418] log likelihood: 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Round [657] log likelihood: -20953.672526 EM: Round [658] log likelihood: -20953.670278 EM: Round [659] log likelihood: -20953.668037 EM: Round [660] log likelihood: -20953.665803 EM: Round [661] log likelihood: -20953.663574 EM: Round [662] log likelihood: -20953.661352 EM: Round [663] log likelihood: -20953.659137 EM: Round [664] log likelihood: -20953.656927 EM: Round [665] log likelihood: -20953.654724 EM: Round [666] log likelihood: -20953.652528 EM: Round [667] log likelihood: -20953.650337 EM: Round [668] log likelihood: -20953.648153 EM: Round [669] log likelihood: -20953.645974 EM: Round [670] log likelihood: -20953.643802 EM: Round [671] log likelihood: -20953.641636 EM: Round [672] log likelihood: -20953.639477 EM: Round [673] log likelihood: -20953.637323 EM: Round [674] log likelihood: -20953.635175 EM: Round [675] log likelihood: -20953.633034 EM: Round [676] log likelihood: -20953.630898 EM: Round [677] log likelihood: -20953.628769 EM: Round [678] log likelihood: 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Round [852] log likelihood: -20953.333458 EM: Round [853] log likelihood: -20953.332139 EM: Round [854] log likelihood: -20953.330823 EM: Round [855] log likelihood: -20953.329510 EM: Round [856] log likelihood: -20953.328201 EM: Round [857] log likelihood: -20953.326895 EM: Round [858] log likelihood: -20953.325592 EM: Round [859] log likelihood: -20953.324293 EM: Round [860] log likelihood: -20953.322998 EM: Round [861] log likelihood: -20953.321705 EM: Round [862] log likelihood: -20953.320417 EM: Round [863] log likelihood: -20953.319131 EM: Round [864] log likelihood: -20953.317849 EM: Round [865] log likelihood: -20953.316570 EM: Round [866] log likelihood: -20953.315295 EM: Round [867] log likelihood: -20953.314023 EM: Round [868] log likelihood: -20953.312754 EM: Round [869] log likelihood: -20953.311489 EM: Round [870] log likelihood: -20953.310227 EM: Round [871] log likelihood: -20953.308968 EM: Round [872] log likelihood: -20953.307712 EM: Round [873] log likelihood: -20953.306460 EM: Round [874] log likelihood: -20953.305211 EM: Round [875] log likelihood: -20953.303966 EM: Round [876] log likelihood: -20953.302723 EM: Round [877] log likelihood: -20953.301484 EM: Round [878] log likelihood: -20953.300248 EM: Round [879] log likelihood: -20953.299015 EM: Round [880] log likelihood: -20953.297786 EM: Round [881] log likelihood: -20953.296559 EM: Round [882] log likelihood: -20953.295336 EM: Round [883] log likelihood: -20953.294116 EM: Round [884] log likelihood: -20953.292900 EM: Round [885] log likelihood: -20953.291686 EM: Round [886] log likelihood: -20953.290476 EM: Round [887] log likelihood: -20953.289268 EM: Round [888] log likelihood: -20953.288064 EM: Round [889] log likelihood: -20953.286863 EM: Round [890] log likelihood: -20953.285665 EM: Round [891] log likelihood: -20953.284471 EM: Round [892] log likelihood: -20953.283279 EM: Round [893] log likelihood: -20953.282090 EM: Round [894] log likelihood: -20953.280905 EM: Round [895] log likelihood: -20953.279723 EM: Round [896] log likelihood: -20953.278543 EM: Round [897] log likelihood: -20953.277367 EM: Round [898] log likelihood: -20953.276194 EM: Round [899] log likelihood: -20953.275024 EM: Round [900] log likelihood: -20953.273856 EM: Round [901] log likelihood: -20953.272692 EM: Round [902] log likelihood: -20953.271531 EM: Round [903] log likelihood: -20953.270373 EM: Round [904] log likelihood: -20953.269218 EM: Round [905] log likelihood: -20953.268066 EM: Round [906] log likelihood: -20953.266917 EM: Round [907] log likelihood: -20953.265771 EM: Round [908] log likelihood: -20953.264627 EM: Round [909] log likelihood: -20953.263487 EM: Round [910] log likelihood: -20953.262350 EM: Round [911] log likelihood: -20953.261216 EM: Round [912] log likelihood: -20953.260084 EM: Round [913] log likelihood: -20953.258956 EM: Round [914] log likelihood: -20953.257830 EM: Round [915] log likelihood: -20953.256707 EM: Round [916] log likelihood: -20953.255588 EM: Round [917] log likelihood: -20953.254471 EM: Round [918] log likelihood: -20953.253357 EM: Round [919] log likelihood: -20953.252246 EM: Round [920] log likelihood: -20953.251137 EM: Round [921] log likelihood: -20953.250032 EM: Round [922] log likelihood: -20953.248929 EM: Round [923] log likelihood: -20953.247830 EM: Round [924] log likelihood: -20953.246733 EM: Round [925] log likelihood: -20953.245639 EM: Round [926] log likelihood: -20953.244547 EM: Round [927] log likelihood: -20953.243459 EM: Round [928] log likelihood: -20953.242373 EM: Round [929] log likelihood: -20953.241291 EM: Round [930] log likelihood: -20953.240211 EM: Round [931] log likelihood: -20953.239133 EM: Round [932] log likelihood: -20953.238059 EM: Round [933] log likelihood: -20953.236987 EM: Round [934] log likelihood: -20953.235918 EM: Round [935] log likelihood: -20953.234852 EM: Round [936] log likelihood: -20953.233788 EM: Round [937] log likelihood: -20953.232728 EM: Round [938] log likelihood: -20953.231669 EM: Round [939] log likelihood: -20953.230614 EM: Round [940] log likelihood: -20953.229561 EM: Round [941] log likelihood: -20953.228512 EM: Round [942] log likelihood: -20953.227464 EM: Round [943] log likelihood: -20953.226420 EM: Round [944] log likelihood: -20953.225378 EM: Round [945] log likelihood: -20953.224339 EM: Round [946] log likelihood: -20953.223302 EM: Round [947] log likelihood: -20953.222268 EM: Round [948] log likelihood: -20953.221237 EM: Round [949] log likelihood: -20953.220208 EM: Round [950] log likelihood: -20953.219182 EM: Round [951] log likelihood: -20953.218159 EM: Round [952] log likelihood: -20953.217138 EM: Round [953] log likelihood: -20953.216120 EM: Round [954] log likelihood: -20953.215105 EM: Round [955] log likelihood: -20953.214092 EM: Round [956] log likelihood: -20953.213081 EM: Round [957] log likelihood: -20953.212074 EM: Round [958] log likelihood: -20953.211069 EM: Round [959] log likelihood: -20953.210066 EM: Round [960] log likelihood: -20953.209066 EM: Round [961] log likelihood: -20953.208068 EM: Round [962] log likelihood: -20953.207073 EM: Round [963] log likelihood: -20953.206081 EM: Round [964] log likelihood: -20953.205091 EM: Round [965] log likelihood: -20953.204104 EM: Round [966] log likelihood: -20953.203119 EM: Round [967] log likelihood: -20953.202137 EM: Round [968] log likelihood: -20953.201157 EM: Round [969] log likelihood: -20953.200179 EM: Round [970] log likelihood: -20953.199205 EM: Round [971] log likelihood: -20953.198232 EM: Round [972] log likelihood: -20953.197262 EM: Round [973] log likelihood: -20953.196295 EM: Round [974] log likelihood: -20953.195330 EM: Round [975] log likelihood: -20953.194367 EM: Round [976] log likelihood: -20953.193407 EM: Round [977] log likelihood: -20953.192450 EM: Round [978] log likelihood: -20953.191495 EM: Round [979] log likelihood: -20953.190542 EM: Round [980] log likelihood: -20953.189592 EM: Round [981] log likelihood: -20953.188644 EM: Round [982] log likelihood: -20953.187698 EM: Round [983] log likelihood: -20953.186755 EM: Round [984] log likelihood: -20953.185814 EM: Round [985] log likelihood: -20953.184876 EM: Round [986] log likelihood: -20953.183940 EM: Round [987] log likelihood: -20953.183006 EM: Round [988] log likelihood: -20953.182075 EM: Round [989] log likelihood: -20953.181146 EM: Round [990] log likelihood: -20953.180220 EM: Round [991] log likelihood: -20953.179296 EM: Round [992] log likelihood: -20953.178374 EM: Round [993] log likelihood: -20953.177455 EM: Round [994] log likelihood: -20953.176537 EM: Round [995] log likelihood: -20953.175623 EM: Round [996] log likelihood: -20953.174710 EM: Round [997] log likelihood: -20953.173800 EM: Round [998] log likelihood: -20953.172892 EM: Round [999] log likelihood: -20953.171986 EM: Round [1000] log likelihood: -20953.171083 EM: Round [1001] log likelihood: -20953.170182 Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam" Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam into /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.86 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa > /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir -done, see /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -20205.185293 EM: Round [1] log likelihood: -20204.696221 EM: Round [2] log likelihood: -20204.661028 EM: Round [3] log likelihood: -20204.626667 EM: Round [4] log likelihood: -20204.592730 EM: Round [5] log likelihood: -20204.559205 EM: Round [6] log likelihood: -20204.526082 EM: Round [7] log likelihood: -20204.493354 EM: Round [8] log likelihood: -20204.461010 EM: Round [9] log likelihood: -20204.429044 EM: Round [10] log likelihood: -20204.397446 EM: Round [11] log likelihood: -20204.366209 EM: Round [12] log likelihood: -20204.335325 EM: Round [13] log likelihood: -20204.304787 EM: Round [14] log likelihood: -20204.274588 EM: Round [15] log likelihood: -20204.244720 EM: Round [16] log likelihood: -20204.215178 EM: Round [17] log likelihood: -20204.185955 EM: Round [18] log likelihood: -20204.157044 EM: Round [19] log likelihood: -20204.128439 EM: Round [20] log likelihood: -20204.100135 EM: Round [21] log likelihood: -20204.072126 EM: Round [22] log likelihood: -20204.044405 EM: Round [23] log likelihood: -20204.016968 EM: Round [24] log likelihood: -20203.989809 EM: Round [25] log likelihood: -20203.962924 EM: Round [26] log likelihood: -20203.936307 EM: Round [27] log likelihood: -20203.909953 EM: Round [28] log likelihood: -20203.883858 EM: Round [29] log likelihood: -20203.858016 EM: Round [30] log likelihood: -20203.832425 EM: Round [31] log likelihood: -20203.807078 EM: Round [32] log likelihood: -20203.781973 EM: Round [33] log likelihood: -20203.757104 EM: Round [34] log likelihood: -20203.732469 EM: Round [35] log likelihood: -20203.708062 EM: Round [36] log likelihood: -20203.683880 EM: Round [37] log likelihood: -20203.659919 EM: Round [38] log likelihood: -20203.636177 EM: Round [39] log likelihood: -20203.612648 EM: Round [40] log likelihood: -20203.589330 EM: Round [41] log likelihood: -20203.566220 EM: Round [42] log likelihood: -20203.543313 EM: Round [43] log likelihood: -20203.520607 EM: Round [44] log likelihood: -20203.498099 EM: Round [45] log likelihood: -20203.475786 EM: Round [46] log likelihood: -20203.453664 EM: Round [47] log likelihood: -20203.431731 EM: Round [48] log likelihood: -20203.409984 EM: Round [49] log likelihood: -20203.388420 EM: Round [50] log likelihood: -20203.367036 EM: Round [51] log likelihood: -20203.345830 EM: Round [52] log likelihood: -20203.324799 EM: Round [53] log likelihood: -20203.303940 EM: Round [54] log likelihood: -20203.283252 EM: Round [55] log likelihood: -20203.262731 EM: Round [56] log likelihood: -20203.242375 EM: Round [57] log likelihood: -20203.222182 EM: Round [58] log likelihood: -20203.202150 EM: Round [59] log likelihood: -20203.182276 EM: Round [60] log likelihood: -20203.162558 EM: Round [61] log likelihood: -20203.142994 EM: Round [62] log likelihood: -20203.123581 EM: Round [63] log likelihood: -20203.104319 EM: Round [64] log likelihood: -20203.085204 EM: Round [65] log likelihood: -20203.066236 EM: Round [66] log likelihood: -20203.047411 EM: Round [67] log likelihood: -20203.028728 EM: Round [68] log likelihood: -20203.010185 EM: Round [69] log likelihood: -20202.991781 EM: Round [70] log likelihood: -20202.973513 EM: Round [71] log likelihood: -20202.955379 EM: Round [72] log likelihood: -20202.937379 EM: Round [73] log likelihood: -20202.919510 EM: Round [74] log likelihood: -20202.901771 EM: Round [75] log likelihood: -20202.884160 EM: Round [76] log likelihood: -20202.866675 EM: Round [77] log likelihood: -20202.849315 EM: Round [78] log likelihood: -20202.832079 EM: Round [79] log likelihood: -20202.814964 EM: Round [80] log likelihood: -20202.797970 EM: Round [81] log likelihood: -20202.781094 EM: Round [82] log likelihood: -20202.764337 EM: Round [83] log likelihood: -20202.747695 EM: Round [84] log likelihood: -20202.731168 EM: Round [85] log likelihood: -20202.714754 EM: Round [86] log likelihood: -20202.698453 EM: Round [87] log likelihood: -20202.682262 EM: Round [88] log likelihood: -20202.666181 EM: Round [89] log likelihood: -20202.650207 EM: Round [90] log likelihood: -20202.634341 EM: Round [91] log likelihood: -20202.618581 EM: Round [92] log likelihood: -20202.602925 EM: Round [93] log likelihood: -20202.587372 EM: Round [94] log likelihood: -20202.571922 EM: Round [95] log likelihood: -20202.556573 EM: Round [96] log likelihood: -20202.541323 EM: Round [97] log likelihood: -20202.526173 EM: Round [98] log likelihood: -20202.511120 EM: Round [99] log likelihood: -20202.496165 EM: Round [100] log likelihood: -20202.481304 EM: Round [101] log likelihood: -20202.466539 EM: Round [102] log likelihood: -20202.451867 EM: Round [103] log likelihood: -20202.437288 EM: Round [104] log likelihood: -20202.422800 EM: Round [105] log likelihood: -20202.408403 EM: Round [106] log likelihood: -20202.394096 EM: Round [107] log likelihood: -20202.379878 EM: Round [108] log likelihood: -20202.365747 EM: Round [109] log likelihood: -20202.351704 EM: Round [110] log likelihood: -20202.337746 EM: Round [111] log likelihood: -20202.323874 EM: Round [112] log likelihood: -20202.310086 EM: Round [113] log likelihood: -20202.296382 EM: Round [114] log likelihood: -20202.282760 EM: Round [115] log likelihood: -20202.269220 EM: Round [116] log likelihood: -20202.255762 EM: Round [117] log likelihood: -20202.242383 EM: Round [118] log likelihood: -20202.229084 EM: Round [119] log likelihood: -20202.215863 EM: Round [120] log likelihood: -20202.202721 EM: Round [121] log likelihood: -20202.189655 EM: Round [122] log likelihood: -20202.176666 EM: Round [123] log likelihood: -20202.163753 EM: Round [124] log likelihood: -20202.150914 EM: Round [125] log likelihood: -20202.138150 EM: Round [126] log likelihood: -20202.125459 EM: Round [127] log likelihood: -20202.112841 EM: Round [128] log likelihood: -20202.100295 EM: Round [129] log likelihood: -20202.087820 EM: Round [130] log likelihood: -20202.075417 EM: Round [131] log likelihood: -20202.063083 EM: Round [132] log likelihood: -20202.050819 EM: Round [133] log likelihood: -20202.038624 EM: Round [134] log likelihood: -20202.026497 EM: Round [135] log likelihood: -20202.014438 EM: Round [136] log likelihood: -20202.002445 EM: Round [137] log likelihood: -20201.990519 EM: Round [138] log likelihood: -20201.978659 EM: Round [139] log likelihood: -20201.966864 EM: Round [140] log likelihood: -20201.955134 EM: Round [141] log likelihood: -20201.943468 EM: Round [142] log likelihood: -20201.931865 EM: Round [143] log likelihood: -20201.920325 EM: Round [144] log likelihood: -20201.908847 EM: Round [145] log likelihood: -20201.897431 EM: Round [146] log likelihood: -20201.886077 EM: Round [147] log likelihood: -20201.874783 EM: Round [148] log likelihood: -20201.863550 EM: Round [149] log likelihood: -20201.852376 EM: Round [150] log likelihood: -20201.841262 EM: Round [151] log likelihood: -20201.830206 EM: Round [152] log likelihood: -20201.819209 EM: Round [153] log likelihood: -20201.808269 EM: Round [154] log likelihood: -20201.797386 EM: Round [155] log likelihood: -20201.786561 EM: Round [156] log likelihood: -20201.775791 EM: Round [157] log likelihood: -20201.765078 EM: Round [158] log likelihood: -20201.754419 EM: Round [159] log likelihood: -20201.743816 EM: Round [160] log likelihood: -20201.733267 EM: Round [161] log likelihood: -20201.722772 EM: Round [162] log likelihood: -20201.712331 EM: Round [163] log likelihood: -20201.701943 EM: Round [164] log likelihood: -20201.691608 EM: Round [165] log likelihood: -20201.681325 EM: Round [166] log likelihood: -20201.671093 EM: Round [167] log likelihood: -20201.660914 EM: Round [168] log likelihood: -20201.650785 EM: Round [169] log likelihood: -20201.640707 EM: Round [170] log likelihood: -20201.630679 EM: Round [171] log likelihood: -20201.620701 EM: Round [172] log likelihood: -20201.610773 EM: Round [173] log likelihood: -20201.600894 EM: Round [174] log likelihood: -20201.591063 EM: Round [175] log likelihood: -20201.581281 EM: Round [176] log likelihood: -20201.571546 EM: Round [177] log likelihood: -20201.561860 EM: Round [178] log likelihood: -20201.552220 EM: Round [179] log likelihood: -20201.542628 EM: Round [180] log likelihood: -20201.533082 EM: Round [181] log likelihood: -20201.523582 EM: Round [182] log likelihood: -20201.514127 EM: Round [183] log likelihood: -20201.504719 EM: Round [184] log likelihood: -20201.495355 EM: Round [185] log likelihood: -20201.486037 EM: Round [186] log likelihood: -20201.476762 EM: Round [187] log likelihood: -20201.467532 EM: Round [188] log likelihood: -20201.458346 EM: Round [189] log likelihood: -20201.449203 EM: Round [190] log likelihood: -20201.440103 EM: Round [191] log likelihood: -20201.431047 EM: Round [192] log likelihood: -20201.422032 EM: Round [193] log likelihood: -20201.413060 EM: Round [194] log likelihood: -20201.404130 EM: Round [195] log likelihood: -20201.395242 EM: Round [196] log likelihood: -20201.386395 EM: Round [197] log likelihood: -20201.377589 EM: Round [198] log likelihood: -20201.368823 EM: Round [199] log likelihood: -20201.360098 EM: Round [200] log likelihood: -20201.351414 EM: Round [201] log likelihood: -20201.342769 EM: Round [202] log likelihood: -20201.334164 EM: Round [203] log likelihood: -20201.325598 EM: Round [204] log likelihood: -20201.317071 EM: 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likelihood: -20199.489194 EM: Round [639] log likelihood: -20199.487225 EM: Round [640] log likelihood: -20199.485261 EM: Round [641] log likelihood: -20199.483303 EM: Round [642] log likelihood: -20199.481350 EM: Round [643] log likelihood: -20199.479402 EM: Round [644] log likelihood: -20199.477460 EM: Round [645] log likelihood: -20199.475523 EM: Round [646] log likelihood: -20199.473591 EM: Round [647] log likelihood: -20199.471665 EM: Round [648] log likelihood: -20199.469744 EM: Round [649] log likelihood: -20199.467828 EM: Round [650] log likelihood: -20199.465918 EM: Round [651] log likelihood: -20199.464013 EM: Round [652] log likelihood: -20199.462113 EM: Round [653] log likelihood: -20199.460218 EM: Round [654] log likelihood: -20199.458328 EM: Round [655] log likelihood: -20199.456444 EM: Round [656] log likelihood: -20199.454564 EM: Round [657] log likelihood: -20199.452690 EM: Round [658] log likelihood: -20199.450821 EM: Round [659] log likelihood: -20199.448957 EM: 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-20199.409208 EM: Round [682] log likelihood: -20199.407457 EM: Round [683] log likelihood: -20199.405711 EM: Round [684] log likelihood: -20199.403969 EM: Round [685] log likelihood: -20199.402232 EM: Round [686] log likelihood: -20199.400500 EM: Round [687] log likelihood: -20199.398773 EM: Round [688] log likelihood: -20199.397050 EM: Round [689] log likelihood: -20199.395332 EM: Round [690] log likelihood: -20199.393618 EM: Round [691] log likelihood: -20199.391909 EM: Round [692] log likelihood: -20199.390205 EM: Round [693] log likelihood: -20199.388505 EM: Round [694] log likelihood: -20199.386810 EM: Round [695] log likelihood: -20199.385119 EM: Round [696] log likelihood: -20199.383433 EM: Round [697] log likelihood: -20199.381751 EM: Round [698] log likelihood: -20199.380074 EM: Round [699] log likelihood: -20199.378401 EM: Round [700] log likelihood: -20199.376733 EM: Round [701] log likelihood: -20199.375069 EM: Round [702] log likelihood: -20199.373410 EM: Round [703] log likelihood: -20199.371755 EM: Round [704] log likelihood: -20199.370105 EM: Round [705] log likelihood: -20199.368459 EM: Round [706] log likelihood: -20199.366817 EM: Round [707] log likelihood: -20199.365180 EM: Round [708] log likelihood: -20199.363547 EM: Round [709] log likelihood: -20199.361919 EM: Round [710] log likelihood: -20199.360295 EM: Round [711] log likelihood: -20199.358675 EM: Round [712] log likelihood: -20199.357059 EM: Round [713] log likelihood: -20199.355448 EM: Round [714] log likelihood: -20199.353841 EM: Round [715] log likelihood: -20199.352239 EM: Round [716] log likelihood: -20199.350640 EM: Round [717] log likelihood: -20199.349046 EM: Round [718] log likelihood: -20199.347456 EM: Round [719] log likelihood: -20199.345871 EM: Round [720] log likelihood: -20199.344289 EM: Round [721] log likelihood: -20199.342712 EM: Round [722] log likelihood: -20199.341139 EM: Round [723] log likelihood: -20199.339570 EM: Round [724] log likelihood: -20199.338005 EM: Round [725] log likelihood: -20199.336445 EM: Round [726] log likelihood: -20199.334888 EM: Round [727] log likelihood: -20199.333336 EM: Round [728] log likelihood: -20199.331788 EM: Round [729] log likelihood: -20199.330244 EM: Round [730] log likelihood: -20199.328704 EM: Round [731] log likelihood: -20199.327168 EM: Round [732] log likelihood: -20199.325636 EM: Round [733] log likelihood: -20199.324108 EM: Round [734] log likelihood: -20199.322584 EM: Round [735] log likelihood: -20199.321064 EM: Round [736] log likelihood: -20199.319549 EM: Round [737] log likelihood: -20199.318037 EM: Round [738] log likelihood: -20199.316529 EM: Round [739] log likelihood: -20199.315025 EM: Round [740] log likelihood: -20199.313525 EM: Round [741] log likelihood: -20199.312029 EM: Round [742] log likelihood: -20199.310537 EM: Round [743] log likelihood: -20199.309049 EM: Round [744] log likelihood: -20199.307565 EM: Round [745] log likelihood: -20199.306085 EM: Round [746] log likelihood: -20199.304609 EM: Round [747] log likelihood: -20199.303136 EM: Round [748] log likelihood: -20199.301667 EM: Round [749] log likelihood: -20199.300203 EM: Round [750] log likelihood: -20199.298742 EM: Round [751] log likelihood: -20199.297285 EM: Round [752] log likelihood: -20199.295831 EM: Round [753] log likelihood: -20199.294382 EM: Round [754] log likelihood: -20199.292936 EM: Round [755] log likelihood: -20199.291494 EM: Round [756] log likelihood: -20199.290056 EM: Round [757] log likelihood: -20199.288622 EM: Round [758] log likelihood: -20199.287191 EM: Round [759] log likelihood: -20199.285765 EM: Round [760] log likelihood: -20199.284342 EM: Round [761] log likelihood: -20199.282922 EM: Round [762] log likelihood: -20199.281506 EM: Round [763] log likelihood: -20199.280094 EM: Round [764] log likelihood: -20199.278686 EM: Round [765] log likelihood: -20199.277282 EM: Round [766] log likelihood: -20199.275881 EM: Round [767] log likelihood: -20199.274483 EM: Round [768] log likelihood: -20199.273090 EM: Round [769] log likelihood: -20199.271700 EM: Round [770] log likelihood: -20199.270313 EM: Round [771] log likelihood: -20199.268930 EM: Round [772] log likelihood: -20199.267551 EM: Round [773] log likelihood: -20199.266175 EM: Round [774] log likelihood: -20199.264803 EM: Round [775] log likelihood: -20199.263435 EM: Round [776] log likelihood: -20199.262070 EM: Round [777] log likelihood: -20199.260709 EM: Round [778] log likelihood: -20199.259351 EM: Round [779] log likelihood: -20199.257996 EM: Round [780] log likelihood: -20199.256646 EM: Round [781] log likelihood: -20199.255298 EM: Round [782] log likelihood: -20199.253955 EM: Round [783] log likelihood: -20199.252614 EM: Round [784] log likelihood: -20199.251277 EM: Round [785] log likelihood: -20199.249944 EM: Round [786] log likelihood: -20199.248614 EM: Round [787] log likelihood: -20199.247288 EM: Round [788] log likelihood: -20199.245964 EM: Round [789] log likelihood: -20199.244645 EM: Round [790] log likelihood: -20199.243329 EM: Round [791] log likelihood: -20199.242016 EM: Round [792] log likelihood: -20199.240706 EM: Round [793] log likelihood: -20199.239400 EM: Round [794] log likelihood: -20199.238098 EM: Round [795] log likelihood: -20199.236798 EM: Round [796] log likelihood: -20199.235502 EM: Round [797] log likelihood: -20199.234210 EM: Round [798] log likelihood: -20199.232920 EM: Round [799] log likelihood: -20199.231634 EM: Round [800] log likelihood: -20199.230352 EM: Round [801] log likelihood: -20199.229072 EM: Round [802] log likelihood: -20199.227796 EM: Round [803] log likelihood: -20199.226524 EM: Round [804] log likelihood: -20199.225254 EM: Round [805] log likelihood: -20199.223988 EM: Round [806] log likelihood: -20199.222725 EM: Round [807] log likelihood: -20199.221465 EM: Round [808] log likelihood: -20199.220209 EM: Round [809] log likelihood: -20199.218956 EM: Round [810] log likelihood: -20199.217705 EM: Round [811] log likelihood: -20199.216459 EM: Round [812] log likelihood: -20199.215215 EM: Round [813] log likelihood: -20199.213975 EM: Round [814] log likelihood: -20199.212737 EM: Round [815] log likelihood: -20199.211503 EM: Round [816] log likelihood: -20199.210272 EM: Round [817] log likelihood: -20199.209045 EM: Round [818] log likelihood: -20199.207820 EM: Round [819] log likelihood: -20199.206598 EM: Round [820] log likelihood: -20199.205380 EM: Round [821] log likelihood: -20199.204165 EM: Round [822] log likelihood: -20199.202953 EM: Round [823] log likelihood: -20199.201744 EM: Round [824] log likelihood: -20199.200538 EM: Round [825] log likelihood: -20199.199335 EM: Round [826] log likelihood: -20199.198135 EM: Round [827] log likelihood: -20199.196938 EM: Round [828] log likelihood: -20199.195745 EM: Round [829] log likelihood: -20199.194554 EM: Round [830] log likelihood: -20199.193366 EM: Round [831] log likelihood: -20199.192182 EM: Round [832] log likelihood: -20199.191000 EM: Round [833] log likelihood: -20199.189822 EM: Round [834] log likelihood: -20199.188646 EM: Round [835] log likelihood: -20199.187474 EM: Round [836] log likelihood: -20199.186304 EM: Round [837] log likelihood: -20199.185138 EM: Round [838] log likelihood: -20199.183974 EM: Round [839] log likelihood: -20199.182814 EM: Round [840] log likelihood: -20199.181656 EM: Round [841] log likelihood: -20199.180501 EM: Round [842] log likelihood: -20199.179349 EM: Round [843] log likelihood: -20199.178201 EM: Round [844] log likelihood: -20199.177055 EM: Round [845] log likelihood: -20199.175912 EM: Round [846] log likelihood: -20199.174771 EM: Round [847] log likelihood: -20199.173634 EM: Round [848] log likelihood: -20199.172500 EM: Round [849] log likelihood: -20199.171368 EM: Round [850] log likelihood: -20199.170240 EM: Round [851] log likelihood: -20199.169114 EM: Round [852] log likelihood: -20199.167991 EM: Round [853] log likelihood: -20199.166871 EM: Round [854] log likelihood: -20199.165754 EM: Round [855] log likelihood: -20199.164640 EM: Round [856] log likelihood: -20199.163528 EM: Round [857] log likelihood: -20199.162419 EM: Round [858] log likelihood: -20199.161313 EM: Round [859] log likelihood: -20199.160210 EM: Round [860] log likelihood: -20199.159110 EM: Round [861] log likelihood: -20199.158012 EM: Round [862] log likelihood: -20199.156917 EM: Round [863] log likelihood: -20199.155825 EM: Round [864] log likelihood: -20199.154736 EM: Round [865] log likelihood: -20199.153650 EM: Round [866] log likelihood: -20199.152566 EM: Round [867] log likelihood: -20199.151485 EM: Round [868] log likelihood: -20199.150407 EM: Round [869] log likelihood: -20199.149331 EM: Round [870] log likelihood: -20199.148258 EM: Round [871] log likelihood: -20199.147188 EM: Round [872] log likelihood: -20199.146120 EM: Round [873] log likelihood: -20199.145056 EM: Round [874] log likelihood: -20199.143994 EM: Round [875] log likelihood: -20199.142934 EM: Round [876] log likelihood: -20199.141877 EM: Round [877] log likelihood: -20199.140823 EM: Round [878] log likelihood: -20199.139772 EM: Round [879] log likelihood: -20199.138723 EM: Round [880] log likelihood: -20199.137677 EM: Round [881] log likelihood: -20199.136633 EM: Round [882] log likelihood: -20199.135592 EM: Round [883] log likelihood: -20199.134554 EM: Round [884] log likelihood: -20199.133518 EM: Round [885] log likelihood: -20199.132485 EM: Round [886] log likelihood: -20199.131455 EM: Round [887] log likelihood: -20199.130427 EM: Round [888] log likelihood: -20199.129402 EM: Round [889] log likelihood: -20199.128379 EM: Round [890] log likelihood: -20199.127359 EM: Round [891] log likelihood: -20199.126341 EM: Round [892] log likelihood: -20199.125326 EM: Round [893] log likelihood: -20199.124313 EM: Round [894] log likelihood: -20199.123303 EM: Round [895] log likelihood: -20199.122296 EM: Round [896] log likelihood: -20199.121291 EM: Round [897] log likelihood: -20199.120289 EM: Round [898] log likelihood: -20199.119289 EM: Round [899] log likelihood: -20199.118291 EM: Round [900] log likelihood: -20199.117296 EM: Round [901] log likelihood: -20199.116304 EM: Round [902] log likelihood: -20199.115314 EM: Round [903] log likelihood: -20199.114326 EM: Round [904] log likelihood: -20199.113341 EM: Round [905] log likelihood: -20199.112359 EM: Round [906] log likelihood: -20199.111379 EM: Round [907] log likelihood: -20199.110401 EM: Round [908] log likelihood: -20199.109426 EM: Round [909] log likelihood: -20199.108453 EM: Round [910] log likelihood: -20199.107483 EM: Round [911] log likelihood: -20199.106515 EM: Round [912] log likelihood: -20199.105549 EM: Round [913] log likelihood: -20199.104586 EM: Round [914] log likelihood: -20199.103625 EM: Round [915] log likelihood: -20199.102667 EM: Round [916] log likelihood: -20199.101711 EM: Round [917] log likelihood: -20199.100758 EM: Round [918] log likelihood: -20199.099806 EM: Round [919] log likelihood: -20199.098858 EM: Round [920] log likelihood: -20199.097911 EM: Round [921] log likelihood: -20199.096967 EM: Round [922] log likelihood: -20199.096025 EM: Round [923] log likelihood: -20199.095086 EM: Round [924] log likelihood: -20199.094149 EM: Round [925] log likelihood: -20199.093214 EM: Round [926] log likelihood: -20199.092282 EM: Round [927] log likelihood: -20199.091352 EM: Round [928] log likelihood: -20199.090424 EM: Round [929] log likelihood: -20199.089498 EM: Round [930] log likelihood: -20199.088575 EM: Round [931] log likelihood: -20199.087654 EM: Round [932] log likelihood: -20199.086736 EM: Round [933] log likelihood: -20199.085819 EM: Round [934] log likelihood: -20199.084905 EM: Round [935] log likelihood: -20199.083993 EM: Round [936] log likelihood: -20199.083084 EM: Round [937] log likelihood: -20199.082177 EM: Round [938] log likelihood: -20199.081272 EM: Round [939] log likelihood: -20199.080369 EM: Round [940] log likelihood: -20199.079468 EM: Round [941] log likelihood: -20199.078570 EM: Round [942] log likelihood: -20199.077674 EM: Round [943] log likelihood: -20199.076780 EM: Round [944] log likelihood: -20199.075888 EM: Round [945] log likelihood: -20199.074999 EM: Round [946] log likelihood: -20199.074112 EM: Round [947] log likelihood: -20199.073226 EM: Round [948] log likelihood: -20199.072344 EM: Round [949] log likelihood: -20199.071463 EM: Round [950] log likelihood: -20199.070584 EM: Round [951] log likelihood: -20199.069708 EM: Round [952] log likelihood: -20199.068834 EM: Round [953] log likelihood: -20199.067962 EM: Round [954] log likelihood: -20199.067092 EM: Round [955] log likelihood: -20199.066224 EM: Round [956] log likelihood: -20199.065359 EM: Round [957] log likelihood: -20199.064495 EM: Round [958] log likelihood: -20199.063634 EM: Round [959] log likelihood: -20199.062775 EM: Round [960] log likelihood: -20199.061918 EM: Round [961] log likelihood: -20199.061063 EM: Round [962] log likelihood: -20199.060210 EM: Round [963] log likelihood: -20199.059359 EM: Round [964] log likelihood: -20199.058510 EM: Round [965] log likelihood: -20199.057664 EM: Round [966] log likelihood: -20199.056819 EM: Round [967] log likelihood: -20199.055977 EM: Round [968] log likelihood: -20199.055136 EM: Round [969] log likelihood: -20199.054298 EM: Round [970] log likelihood: -20199.053462 EM: Round [971] log likelihood: -20199.052628 EM: Round [972] log likelihood: -20199.051796 EM: Round [973] log likelihood: -20199.050966 EM: Round [974] log likelihood: -20199.050138 EM: Round [975] log likelihood: -20199.049312 EM: Round [976] log likelihood: -20199.048488 EM: Round [977] log likelihood: -20199.047666 EM: Round [978] log likelihood: -20199.046846 EM: Round [979] log likelihood: -20199.046028 EM: Round [980] log likelihood: -20199.045212 EM: Round [981] log likelihood: -20199.044398 EM: Round [982] log likelihood: -20199.043586 EM: Round [983] log likelihood: -20199.042776 EM: Round [984] log likelihood: -20199.041968 EM: Round [985] log likelihood: -20199.041162 EM: Round [986] log likelihood: -20199.040358 EM: Round [987] log likelihood: -20199.039557 EM: Round [988] log likelihood: -20199.038756 EM: Round [989] log likelihood: -20199.037958 EM: Round [990] log likelihood: -20199.037162 EM: Round [991] log likelihood: -20199.036368 EM: Round [992] log likelihood: -20199.035576 EM: Round [993] log likelihood: -20199.034786 EM: Round [994] log likelihood: -20199.033997 EM: Round [995] log likelihood: -20199.033211 EM: Round [996] log likelihood: -20199.032426 EM: Round [997] log likelihood: -20199.031644 EM: Round [998] log likelihood: -20199.030863 EM: Round [999] log likelihood: -20199.030084 EM: Round [1000] log likelihood: -20199.029308 EM: Round [1001] log likelihood: -20199.028533 Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz: 294568972 Execution Time = 5.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --gtf /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/fi_workdir/microH.dat Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fa --gtf /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gtf > /tmp/nxf.b9RdbAI3hE/fi_workdir/microH.dat Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.b9RdbAI3hE/fi_workdir/microH.dat /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_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.b9RdbAI3hE/fi_workdir/microH.dat /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.b9RdbAI3hE --json_outfile /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.json --file_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.b9RdbAI3hE --json_outfile /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.json --file_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1 Running: touch /tmp/nxf.b9RdbAI3hE/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.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --html_output /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix Hs746T_FFPE_RNA_0001_23LG7FLT4_1 --html_output /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000231365.6] WARNING, no entry stored in dbm for [ENSG00000231365.6] WARNING, no entry stored in dbm for [ENSG00000231365.6] WARNING, no entry stored in dbm for [ENSG00000231365.6] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000230534.6] WARNING, no entry stored in dbm for [ENSG00000216829.6] WARNING, no entry stored in dbm for [ENSG00000216829.6] WARNING, no entry stored in dbm for [ENSG00000229180.7] WARNING, no entry stored in dbm for [ENSG00000229180.7] WARNING, no entry stored in dbm for [ENSG00000261235.1] WARNING, no entry stored in dbm for [ENSG00000261235.1] WARNING, no entry stored in dbm for [ENSG00000261235.1] WARNING, no entry stored in dbm for [ENSG00000267052.3] WARNING, no entry stored in dbm for [ENSG00000267052.3] WARNING, no entry stored in dbm for [ENSG00000267052.3] WARNING, no entry stored in dbm for [ENSG00000237813.4] WARNING, no entry stored in dbm for [ENSG00000237813.4] WARNING, no entry stored in dbm for [ENSG00000237813.4] WARNING, no entry stored in dbm for [ENSG00000237813.4] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000243797.6] WARNING, no entry stored in dbm for [ENSG00000254083.6] WARNING, no entry stored in dbm for [ENSG00000254083.6] WARNING, no entry stored in dbm for [ENSG00000254083.6] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.b9RdbAI3hE/ctat_genome_lib_build_dir > /tmp/nxf.b9RdbAI3hE/Hs746T_FFPE_RNA_0001_23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.b9RdbAI3hE/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory