Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/fead9c10c47bacfabd13e68a928eb1/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/3d7ee2b28f1612993d80273cf66a27/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/3d7ee2b28f1612993d80273cf66a27/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/fead9c10c47bacfabd13e68a928eb1/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/7daadbf5b907f622d438afd404616f/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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 aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/cytoBand.txt Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.4vpUnjdFeW/fi_workdir --reads "/tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 03 20:23:28 ..... started STAR run Jun 03 20:23:28 ..... loading genome Jun 03 20:25:12 ... generating Suffix Array index Jun 03 20:28:58 ... completed Suffix Array index Jun 03 20:28:58 ..... processing annotations GTF Jun 03 20:28:59 ..... inserting junctions into the genome indices Jun 03 20:30:00 ..... started mapping Jun 03 20:59:58 ..... finished mapping Jun 03 20:59:59 ..... started sorting BAM Jun 03 21:00:01 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 36.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.4vpUnjdFeW/fi_workdir --reads "/tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 21:00:27 : INFO : Done. Execution Time = 0.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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] [3430000] [3440000] [3450000] [3460000] [3470000] [3480000] [3490000] [3500000] [3510000] [3520000] [3530000] [3540000] [3550000] [3560000] [3570000] [3580000] [3590000] [3600000] [3610000] [3620000] [3630000] [3640000] [3650000] [3660000] [3670000] [3680000] [3690000] [3700000] [3710000] [3720000] [3730000] [3740000] [3750000] [3760000] [3770000] [3780000] [3790000] [3800000] [3810000] [3820000] [3830000] [3840000] [3850000] [3860000] [3870000] [3880000] [3890000] [3900000] [3910000] [3920000] [3930000] [3940000] [3950000] [3960000] [3970000] [3980000] [3990000] [4000000] [4010000] [4020000] [4030000] [4040000] [4050000] [4060000] [4070000] [4080000] [4090000] [4100000] [4110000] [4120000] -done parsing /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 18, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 189, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 70, 'excessive soft clipping' => 24159, 'per_id < 96' => 14320, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 40, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 348, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 24, 'num genes matched < 2' => 75, 'small anchor length' => 17, 'exons hit < 2' => 13, ' ** passed ** ' => 8539, 'seq-similar region overlap' => 299, 'low complexity anchor region' => 43, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 36, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6 }; -writing fusion junction support info. Execution Time = 2.27 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L [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: AC026412.1--SDHAP1 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: AC242842.2--KCNN3 [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] 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[290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] -fusion SPANNING read extraction for scaff: ACACA--ETV2 [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] -fusion SPANNING read extraction for scaff: AGO2--TRAPPC9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: BCAS3--CASC17 [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] 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[514000] [515000] [516000] [517000] [518000] [519000] [520000] [521000] [522000] [523000] [524000] [525000] [526000] [527000] [528000] [529000] [530000] [531000] [532000] [533000] [534000] [535000] [536000] [537000] [538000] [539000] [540000] [541000] [542000] [543000] [544000] [545000] [546000] [547000] [548000] [549000] [550000] [551000] [552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] [589000] [590000] [591000] [592000] [593000] [594000] -fusion SPANNING read extraction for scaff: BRD4--NOTCH3 [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] -fusion SPANNING read extraction for scaff: C1orf112--F5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] -fusion SPANNING read extraction for scaff: CERCAM--VDAC3 [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] -fusion SPANNING read extraction for scaff: CERCAM--SLC20A2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] -fusion SPANNING read extraction for scaff: CNPPD1--GAPDHP49 [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] -fusion SPANNING read extraction for scaff: DIAPH1--PCDH1 [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] -fusion SPANNING read extraction for scaff: ELK1--SYN1 [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] -fusion SPANNING read extraction for scaff: FBXL20--PAMR1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: FBXL20--SH3RF3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] -fusion SPANNING read extraction for scaff: GSK3A--CIC [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: IGF1R--TRIM37 [1000] [2000] -fusion SPANNING read extraction for scaff: ING5--FP236383.3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] -fusion SPANNING read extraction for scaff: INPPL1--GHSR [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] -fusion SPANNING read extraction for scaff: INPPL1--TNFSF10 [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: INTS10--AC018541.1 [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: INTS2--BCAS3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: INTS9--DLGAP2 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: KLF15--ALG1L2 [1000] [2000] -fusion SPANNING read extraction for scaff: LINC00937--AC083906.5 [1000] -fusion SPANNING read extraction for scaff: LINC00937--AC083906.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: MAD1L1--SDK1 [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] -fusion SPANNING read extraction for scaff: MARK2--AC019211.1 [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: NEK6--AC092958.4 [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: NEK8--EPHA6 [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] -fusion SPANNING read extraction for scaff: NF1--AL353742.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] -fusion SPANNING read extraction for scaff: NF1--AL669983.1 [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] -fusion SPANNING read extraction for scaff: PARG--BMS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] -fusion SPANNING read extraction for scaff: PHF21A--KIT [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] -fusion SPANNING read extraction for scaff: PIGS--SPAG5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PSMD14--AC005040.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PSMD14--LINC01789 [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: PTK2--AGO2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] -fusion SPANNING read extraction for scaff: PTPRF--AC099671.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] -fusion SPANNING read extraction for scaff: QKI--AL449043.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [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] -fusion SPANNING read extraction for scaff: QKI--WASHC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: RFC1--WDR19 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: RSRC1--IL12A-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] -fusion SPANNING read extraction for scaff: SCARB1--DHX37 [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] -fusion SPANNING read extraction for scaff: SDHA--PLEKHG4B [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: SRP68--ZMAT3 [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: TBC1D8--AGFG1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -fusion SPANNING read extraction for scaff: TERF1--KCNB2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: TRIM37--AC022523.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -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] -fusion SPANNING read extraction for scaff: USP37--AC008281.1 [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] -fusion SPANNING read extraction for scaff: USP37--AC009310.1 [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: UXS1--NHEJ1 [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: VMP1--PINX1 [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: VPS72--AC137761.1 [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: WT1--AC006504.5 [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] -fusion SPANNING read extraction for scaff: WT1--AC006504.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: WT1--AC005357.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [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] -fusion SPANNING read extraction for scaff: XPO1--USP34 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: ZFP3--TM4SF5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 32227, 'lacks exon overlap' => 58169 }; Execution Time = 6.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -15391.992536 EM: Round [1] log likelihood: -15386.108100 EM: Round [2] log likelihood: -15385.060296 EM: Round [3] log likelihood: -15384.181845 EM: Round [4] log likelihood: -15383.427892 EM: Round [5] log likelihood: -15382.775760 EM: Round [6] log likelihood: -15382.207868 EM: Round [7] log likelihood: -15381.710317 EM: Round [8] log likelihood: -15381.271962 EM: Round [9] log likelihood: -15380.883760 EM: Round [10] log likelihood: -15380.538305 EM: Round [11] log likelihood: -15380.229472 EM: Round [12] log likelihood: -15379.952166 EM: Round [13] log likelihood: -15379.702117 EM: Round [14] log likelihood: -15379.475729 EM: Round [15] log likelihood: -15379.269959 EM: Round [16] log likelihood: -15379.082219 EM: Round [17] log likelihood: -15378.910303 EM: Round [18] log likelihood: -15378.752320 EM: Round [19] log likelihood: -15378.606649 EM: Round [20] log likelihood: -15378.471890 EM: Round [21] log likelihood: -15378.346837 EM: Round [22] log likelihood: -15378.230444 EM: Round [23] log likelihood: -15378.121804 EM: Round [24] log likelihood: -15378.020126 EM: Round [25] log likelihood: -15377.924723 EM: Round [26] log likelihood: -15377.834990 EM: Round [27] log likelihood: -15377.750402 EM: Round [28] log likelihood: -15377.670494 EM: Round [29] log likelihood: -15377.594858 EM: Round [30] log likelihood: -15377.523133 EM: Round [31] log likelihood: -15377.455001 EM: Round [32] log likelihood: -15377.390179 EM: Round [33] log likelihood: -15377.328414 EM: Round [34] log likelihood: -15377.269482 EM: Round [35] log likelihood: -15377.213184 EM: Round [36] log likelihood: -15377.159337 EM: Round [37] log likelihood: -15377.107781 EM: Round [38] log likelihood: -15377.058369 EM: Round [39] log likelihood: -15377.010969 EM: Round [40] log likelihood: -15376.965461 EM: Round [41] log likelihood: -15376.921736 EM: Round [42] log likelihood: -15376.879695 EM: Round [43] log likelihood: -15376.839245 EM: Round [44] log likelihood: -15376.800304 EM: Round [45] log likelihood: -15376.762794 EM: Round [46] log likelihood: -15376.726645 EM: Round [47] log likelihood: -15376.691790 EM: Round [48] log likelihood: -15376.658169 EM: Round [49] log likelihood: -15376.625724 EM: Round [50] log likelihood: -15376.594403 EM: Round [51] log likelihood: -15376.564157 EM: Round [52] log likelihood: -15376.534938 EM: Round [53] log likelihood: -15376.506704 EM: Round [54] log likelihood: -15376.479413 EM: Round [55] log likelihood: -15376.453028 EM: Round [56] log likelihood: -15376.427511 EM: Round [57] log likelihood: -15376.402829 EM: Round [58] log likelihood: -15376.378948 EM: Round [59] log likelihood: -15376.355838 EM: Round [60] log likelihood: -15376.333470 EM: Round [61] log likelihood: -15376.311816 EM: Round [62] log likelihood: -15376.290849 EM: Round [63] log likelihood: -15376.270544 EM: Round [64] log likelihood: -15376.250876 EM: Round [65] log likelihood: -15376.231824 EM: Round [66] log likelihood: -15376.213364 EM: Round [67] log likelihood: -15376.195477 EM: Round [68] log likelihood: -15376.178141 EM: Round [69] log likelihood: -15376.161337 EM: Round [70] log likelihood: -15376.145047 EM: Round [71] log likelihood: -15376.129254 EM: Round [72] log likelihood: -15376.113940 EM: Round [73] log likelihood: -15376.099088 EM: Round [74] log likelihood: -15376.084684 EM: Round [75] log likelihood: -15376.070712 EM: Round [76] log likelihood: -15376.057157 EM: Round [77] log likelihood: -15376.044007 EM: Round [78] log likelihood: -15376.031246 EM: Round [79] log likelihood: -15376.018863 EM: Round [80] log likelihood: -15376.006845 EM: Round [81] log likelihood: -15375.995179 EM: Round [82] log likelihood: -15375.983856 EM: Round [83] log likelihood: -15375.972862 EM: Round [84] log likelihood: -15375.962188 EM: Round [85] log likelihood: -15375.951824 EM: Round [86] log likelihood: -15375.941758 EM: Round [87] log likelihood: -15375.931983 EM: Round [88] log likelihood: -15375.922488 EM: Round [89] log likelihood: -15375.913264 EM: Round [90] log likelihood: -15375.904304 EM: Round [91] log likelihood: -15375.895598 EM: Round [92] log likelihood: -15375.887138 EM: Round [93] log likelihood: -15375.878918 EM: Round [94] log likelihood: -15375.870928 EM: Round [95] log likelihood: -15375.863163 EM: Round [96] log likelihood: -15375.855615 EM: Round [97] log likelihood: -15375.848276 EM: Round [98] log likelihood: -15375.841142 EM: Round [99] log likelihood: -15375.834205 EM: Round [100] log likelihood: -15375.827460 EM: Round [101] log likelihood: -15375.820899 EM: Round [102] log likelihood: -15375.814519 EM: Round [103] log likelihood: -15375.808313 EM: Round [104] log likelihood: -15375.802276 EM: Round [105] log likelihood: -15375.796402 EM: Round [106] log likelihood: -15375.790687 EM: Round [107] log likelihood: -15375.785126 EM: Round [108] log likelihood: -15375.779715 EM: Round [109] log likelihood: -15375.774448 EM: Round [110] log likelihood: -15375.769322 EM: Round [111] log likelihood: -15375.764331 EM: Round [112] log likelihood: -15375.759473 EM: Round [113] log likelihood: -15375.754743 EM: Round [114] log likelihood: -15375.750137 EM: Round [115] log likelihood: -15375.745652 EM: Round [116] log likelihood: -15375.741284 EM: Round [117] log likelihood: -15375.737029 EM: Round [118] log likelihood: -15375.732885 EM: Round [119] log likelihood: -15375.728847 EM: Round [120] log likelihood: -15375.724914 EM: Round [121] log likelihood: -15375.721081 EM: Round [122] log likelihood: -15375.717346 EM: Round [123] log likelihood: -15375.713705 EM: Round [124] log likelihood: -15375.710157 EM: Round [125] log likelihood: -15375.706698 EM: Round [126] log likelihood: -15375.703326 EM: Round [127] log likelihood: -15375.700039 EM: Round [128] log likelihood: -15375.696833 EM: Round [129] log likelihood: -15375.693707 EM: Round [130] log likelihood: -15375.690658 EM: Round [131] log likelihood: -15375.687684 EM: Round [132] log likelihood: -15375.684783 EM: Round [133] log likelihood: -15375.681953 EM: Round [134] log likelihood: -15375.679192 EM: Round [135] log likelihood: -15375.676497 EM: Round [136] log likelihood: -15375.673867 EM: Round [137] log likelihood: -15375.671301 EM: Round [138] log likelihood: -15375.668796 EM: Round [139] log likelihood: -15375.666350 EM: Round [140] log likelihood: -15375.663962 EM: Round [141] log likelihood: -15375.661631 EM: Round [142] log likelihood: -15375.659354 EM: Round [143] log likelihood: -15375.657130 EM: Round [144] log likelihood: -15375.654958 EM: Round [145] log likelihood: -15375.652836 EM: Round [146] log likelihood: -15375.650764 EM: Round [147] log likelihood: -15375.648738 EM: Round [148] log likelihood: -15375.646759 EM: Round [149] log likelihood: -15375.644825 EM: Round [150] log likelihood: -15375.642935 EM: Round [151] log likelihood: -15375.641087 EM: Round [152] log likelihood: -15375.639280 EM: Round [153] log likelihood: -15375.637514 EM: Round [154] log likelihood: -15375.635787 EM: Round [155] log likelihood: -15375.634098 EM: Round [156] log likelihood: -15375.632446 EM: Round [157] log likelihood: -15375.630830 EM: Round [158] log likelihood: -15375.629250 EM: Round [159] log likelihood: -15375.627703 EM: Round [160] log likelihood: -15375.626190 EM: Round [161] log likelihood: -15375.624709 EM: Round [162] log likelihood: -15375.623260 EM: Round [163] log likelihood: -15375.621841 EM: Round [164] log likelihood: -15375.620452 EM: Round [165] log likelihood: -15375.619092 EM: Round [166] log likelihood: -15375.617761 EM: Round [167] log likelihood: -15375.616457 EM: Round [168] log likelihood: -15375.615181 EM: Round [169] log likelihood: -15375.613930 EM: Round [170] log likelihood: -15375.612705 EM: Round [171] log likelihood: -15375.611505 EM: Round [172] log likelihood: -15375.610329 EM: Round [173] log likelihood: -15375.609177 EM: Round [174] log likelihood: -15375.608047 EM: Round [175] log likelihood: -15375.606940 EM: Round [176] log likelihood: -15375.605855 EM: Round [177] log likelihood: -15375.604792 EM: Round [178] log likelihood: -15375.603749 EM: Round [179] log likelihood: -15375.602726 EM: Round [180] log likelihood: -15375.601723 EM: Round [181] log likelihood: -15375.600740 EM: Round [182] log likelihood: -15375.599775 EM: Round [183] log likelihood: -15375.598828 EM: Round [184] log likelihood: -15375.597900 EM: Round [185] log likelihood: -15375.596989 EM: Round [186] log likelihood: -15375.596095 EM: Round [187] log likelihood: -15375.595217 EM: Round [188] log likelihood: -15375.594356 EM: Round [189] log likelihood: -15375.593510 EM: Round [190] log likelihood: -15375.592680 EM: Round [191] log likelihood: -15375.591866 EM: Round [192] log likelihood: -15375.591065 EM: Round [193] log likelihood: -15375.590280 EM: Round [194] log likelihood: -15375.589508 EM: Round [195] log likelihood: -15375.588750 EM: Round [196] log likelihood: -15375.588005 EM: Round [197] log likelihood: -15375.587273 EM: Round [198] log likelihood: -15375.586555 EM: Round [199] log likelihood: -15375.585848 EM: Round [200] log likelihood: -15375.585154 EM: Round [201] log likelihood: -15375.584472 EM: Round [202] log likelihood: -15375.583801 EM: Round [203] log likelihood: -15375.583142 EM: Round [204] log likelihood: -15375.582494 EM: Round [205] log likelihood: -15375.581857 EM: Round [206] log likelihood: -15375.581230 EM: Round [207] log likelihood: -15375.580614 EM: Round [208] log likelihood: -15375.580008 EM: Round [209] log likelihood: -15375.579412 EM: Round [210] log likelihood: -15375.578826 EM: Round [211] log likelihood: -15375.578249 EM: Round [212] log likelihood: -15375.577682 EM: Round [213] log likelihood: -15375.577124 EM: Round [214] log likelihood: -15375.576574 EM: Round [215] log likelihood: -15375.576033 EM: Round [216] log likelihood: -15375.575501 EM: Round [217] log likelihood: -15375.574978 EM: Round [218] log likelihood: -15375.574462 EM: Round [219] log likelihood: -15375.573954 EM: Round [220] log likelihood: -15375.573455 EM: Round [221] log likelihood: -15375.572963 EM: Round [222] log likelihood: -15375.572478 EM: Round [223] log likelihood: -15375.572001 EM: Round [224] log likelihood: -15375.571531 EM: Round [225] log likelihood: -15375.571068 EM: Round [226] log likelihood: -15375.570612 EM: Round [227] log likelihood: -15375.570163 EM: Round [228] log likelihood: -15375.569721 EM: Round [229] log likelihood: -15375.569285 EM: Round [230] log likelihood: -15375.568856 EM: Round [231] log likelihood: -15375.568432 EM: Round [232] log likelihood: -15375.568015 EM: Round [233] log likelihood: -15375.567604 EM: Round [234] log likelihood: -15375.567199 EM: Round [235] log likelihood: -15375.566800 EM: Round [236] log likelihood: -15375.566406 EM: Round [237] log likelihood: -15375.566018 EM: Round [238] log likelihood: -15375.565636 EM: Round [239] log likelihood: -15375.565259 EM: Round [240] log likelihood: -15375.564887 EM: Round [241] log likelihood: -15375.564520 EM: Round [242] log likelihood: -15375.564158 EM: Round [243] log likelihood: -15375.563802 EM: Round [244] log likelihood: -15375.563450 EM: Round [245] log likelihood: -15375.563103 EM: Round [246] log likelihood: -15375.562761 EM: Round [247] log likelihood: -15375.562423 EM: Round [248] log likelihood: -15375.562090 EM: Round [249] log likelihood: -15375.561762 EM: Round [250] log likelihood: -15375.561438 EM: Round [251] log likelihood: -15375.561118 EM: Round [252] log likelihood: -15375.560802 EM: Round [253] log likelihood: -15375.560491 EM: Round [254] log likelihood: -15375.560183 EM: Round [255] log likelihood: -15375.559880 EM: Round [256] log likelihood: -15375.559581 EM: Round [257] log likelihood: -15375.559285 EM: Round [258] log likelihood: -15375.558994 EM: Round [259] log likelihood: -15375.558706 EM: Round [260] log likelihood: -15375.558422 EM: Round [261] log likelihood: -15375.558141 EM: Round [262] log likelihood: -15375.557864 EM: Round [263] log likelihood: -15375.557591 EM: Round [264] log likelihood: -15375.557321 EM: Round [265] log likelihood: -15375.557054 EM: Round [266] log likelihood: -15375.556791 EM: Round [267] log likelihood: -15375.556531 EM: Round [268] log likelihood: -15375.556274 EM: Round [269] log likelihood: -15375.556021 EM: Round [270] log likelihood: -15375.555771 EM: Round [271] log likelihood: -15375.555523 EM: Round [272] log likelihood: -15375.555279 EM: Round [273] log likelihood: -15375.555038 EM: Round [274] log likelihood: -15375.554800 EM: Round [275] log likelihood: -15375.554564 EM: Round [276] log likelihood: -15375.554332 EM: Round [277] log likelihood: -15375.554102 EM: Round [278] log likelihood: -15375.553875 EM: Round [279] log likelihood: -15375.553651 EM: Round [280] log likelihood: -15375.553429 EM: Round [281] log likelihood: -15375.553211 EM: Round [282] log likelihood: -15375.552994 EM: Round [283] log likelihood: -15375.552781 EM: Round [284] log likelihood: -15375.552569 EM: Round [285] log likelihood: -15375.552361 EM: Round [286] log likelihood: -15375.552155 EM: Round [287] log likelihood: -15375.551951 EM: Round [288] log likelihood: -15375.551749 EM: Round [289] log likelihood: -15375.551550 EM: Round [290] log likelihood: -15375.551354 EM: Round [291] log likelihood: -15375.551159 EM: Round [292] log likelihood: -15375.550967 EM: Round [293] log likelihood: -15375.550777 EM: Round [294] log likelihood: -15375.550589 EM: Round [295] log likelihood: -15375.550404 EM: Round [296] log likelihood: -15375.550220 EM: Round [297] log likelihood: -15375.550039 EM: Round [298] log likelihood: -15375.549860 EM: Round [299] log likelihood: -15375.549682 EM: Round [300] log likelihood: -15375.549507 EM: Round [301] log likelihood: -15375.549334 EM: Round [302] log likelihood: -15375.549163 EM: Round [303] log likelihood: -15375.548993 EM: Round [304] log likelihood: -15375.548826 EM: Round [305] log likelihood: -15375.548660 EM: Round [306] log likelihood: -15375.548497 EM: Round [307] log likelihood: -15375.548335 EM: Round [308] log likelihood: -15375.548175 EM: Round [309] log likelihood: -15375.548017 EM: Round [310] log likelihood: -15375.547860 EM: Round [311] log likelihood: -15375.547705 EM: Round [312] log likelihood: -15375.547552 EM: Round [313] log likelihood: -15375.547401 EM: Round [314] log likelihood: -15375.547251 EM: Round [315] log likelihood: -15375.547103 EM: Round [316] log likelihood: -15375.546957 EM: Round [317] log likelihood: -15375.546812 EM: Round [318] log likelihood: -15375.546669 EM: Round [319] log likelihood: -15375.546527 EM: Round [320] log likelihood: -15375.546387 EM: Round [321] log likelihood: -15375.546249 EM: Round [322] log likelihood: -15375.546112 EM: Round [323] log likelihood: -15375.545976 EM: Round [324] log likelihood: -15375.545842 EM: Round [325] log likelihood: -15375.545709 EM: Round [326] log likelihood: -15375.545578 EM: Round [327] log likelihood: -15375.545449 EM: Round [328] log likelihood: -15375.545320 EM: Round [329] log likelihood: -15375.545193 EM: Round [330] log likelihood: -15375.545068 EM: Round [331] log likelihood: -15375.544943 EM: Round [332] log likelihood: -15375.544820 EM: Round [333] log likelihood: -15375.544699 EM: Round [334] log likelihood: -15375.544579 EM: Round [335] log likelihood: -15375.544459 EM: Round [336] log likelihood: -15375.544342 EM: Round [337] log likelihood: -15375.544225 EM: Round [338] log likelihood: -15375.544110 EM: Round [339] log likelihood: -15375.543996 EM: Round [340] log likelihood: -15375.543883 EM: Round [341] log likelihood: -15375.543772 EM: Round [342] log likelihood: -15375.543661 EM: Round [343] log likelihood: -15375.543552 EM: Round [344] log likelihood: -15375.543444 EM: Round [345] log likelihood: -15375.543337 EM: Round [346] log likelihood: -15375.543231 EM: Round [347] log likelihood: -15375.543126 EM: Round [348] log likelihood: -15375.543023 EM: Round [349] log likelihood: -15375.542920 EM: Round [350] log likelihood: -15375.542819 EM: Round [351] log likelihood: -15375.542718 EM: Round [352] log likelihood: -15375.542619 EM: Stopping iterations at round 352 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa > /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir -done, see /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -13858.419657 EM: Round [1] log likelihood: -13856.576383 EM: Round [2] log likelihood: -13856.560456 EM: Round [3] log likelihood: -13856.560374 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 154970419 Execution Time = 3.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.gtf > /tmp/nxf.4vpUnjdFeW/fi_workdir/microH.dat Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.4vpUnjdFeW/fi_workdir/microH.dat /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/fi_workdir/microH.dat /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.4vpUnjdFeW --json_outfile /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.4vpUnjdFeW --json_outfile /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.4vpUnjdFeW/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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --html_output /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_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.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-8e3550-R1_A23YTGFLT4_1 --html_output /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000267575.7] WARNING, no entry stored in dbm for [ENSG00000267575.7] WARNING, no entry stored in dbm for [ENSG00000267575.7] WARNING, no entry stored in dbm for [ENSG00000267575.7] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286065.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000234285.1] WARNING, no entry stored in dbm for [ENSG00000267623.3] WARNING, no entry stored in dbm for [ENSG00000284964.1] WARNING, no entry stored in dbm for [ENSG00000284964.1] WARNING, no entry stored in dbm for [ENSG00000188002.10] WARNING, no entry stored in dbm for [ENSG00000185485.14] WARNING, no entry stored in dbm for [ENSG00000260158.1] WARNING, no entry stored in dbm for [ENSG00000260785.2] WARNING, no entry stored in dbm for [ENSG00000239498.1] WARNING, no entry stored in dbm for [ENSG00000285409.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000280441.3] WARNING, no entry stored in dbm for [ENSG00000280441.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.4vpUnjdFeW/ctat_genome_lib_build_dir > /tmp/nxf.4vpUnjdFeW/aih-tih-sc-8e3550-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.4vpUnjdFeW/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory