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/cb/e4849de20220debe757fa3abdb1467/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/e4849de20220debe757fa3abdb1467/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/5f1b58950886125572f51223428af3/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/e81a6ca03cf9d7ef81a56126a150b0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/e81a6ca03cf9d7ef81a56126a150b0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/cytoBand.txt Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed -parsing GTF file: /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok Running: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok Running: samtools faidx /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.fqPNrqQpK0/fi_workdir --reads "/tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 11:09:55 ..... started STAR run Jun 08 11:09:55 ..... loading genome Jun 08 11:11:35 ... generating Suffix Array index Jun 08 11:15:13 ... completed Suffix Array index Jun 08 11:15:14 ..... processing annotations GTF Jun 08 11:15:14 ..... inserting junctions into the genome indices Jun 08 11:16:14 ..... started mapping Jun 08 12:08:01 ..... finished mapping Jun 08 12:08:02 ..... started sorting BAM Jun 08 12:08:03 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam Execution Time = 58.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.fqPNrqQpK0/fi_workdir --reads "/tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups 12:08:18 : INFO : Done. Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf -parsing /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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] -done parsing /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 71, 'per_id < 96' => 23779, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 110, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4, 'small anchor length' => 191, 'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6, 'seq-similar region overlap' => 398, ' ** passed ** ' => 25067, 'num genes matched < 2' => 64, 'excessive soft clipping' => 18690, 'low complexity anchor region' => 22, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 38, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 402, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 4 }; -writing fusion junction support info. Execution Time = 1.40 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] -fusion SPANNING read extraction for scaff: AC138035.1--SEPTIN14 [1000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] 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[205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] -fusion SPANNING read extraction for scaff: CPSF6--DUX4 [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] -fusion SPANNING read extraction for scaff: EPC1--PHC2 [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] -fusion SPANNING read extraction for scaff: EPC1--TLR12P [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] -fusion SPANNING read extraction for scaff: FBXO10--SETD2 [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: FP325317.1--BMS1P10 [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: FXYD1--FXYD5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] -fusion SPANNING read extraction for scaff: KDM4C--ZCCHC7 [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] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [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: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -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] [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] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3 [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: PCDHGA3--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [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: PCDHGA3--PCDHGA10 [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] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [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: PCDHGA3--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [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: PCDHGA3--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [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: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -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] -fusion SPANNING read extraction for scaff: ZCCHC7--AL513412.1 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 121957, 'lacks exon overlap' => 6159 }; Execution Time = 3.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -7880.709345 EM: Round [1] log likelihood: -7875.243300 EM: Round [2] log likelihood: -7872.563037 EM: Round [3] log likelihood: -7870.373075 EM: Round [4] log likelihood: -7868.569623 EM: Round [5] log likelihood: -7867.074523 EM: Round [6] log likelihood: -7865.827336 EM: Round [7] log likelihood: -7864.780710 EM: Round [8] log likelihood: -7863.897176 EM: Round [9] log likelihood: -7863.146856 EM: Round [10] log likelihood: -7862.505778 EM: Round [11] log likelihood: -7861.954612 EM: Round [12] log likelihood: -7861.477710 EM: Round [13] log likelihood: -7861.062359 EM: Round [14] log likelihood: -7860.698200 EM: Round [15] log likelihood: -7860.376773 EM: Round [16] log likelihood: -7860.091149 EM: Round [17] log likelihood: -7859.835643 EM: Round [18] log likelihood: -7859.605579 EM: Round [19] log likelihood: -7859.397105 EM: Round [20] log likelihood: -7859.207039 EM: Round [21] log likelihood: -7859.032748 EM: Round [22] log likelihood: -7858.872046 EM: Round [23] log likelihood: -7858.723118 EM: Round [24] log likelihood: -7858.584447 EM: Round [25] log likelihood: -7858.454766 EM: Round [26] log likelihood: -7858.333011 EM: Round [27] log likelihood: -7858.218286 EM: Round [28] log likelihood: -7858.109835 EM: Round [29] log likelihood: -7858.007013 EM: Round [30] log likelihood: -7857.909273 EM: Round [31] log likelihood: -7857.816145 EM: Round [32] log likelihood: -7857.727223 EM: Round [33] log likelihood: -7857.642158 EM: Round [34] log likelihood: -7857.560645 EM: Round [35] log likelihood: -7857.482416 EM: Round [36] log likelihood: -7857.407235 EM: Round [37] log likelihood: -7857.334894 EM: Round [38] log likelihood: -7857.265207 EM: Round [39] log likelihood: -7857.198008 EM: Round [40] log likelihood: -7857.133147 EM: Round [41] log likelihood: -7857.070486 EM: Round [42] log likelihood: -7857.009903 EM: Round [43] log likelihood: -7856.951284 EM: Round [44] log likelihood: -7856.894524 EM: Round [45] log likelihood: -7856.839529 EM: Round [46] log likelihood: -7856.786207 EM: Round [47] log likelihood: -7856.734477 EM: Round [48] log likelihood: -7856.684262 EM: Round [49] log likelihood: -7856.635488 EM: Round [50] log likelihood: -7856.588090 EM: Round [51] log likelihood: -7856.542003 EM: Round [52] log likelihood: -7856.497167 EM: Round [53] log likelihood: -7856.453527 EM: Round [54] log likelihood: -7856.411029 EM: Round [55] log likelihood: -7856.369623 EM: Round [56] log likelihood: -7856.329262 EM: Round [57] log likelihood: -7856.289900 EM: Round [58] log likelihood: -7856.251496 EM: Round [59] log likelihood: -7856.214009 EM: Round [60] log likelihood: -7856.177400 EM: Round [61] log likelihood: -7856.141634 EM: Round [62] log likelihood: -7856.106675 EM: Round [63] log likelihood: -7856.072492 EM: Round [64] log likelihood: -7856.039053 EM: Round [65] log likelihood: -7856.006328 EM: Round [66] log likelihood: -7855.974290 EM: Round [67] log likelihood: -7855.942911 EM: Round [68] log likelihood: -7855.912166 EM: Round [69] log likelihood: -7855.882031 EM: Round [70] log likelihood: -7855.852484 EM: Round [71] log likelihood: -7855.823501 EM: Round [72] log likelihood: -7855.795062 EM: Round [73] log likelihood: -7855.767147 EM: Round [74] log likelihood: -7855.739738 EM: Round [75] log likelihood: -7855.712816 EM: Round [76] log likelihood: -7855.686365 EM: Round [77] log likelihood: -7855.660367 EM: Round [78] log likelihood: -7855.634807 EM: Round [79] log likelihood: -7855.609671 EM: Round [80] log likelihood: -7855.584944 EM: Round [81] log likelihood: -7855.560612 EM: Round [82] log likelihood: -7855.536664 EM: Round [83] log likelihood: -7855.513086 EM: Round [84] log likelihood: -7855.489867 EM: Round [85] log likelihood: -7855.466996 EM: Round [86] log likelihood: -7855.444462 EM: Round [87] log likelihood: -7855.422254 EM: Round [88] log likelihood: -7855.400364 EM: Round [89] log likelihood: -7855.378782 EM: Round [90] log likelihood: -7855.357499 EM: Round [91] log likelihood: -7855.336506 EM: Round [92] log likelihood: -7855.315795 EM: Round [93] log likelihood: -7855.295359 EM: Round [94] log likelihood: -7855.275191 EM: Round [95] log likelihood: -7855.255282 EM: Round [96] log likelihood: -7855.235627 EM: Round [97] log likelihood: -7855.216218 EM: Round [98] log likelihood: -7855.197050 EM: Round [99] log likelihood: -7855.178117 EM: Round [100] log likelihood: -7855.159412 EM: Round [101] log likelihood: -7855.140931 EM: Round [102] log likelihood: -7855.122667 EM: Round [103] log likelihood: -7855.104617 EM: Round [104] log likelihood: -7855.086775 EM: Round [105] log likelihood: -7855.069136 EM: Round [106] log likelihood: -7855.051696 EM: Round [107] log likelihood: -7855.034450 EM: Round [108] log likelihood: -7855.017395 EM: Round [109] log likelihood: -7855.000527 EM: Round [110] log likelihood: -7854.983841 EM: Round [111] log likelihood: -7854.967334 EM: Round [112] log likelihood: -7854.951002 EM: Round [113] log likelihood: -7854.934842 EM: Round [114] log likelihood: -7854.918850 EM: Round [115] log likelihood: -7854.903024 EM: Round [116] log likelihood: -7854.887360 EM: Round [117] log likelihood: -7854.871855 EM: Round [118] log likelihood: -7854.856506 EM: Round [119] log likelihood: -7854.841311 EM: Round [120] log likelihood: -7854.826267 EM: Round [121] log likelihood: -7854.811370 EM: Round [122] log likelihood: -7854.796619 EM: Round [123] log likelihood: -7854.782012 EM: Round [124] log likelihood: -7854.767545 EM: Round [125] log likelihood: -7854.753216 EM: Round [126] log likelihood: -7854.739024 EM: Round [127] log likelihood: -7854.724966 EM: Round [128] log likelihood: -7854.711039 EM: Round [129] log likelihood: -7854.697243 EM: Round [130] log likelihood: -7854.683574 EM: Round [131] log likelihood: -7854.670031 EM: Round [132] log likelihood: -7854.656612 EM: Round [133] log likelihood: -7854.643315 EM: Round [134] log likelihood: -7854.630138 EM: Round [135] log likelihood: -7854.617081 EM: Round [136] log likelihood: -7854.604140 EM: Round [137] log likelihood: -7854.591314 EM: Round [138] log likelihood: -7854.578602 EM: Round [139] log likelihood: -7854.566002 EM: Round [140] log likelihood: -7854.553513 EM: Round [141] log likelihood: -7854.541132 EM: Round [142] log likelihood: -7854.528859 EM: Round [143] log likelihood: -7854.516693 EM: Round [144] log likelihood: -7854.504631 EM: Round [145] log likelihood: -7854.492672 EM: Round [146] log likelihood: -7854.480816 EM: Round [147] log likelihood: -7854.469060 EM: Round [148] log likelihood: -7854.457403 EM: Round [149] log likelihood: -7854.445845 EM: Round [150] log likelihood: -7854.434384 EM: Round [151] log likelihood: -7854.423019 EM: Round [152] log likelihood: -7854.411748 EM: Round [153] log likelihood: -7854.400571 EM: Round [154] log likelihood: -7854.389486 EM: Round [155] log likelihood: -7854.378492 EM: Round [156] log likelihood: -7854.367588 EM: Round [157] log likelihood: -7854.356774 EM: Round [158] log likelihood: -7854.346047 EM: Round [159] log likelihood: -7854.335408 EM: Round [160] log likelihood: -7854.324854 EM: Round [161] log likelihood: -7854.314386 EM: Round [162] log likelihood: -7854.304001 EM: Round [163] log likelihood: -7854.293700 EM: Round [164] log likelihood: -7854.283481 EM: Round [165] log likelihood: -7854.273343 EM: Round [166] log likelihood: -7854.263285 EM: Round [167] log likelihood: -7854.253307 EM: Round [168] log likelihood: -7854.243408 EM: Round [169] log likelihood: -7854.233586 EM: Round [170] log likelihood: -7854.223841 EM: Round [171] log likelihood: -7854.214172 EM: Round [172] log likelihood: -7854.204579 EM: Round [173] log likelihood: -7854.195060 EM: Round [174] log likelihood: -7854.185614 EM: Round [175] log likelihood: -7854.176241 EM: Round [176] log likelihood: -7854.166941 EM: Round [177] log likelihood: -7854.157712 EM: Round [178] log likelihood: -7854.148553 EM: Round [179] log likelihood: -7854.139465 EM: Round [180] log likelihood: -7854.130445 EM: Round [181] log likelihood: -7854.121494 EM: Round [182] log likelihood: -7854.112611 EM: Round [183] log likelihood: -7854.103795 EM: Round [184] log 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likelihood: -7852.841338 EM: Round [603] log likelihood: -7852.840625 EM: Round [604] log likelihood: -7852.839916 EM: Round [605] log likelihood: -7852.839210 EM: Round [606] log likelihood: -7852.838508 EM: Round [607] log likelihood: -7852.837810 EM: Round [608] log likelihood: -7852.837116 EM: Round [609] log likelihood: -7852.836425 EM: Round [610] log likelihood: -7852.835738 EM: Round [611] log likelihood: -7852.835055 EM: Round [612] log likelihood: -7852.834375 EM: Round [613] log likelihood: -7852.833699 EM: Round [614] log likelihood: -7852.833027 EM: Round [615] log likelihood: -7852.832358 EM: Round [616] log likelihood: -7852.831693 EM: Round [617] log likelihood: -7852.831031 EM: Round [618] log likelihood: -7852.830373 EM: Round [619] log likelihood: -7852.829718 EM: Round [620] log likelihood: -7852.829067 EM: Round [621] log likelihood: -7852.828420 EM: Round [622] log likelihood: -7852.827775 EM: Round [623] log likelihood: -7852.827135 EM: Round [624] log 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likelihood: -7852.813305 EM: Round [647] log likelihood: -7852.812742 EM: Round [648] log likelihood: -7852.812181 EM: Round [649] log likelihood: -7852.811624 EM: Round [650] log likelihood: -7852.811069 EM: Round [651] log likelihood: -7852.810517 EM: Round [652] log likelihood: -7852.809969 EM: Round [653] log likelihood: -7852.809423 EM: Round [654] log likelihood: -7852.808880 EM: Round [655] log likelihood: -7852.808340 EM: Round [656] log likelihood: -7852.807802 EM: Round [657] log likelihood: -7852.807268 EM: Round [658] log likelihood: -7852.806737 EM: Round [659] log likelihood: -7852.806208 EM: Round [660] log likelihood: -7852.805682 EM: Round [661] log likelihood: -7852.805159 EM: Round [662] log likelihood: -7852.804639 EM: Round [663] log likelihood: -7852.804121 EM: Round [664] log likelihood: -7852.803606 EM: Round [665] log likelihood: -7852.803094 EM: Round [666] log likelihood: -7852.802585 EM: Round [667] log likelihood: -7852.802078 EM: Round [668] log likelihood: -7852.801574 EM: Round [669] log likelihood: -7852.801073 EM: Round [670] log likelihood: -7852.800574 EM: Round [671] log likelihood: -7852.800078 EM: Round [672] log likelihood: -7852.799585 EM: Round [673] log likelihood: -7852.799094 EM: Round [674] log likelihood: -7852.798606 EM: Round [675] log likelihood: -7852.798121 EM: Round [676] log likelihood: -7852.797638 EM: Round [677] log likelihood: -7852.797157 EM: Round [678] log likelihood: -7852.796679 EM: Round [679] log likelihood: -7852.796204 EM: Round [680] log likelihood: -7852.795731 EM: Round [681] log likelihood: -7852.795261 EM: Round [682] log likelihood: -7852.794793 EM: Round [683] log likelihood: -7852.794328 EM: Round [684] log likelihood: -7852.793865 EM: Round [685] log likelihood: -7852.793404 EM: Round [686] log likelihood: -7852.792946 EM: Round [687] log likelihood: -7852.792491 EM: Round [688] log likelihood: -7852.792038 EM: Round [689] log likelihood: -7852.791587 EM: Round [690] log likelihood: -7852.791138 EM: Round [691] log likelihood: -7852.790692 EM: Round [692] log likelihood: -7852.790249 EM: Round [693] log likelihood: -7852.789807 EM: Round [694] log likelihood: -7852.789368 EM: Round [695] log likelihood: -7852.788932 EM: Round [696] log likelihood: -7852.788497 EM: Round [697] log likelihood: -7852.788065 EM: Round [698] log likelihood: -7852.787636 EM: Round [699] log likelihood: -7852.787208 EM: Round [700] log likelihood: -7852.786783 EM: Round [701] log likelihood: -7852.786360 EM: Round [702] log likelihood: -7852.785939 EM: Round [703] log likelihood: -7852.785521 EM: Round [704] log likelihood: -7852.785104 EM: Round [705] log likelihood: -7852.784690 EM: Round [706] log likelihood: -7852.784278 EM: Round [707] log likelihood: -7852.783868 EM: Round [708] log likelihood: -7852.783461 EM: Round [709] log likelihood: -7852.783055 EM: Round [710] log likelihood: -7852.782652 EM: Round [711] log likelihood: -7852.782251 EM: Round [712] log likelihood: -7852.781852 EM: Round [713] log likelihood: -7852.781455 EM: Round [714] log likelihood: -7852.781060 EM: Round [715] log likelihood: -7852.780667 EM: Round [716] log likelihood: -7852.780276 EM: Round [717] log likelihood: -7852.779888 EM: Round [718] log likelihood: -7852.779501 EM: Round [719] log likelihood: -7852.779117 EM: Round [720] log likelihood: -7852.778734 EM: Round [721] log likelihood: -7852.778354 EM: Round [722] log likelihood: -7852.777975 EM: Round [723] log likelihood: -7852.777599 EM: Round [724] log likelihood: -7852.777224 EM: Round [725] log likelihood: -7852.776851 EM: Round [726] log likelihood: -7852.776481 EM: Round [727] log likelihood: -7852.776112 EM: Round [728] log likelihood: -7852.775746 EM: Round [729] log likelihood: -7852.775381 EM: Round [730] log likelihood: -7852.775018 EM: Round [731] log likelihood: -7852.774657 EM: Round [732] log likelihood: -7852.774298 EM: Round [733] log likelihood: -7852.773941 EM: Round [734] log likelihood: -7852.773586 EM: Round [735] log likelihood: -7852.773232 EM: Round [736] log likelihood: -7852.772881 EM: Round [737] log likelihood: -7852.772531 EM: Round [738] log likelihood: -7852.772183 EM: Round [739] log likelihood: -7852.771837 EM: Round [740] log likelihood: -7852.771493 EM: Round [741] log likelihood: -7852.771150 EM: Round [742] log likelihood: -7852.770810 EM: Round [743] log likelihood: -7852.770471 EM: Round [744] log likelihood: -7852.770134 EM: Round [745] log likelihood: -7852.769799 EM: Round [746] log likelihood: -7852.769465 EM: Round [747] log likelihood: -7852.769134 EM: Round [748] log likelihood: -7852.768804 EM: Round [749] log likelihood: -7852.768475 EM: Round [750] log likelihood: -7852.768149 EM: Round [751] log likelihood: -7852.767824 EM: Round [752] log likelihood: -7852.767501 EM: Round [753] log likelihood: -7852.767180 EM: Round [754] log likelihood: -7852.766860 EM: Round [755] log likelihood: -7852.766542 EM: Round [756] log likelihood: -7852.766226 EM: Round [757] log likelihood: -7852.765911 EM: Round [758] log likelihood: -7852.765598 EM: Round [759] log likelihood: -7852.765287 EM: Round [760] log likelihood: -7852.764977 EM: Round [761] log likelihood: -7852.764669 EM: Round [762] log likelihood: -7852.764362 EM: Round [763] log likelihood: -7852.764057 EM: Round [764] log likelihood: -7852.763754 EM: Round [765] log likelihood: -7852.763452 EM: Round [766] log likelihood: -7852.763152 EM: Round [767] log likelihood: -7852.762854 EM: Round [768] log likelihood: -7852.762557 EM: Round [769] log likelihood: -7852.762261 EM: Round [770] log likelihood: -7852.761967 EM: Round [771] log likelihood: -7852.761675 EM: Round [772] log likelihood: -7852.761384 EM: Round [773] log likelihood: -7852.761095 EM: Round [774] log likelihood: -7852.760807 EM: Round [775] log likelihood: -7852.760521 EM: Round [776] log likelihood: -7852.760236 EM: Round [777] log likelihood: -7852.759953 EM: Round [778] log likelihood: -7852.759671 EM: Round [779] log likelihood: -7852.759391 EM: Round [780] log likelihood: -7852.759112 EM: Round [781] log likelihood: -7852.758835 EM: Round [782] log likelihood: -7852.758559 EM: Round [783] log likelihood: -7852.758284 EM: Round [784] log likelihood: -7852.758011 EM: Round [785] log likelihood: -7852.757740 EM: Round [786] log likelihood: -7852.757470 EM: Round [787] log likelihood: -7852.757201 EM: Round [788] log likelihood: -7852.756934 EM: Round [789] log likelihood: -7852.756668 EM: Round [790] log likelihood: -7852.756403 EM: Round [791] log likelihood: -7852.756140 EM: Round [792] log likelihood: -7852.755878 EM: Round [793] log likelihood: -7852.755618 EM: Round [794] log likelihood: -7852.755359 EM: Round [795] log likelihood: -7852.755101 EM: Round [796] log likelihood: -7852.754845 EM: Round [797] log likelihood: -7852.754590 EM: Round [798] log likelihood: -7852.754336 EM: Round [799] log likelihood: -7852.754084 EM: Round [800] log likelihood: -7852.753833 EM: Round [801] log likelihood: -7852.753583 EM: Round [802] log likelihood: -7852.753335 EM: Round [803] log likelihood: -7852.753088 EM: Round [804] log likelihood: -7852.752842 EM: Round [805] log likelihood: -7852.752598 EM: Round [806] log likelihood: -7852.752354 EM: Round [807] log likelihood: -7852.752112 EM: Round [808] log likelihood: -7852.751872 EM: Round [809] log likelihood: -7852.751632 EM: Round [810] log likelihood: -7852.751394 EM: Round [811] log likelihood: -7852.751157 EM: Round [812] log likelihood: -7852.750922 EM: Round [813] log likelihood: -7852.750687 EM: Round [814] log likelihood: -7852.750454 EM: Round [815] log likelihood: -7852.750222 EM: Round [816] log likelihood: -7852.749991 EM: Round [817] log likelihood: -7852.749762 EM: Round [818] log likelihood: -7852.749533 EM: Round [819] log likelihood: -7852.749306 EM: Round [820] log likelihood: -7852.749080 EM: Round [821] log likelihood: -7852.748855 EM: Round [822] log likelihood: -7852.748632 EM: Round [823] log likelihood: -7852.748409 EM: Round [824] log likelihood: -7852.748188 EM: Round [825] log likelihood: -7852.747968 EM: Round [826] log likelihood: -7852.747749 EM: Round [827] log likelihood: -7852.747531 EM: Round [828] log likelihood: -7852.747314 EM: Round [829] log likelihood: -7852.747099 EM: Round [830] log likelihood: -7852.746884 EM: Round [831] log likelihood: -7852.746671 EM: Round [832] log likelihood: -7852.746459 EM: Round [833] log likelihood: -7852.746248 EM: Round [834] log likelihood: -7852.746038 EM: Round [835] log likelihood: -7852.745829 EM: Round [836] log likelihood: -7852.745621 EM: Round [837] log likelihood: -7852.745414 EM: Round [838] log likelihood: -7852.745209 EM: Round [839] log likelihood: -7852.745004 EM: Round [840] log likelihood: -7852.744801 EM: Round [841] log likelihood: -7852.744598 EM: Round [842] log likelihood: -7852.744397 EM: Round [843] log likelihood: -7852.744196 EM: Round [844] log likelihood: -7852.743997 EM: Round [845] log likelihood: -7852.743799 EM: Round [846] log likelihood: -7852.743602 EM: Round [847] log likelihood: -7852.743406 EM: Round [848] log likelihood: -7852.743210 EM: Round [849] log likelihood: -7852.743016 EM: Round [850] log likelihood: -7852.742823 EM: Round [851] log likelihood: -7852.742631 EM: Round [852] log likelihood: -7852.742440 EM: Round [853] log likelihood: -7852.742250 EM: Round [854] log likelihood: -7852.742061 EM: Round [855] log likelihood: -7852.741873 EM: Round [856] log likelihood: -7852.741686 EM: Round [857] log likelihood: -7852.741499 EM: Round [858] log likelihood: -7852.741314 EM: Round [859] log likelihood: -7852.741130 EM: Round [860] log likelihood: -7852.740947 EM: Round [861] log likelihood: -7852.740764 EM: Round [862] log likelihood: -7852.740583 EM: Round [863] log likelihood: -7852.740403 EM: Round [864] log likelihood: -7852.740223 EM: Round [865] log likelihood: -7852.740045 EM: Round [866] log likelihood: -7852.739867 EM: Round [867] log likelihood: -7852.739690 EM: Round [868] log likelihood: -7852.739515 EM: Round [869] log likelihood: -7852.739340 EM: Round [870] log likelihood: -7852.739166 EM: Round [871] log likelihood: -7852.738993 EM: Round [872] log likelihood: -7852.738821 EM: Round [873] log likelihood: -7852.738649 EM: Round [874] log likelihood: -7852.738479 EM: Round [875] log likelihood: -7852.738310 EM: Round [876] log likelihood: -7852.738141 EM: Round [877] log likelihood: -7852.737974 EM: Round [878] log likelihood: -7852.737807 EM: Round [879] log likelihood: -7852.737641 EM: Round [880] log likelihood: -7852.737476 EM: Round [881] log likelihood: -7852.737312 EM: Round [882] log likelihood: -7852.737148 EM: Round [883] log likelihood: -7852.736986 EM: Round [884] log likelihood: -7852.736824 EM: Round [885] log likelihood: -7852.736663 EM: Round [886] log likelihood: -7852.736503 EM: Round [887] log likelihood: -7852.736344 EM: Round [888] log likelihood: -7852.736186 EM: Round [889] log likelihood: -7852.736028 EM: Round [890] log likelihood: -7852.735872 EM: Round [891] log likelihood: -7852.735716 EM: Round [892] log likelihood: -7852.735561 EM: Round [893] log likelihood: -7852.735407 EM: Round [894] log likelihood: -7852.735253 EM: Round [895] log likelihood: -7852.735101 EM: Round [896] log likelihood: -7852.734949 EM: Round [897] log likelihood: -7852.734798 EM: Round [898] log likelihood: -7852.734648 EM: Round [899] log likelihood: -7852.734498 EM: Round [900] log likelihood: -7852.734349 EM: Round [901] log likelihood: -7852.734202 EM: Round [902] log likelihood: -7852.734054 EM: Round [903] log likelihood: -7852.733908 EM: Round [904] log likelihood: -7852.733762 EM: Round [905] log likelihood: -7852.733618 EM: Round [906] log likelihood: -7852.733473 EM: Round [907] log likelihood: -7852.733330 EM: Round [908] log likelihood: -7852.733188 EM: Round [909] log likelihood: -7852.733046 EM: Round [910] log likelihood: -7852.732905 EM: Round [911] log likelihood: -7852.732764 EM: Round [912] log likelihood: -7852.732625 EM: Round [913] log likelihood: -7852.732486 EM: Round [914] log likelihood: -7852.732347 EM: Round [915] log likelihood: -7852.732210 EM: Round [916] log likelihood: -7852.732073 EM: Round [917] log likelihood: -7852.731937 EM: Round [918] log likelihood: -7852.731802 EM: Round [919] log likelihood: -7852.731667 EM: Round [920] log likelihood: -7852.731533 EM: Round [921] log likelihood: -7852.731400 EM: Round [922] log likelihood: -7852.731267 EM: Round [923] log likelihood: -7852.731136 EM: Round [924] log likelihood: -7852.731004 EM: Round [925] log likelihood: -7852.730874 EM: Round [926] log likelihood: -7852.730744 EM: Round [927] log likelihood: -7852.730615 EM: Round [928] log likelihood: -7852.730487 EM: Round [929] log likelihood: -7852.730359 EM: Round [930] log likelihood: -7852.730232 EM: Round [931] log likelihood: -7852.730105 EM: Round [932] log likelihood: -7852.729979 EM: Round [933] log likelihood: -7852.729854 EM: Round [934] log likelihood: -7852.729730 EM: Round [935] log likelihood: -7852.729606 EM: Round [936] log likelihood: -7852.729483 EM: Round [937] log likelihood: -7852.729360 EM: Round [938] log likelihood: -7852.729238 EM: Round [939] log likelihood: -7852.729117 EM: Round [940] log likelihood: -7852.728996 EM: Round [941] log likelihood: -7852.728876 EM: Round [942] log likelihood: -7852.728757 EM: Round [943] log likelihood: -7852.728638 EM: Round [944] log likelihood: -7852.728520 EM: Round [945] log likelihood: -7852.728402 EM: Round [946] log likelihood: -7852.728285 EM: Round [947] log likelihood: -7852.728169 EM: Round [948] log likelihood: -7852.728053 EM: Round [949] log likelihood: -7852.727938 EM: Round [950] log likelihood: -7852.727824 EM: Round [951] log likelihood: -7852.727710 EM: Round [952] log likelihood: -7852.727596 EM: Round [953] log likelihood: -7852.727484 EM: Round [954] log likelihood: -7852.727371 EM: Round [955] log likelihood: -7852.727260 EM: Round [956] log likelihood: -7852.727149 EM: Round [957] log likelihood: -7852.727038 EM: Round [958] log likelihood: -7852.726929 EM: Round [959] log likelihood: -7852.726819 EM: Round [960] log likelihood: -7852.726711 EM: Round [961] log likelihood: -7852.726602 EM: Round [962] log likelihood: -7852.726495 EM: Round [963] log likelihood: -7852.726388 EM: Round [964] log likelihood: -7852.726281 EM: Round [965] log likelihood: -7852.726175 EM: Round [966] log likelihood: -7852.726070 EM: Round [967] log likelihood: -7852.725965 EM: Round [968] log likelihood: -7852.725861 EM: Round [969] log likelihood: -7852.725757 EM: Round [970] log likelihood: -7852.725654 EM: Round [971] log likelihood: -7852.725551 EM: Round [972] log likelihood: -7852.725449 EM: Round [973] log likelihood: -7852.725348 EM: Round [974] log likelihood: -7852.725247 EM: Round [975] log likelihood: -7852.725146 EM: Round [976] log likelihood: -7852.725046 EM: Round [977] log likelihood: -7852.724947 EM: Stopping iterations at round 977 due to insufficient improvement in likelihood. Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam" Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords CMD: touch /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir -done, see /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -7097.961224 EM: Round [1] log likelihood: -7097.914278 EM: Round [2] log likelihood: -7097.914258 EM: Stopping iterations at round 2 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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 295604458 Execution Time = 5.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/fi_workdir/microH.dat Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.fqPNrqQpK0/fi_workdir/microH.dat Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.fqPNrqQpK0/fi_workdir/microH.dat /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.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.fqPNrqQpK0/fi_workdir/microH.dat /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.fqPNrqQpK0 --json_outfile /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.fqPNrqQpK0 --json_outfile /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 Running: touch /tmp/nxf.fqPNrqQpK0/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.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000238035.8] WARNING, no entry stored in dbm for [ENSG00000238035.8] WARNING, no entry stored in dbm for [ENSG00000238035.8] WARNING, no entry stored in dbm for [ENSG00000277737.3] WARNING, no entry stored in dbm for [ENSG00000237238.3] WARNING, no entry stored in dbm for [ENSG00000277737.3] WARNING, no entry stored in dbm for [ENSG00000237238.3] WARNING, no entry stored in dbm for [ENSG00000277737.3] WARNING, no entry stored in dbm for [ENSG00000237238.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.fqPNrqQpK0/ctat_genome_lib_build_dir > /tmp/nxf.fqPNrqQpK0/1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.fqPNrqQpK0/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory