Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/fdfd3a144f13f3a0eadba38f8641d6/tih_rna_sample_00650_B23MVV7LT4_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/9c/ce718bf930bc0dc3880e21a9a0c407/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/c7ea523117b40fddc5555c4881c498/tih_rna_sample_00650_B23MVV7LT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/ce718bf930bc0dc3880e21a9a0c407/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/fdfd3a144f13f3a0eadba38f8641d6/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00650_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1 --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 tih_rna_sample_00650_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/cytoBand.txt Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed -parsing GTF file: /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00650_B23MVV7LT4_1.star --out_dir /tmp/nxf.HJZ3GQTWH8/fi_workdir --reads "/tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:27:00 ..... started STAR run Jun 08 10:27:00 ..... loading genome Jun 08 10:28:50 ... generating Suffix Array index Jun 08 10:32:57 ... completed Suffix Array index Jun 08 10:32:57 ..... processing annotations GTF Jun 08 10:32:57 ..... inserting junctions into the genome indices Jun 08 10:34:08 ..... started mapping Jun 08 12:14:44 ..... finished mapping Jun 08 12:14:47 ..... started sorting BAM Jun 08 12:14:48 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00650_B23MVV7LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00650_B23MVV7LT4_1.star.sortedByCoord.out.bam Execution Time = 107.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00650_B23MVV7LT4_1.star --out_dir /tmp/nxf.HJZ3GQTWH8/fi_workdir --reads "/tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups 12:15:06 : INFO : Done. Execution Time = 0.25 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf -parsing /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_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] -done parsing /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'exons hit < 2' => 3, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6, 'num genes matched < 2' => 306, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 157, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 1090, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 138, 'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 72, 'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 520, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 135, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2, 'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 6, ' ** passed ** ' => 15809, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 184, 'low complexity anchor region' => 11, 'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 78, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 37, 'per_id < 96' => 10646, 'excessive soft clipping' => 16500, 'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 8, 'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4, 'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 8, 'small anchor length' => 51, 'seq-similar region overlap' => 4, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 42 }; -writing fusion junction support info. Execution Time = 1.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: AC079781.4--ASNS [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] -fusion SPANNING read extraction for scaff: AGAP12P--FRMPD2 [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] 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[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] -fusion SPANNING read extraction for scaff: AHR--KANK1 [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: AL512590.2--CCDC180 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: AL669831.1--SEPTIN14 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] -fusion SPANNING read extraction for scaff: CCDC198--NPIPB12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: CDKN2B--IFNA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: CDKN2B--IFNA2 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] -fusion SPANNING read extraction for scaff: EML4--ALK [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: IGFL1P2--HIF3A [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] -fusion SPANNING read extraction for scaff: IL9RP2--EML4 [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] -fusion SPANNING read extraction for scaff: KANK1--LRRK2 [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: LRRK2--AHR [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] -fusion SPANNING read extraction for scaff: PCDHA6--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] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [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: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -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] -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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [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] -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] -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] -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] -fusion SPANNING read extraction for scaff: PTPN2--NPIPB12 [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: RITA1--LRRK2 [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: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [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] -fusion SPANNING read extraction for scaff: TUBA4B--SVIL [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] -fusion SPANNING read extraction for scaff: TUBB8--EML4 [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: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 27083, 'seq similar region alignment' => 29889 }; Execution Time = 3.98 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -12041.010151 EM: Round [1] log likelihood: -12017.738479 EM: Round [2] log likelihood: -12017.403755 EM: Round [3] log likelihood: -12017.343390 EM: Round [4] log likelihood: -12017.316950 EM: Round [5] log likelihood: -12017.301645 EM: Round [6] log likelihood: -12017.290104 EM: Round [7] log likelihood: -12017.279882 EM: Round [8] log likelihood: -12017.270162 EM: Round [9] log likelihood: -12017.260674 EM: Round [10] log likelihood: -12017.251325 EM: Round [11] log likelihood: -12017.242083 EM: Round [12] log likelihood: -12017.232939 EM: Round [13] log likelihood: -12017.223887 EM: Round [14] log likelihood: -12017.214924 EM: Round [15] log likelihood: -12017.206050 EM: Round [16] log likelihood: -12017.197264 EM: Round [17] log likelihood: -12017.188563 EM: Round [18] log likelihood: -12017.179947 EM: Round [19] log likelihood: -12017.171415 EM: Round [20] log likelihood: -12017.162966 EM: Round [21] log likelihood: -12017.154599 EM: Round [22] log likelihood: -12017.146312 EM: Round [23] log likelihood: -12017.138105 EM: Round [24] log likelihood: -12017.129977 EM: Round [25] log likelihood: -12017.121927 EM: Round [26] log likelihood: -12017.113953 EM: Round [27] log likelihood: -12017.106056 EM: Round [28] log likelihood: -12017.098233 EM: Round [29] log likelihood: -12017.090485 EM: Round [30] log likelihood: -12017.082810 EM: Round [31] log likelihood: -12017.075207 EM: Round [32] log likelihood: -12017.067675 EM: Round [33] log likelihood: -12017.060214 EM: Round [34] log likelihood: -12017.052823 EM: Round [35] log likelihood: -12017.045501 EM: Round [36] log likelihood: -12017.038247 EM: Round [37] log likelihood: -12017.031060 EM: Round [38] log likelihood: -12017.023940 EM: Round [39] log likelihood: -12017.016886 EM: Round [40] log likelihood: -12017.009897 EM: Round [41] log likelihood: -12017.002972 EM: Round [42] log likelihood: -12016.996110 EM: Round [43] log likelihood: -12016.989312 EM: Round [44] log likelihood: -12016.982575 EM: Round [45] log likelihood: -12016.975900 EM: Round [46] log likelihood: -12016.969286 EM: Round [47] log likelihood: -12016.962732 EM: Round [48] log likelihood: -12016.956237 EM: Round [49] log likelihood: -12016.949800 EM: Round [50] log likelihood: -12016.943422 EM: Round [51] log likelihood: -12016.937101 EM: Round [52] log likelihood: -12016.930837 EM: Round [53] log likelihood: -12016.924629 EM: Round [54] log likelihood: -12016.918476 EM: Round [55] log likelihood: -12016.912379 EM: Round [56] log likelihood: -12016.906335 EM: Round [57] log likelihood: -12016.900346 EM: Round [58] log likelihood: -12016.894409 EM: Round [59] log likelihood: -12016.888525 EM: Round [60] log likelihood: -12016.882693 EM: Round [61] log likelihood: -12016.876913 EM: Round [62] log likelihood: -12016.871183 EM: Round [63] log likelihood: -12016.865504 EM: Round [64] log likelihood: -12016.859874 EM: Round [65] log likelihood: -12016.854294 EM: Round [66] log likelihood: -12016.848763 EM: Round [67] log likelihood: -12016.843279 EM: Round [68] log likelihood: -12016.837844 EM: Round [69] log likelihood: -12016.832455 EM: Round [70] log likelihood: -12016.827114 EM: Round [71] log likelihood: -12016.821818 EM: Round [72] log likelihood: -12016.816569 EM: Round [73] log likelihood: -12016.811364 EM: Round [74] log likelihood: -12016.806205 EM: Round [75] log likelihood: -12016.801090 EM: Round [76] log likelihood: -12016.796018 EM: Round [77] log likelihood: -12016.790991 EM: Round [78] log likelihood: -12016.786006 EM: Round [79] log likelihood: -12016.781063 EM: Round [80] log likelihood: -12016.776163 EM: Round [81] log likelihood: -12016.771305 EM: Round [82] log likelihood: -12016.766488 EM: Round [83] log likelihood: -12016.761712 EM: Round [84] log likelihood: -12016.756976 EM: Round [85] log likelihood: -12016.752280 EM: Round [86] log likelihood: -12016.747624 EM: Round [87] log likelihood: -12016.743007 EM: Round [88] log likelihood: -12016.738429 EM: Round [89] log likelihood: -12016.733890 EM: Round [90] log likelihood: -12016.729388 EM: Round [91] log likelihood: -12016.724925 EM: Round [92] log likelihood: -12016.720498 EM: Round [93] log likelihood: -12016.716109 EM: Round [94] log likelihood: -12016.711756 EM: Round [95] log likelihood: -12016.707440 EM: Round [96] log likelihood: -12016.703159 EM: Round [97] log likelihood: -12016.698914 EM: Round [98] log likelihood: -12016.694704 EM: Round [99] log likelihood: -12016.690529 EM: Round [100] log likelihood: -12016.686389 EM: Round [101] log likelihood: -12016.682283 EM: Round [102] log likelihood: -12016.678211 EM: Round [103] log likelihood: -12016.674172 EM: Round [104] log likelihood: -12016.670166 EM: Round [105] log likelihood: -12016.666194 EM: Round [106] log likelihood: -12016.662254 EM: Round [107] log likelihood: -12016.658346 EM: Round [108] log likelihood: -12016.654470 EM: Round [109] log likelihood: -12016.650626 EM: Round [110] log likelihood: -12016.646814 EM: Round [111] log likelihood: -12016.643032 EM: Round [112] log likelihood: -12016.639282 EM: Round [113] log likelihood: -12016.635561 EM: Round [114] log likelihood: -12016.631871 EM: Round [115] log likelihood: -12016.628211 EM: Round [116] log likelihood: -12016.624581 EM: Round [117] log likelihood: -12016.620980 EM: Round [118] log likelihood: -12016.617408 EM: Round [119] log likelihood: -12016.613865 EM: Round [120] log likelihood: -12016.610350 EM: Round [121] log likelihood: -12016.606864 EM: Round [122] log likelihood: -12016.603406 EM: Round [123] log likelihood: -12016.599975 EM: Round [124] log likelihood: -12016.596572 EM: Round [125] log likelihood: -12016.593197 EM: Round [126] log likelihood: -12016.589848 EM: Round [127] log likelihood: -12016.586527 EM: Round [128] log likelihood: -12016.583232 EM: Round [129] log likelihood: -12016.579963 EM: Round [130] log likelihood: -12016.576720 EM: Round [131] log likelihood: -12016.573503 EM: Round [132] log likelihood: -12016.570312 EM: Round [133] log likelihood: -12016.567146 EM: Round [134] log likelihood: -12016.564005 EM: Round [135] log likelihood: -12016.560889 EM: Round [136] log likelihood: -12016.557797 EM: Round [137] log likelihood: -12016.554731 EM: Round [138] log likelihood: -12016.551688 EM: Round [139] log likelihood: -12016.548670 EM: Round [140] log likelihood: -12016.545675 EM: Round [141] log likelihood: -12016.542704 EM: Round [142] log likelihood: -12016.539756 EM: Round [143] log likelihood: -12016.536832 EM: Round [144] log likelihood: -12016.533930 EM: Round [145] log likelihood: -12016.531052 EM: Round [146] log likelihood: -12016.528196 EM: Round [147] log likelihood: -12016.525362 EM: Round [148] log likelihood: -12016.522550 EM: Round [149] log likelihood: -12016.519761 EM: Round [150] log likelihood: -12016.516993 EM: Round [151] log likelihood: -12016.514247 EM: Round [152] log likelihood: -12016.511522 EM: Round [153] log likelihood: -12016.508819 EM: Round [154] log likelihood: -12016.506137 EM: Round [155] log likelihood: -12016.503475 EM: Round [156] log likelihood: -12016.500834 EM: Round [157] log likelihood: -12016.498214 EM: Round [158] log 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Round [180] log likelihood: -12016.443223 EM: Round [181] log likelihood: -12016.441046 EM: Round [182] log likelihood: -12016.438885 EM: Round [183] log likelihood: -12016.436741 EM: Round [184] log likelihood: -12016.434613 EM: Round [185] log likelihood: -12016.432502 EM: Round [186] log likelihood: -12016.430406 EM: Round [187] log likelihood: -12016.428326 EM: Round [188] log likelihood: -12016.426262 EM: Round [189] log likelihood: -12016.424214 EM: Round [190] log likelihood: -12016.422181 EM: Round [191] log likelihood: -12016.420163 EM: Round [192] log likelihood: -12016.418161 EM: Round [193] log likelihood: -12016.416174 EM: Round [194] log likelihood: -12016.414202 EM: Round [195] log likelihood: -12016.412245 EM: Round [196] log likelihood: -12016.410302 EM: Round [197] log likelihood: -12016.408375 EM: Round [198] log likelihood: -12016.406461 EM: Round [199] log likelihood: -12016.404562 EM: Round [200] log likelihood: -12016.402678 EM: Round [201] log likelihood: -12016.400807 EM: Round [202] log likelihood: -12016.398951 EM: Round [203] log likelihood: -12016.397109 EM: Round [204] log likelihood: -12016.395280 EM: Round [205] log likelihood: -12016.393465 EM: Round [206] log likelihood: -12016.391664 EM: Round [207] log likelihood: -12016.389876 EM: Round [208] log likelihood: -12016.388102 EM: Round [209] log likelihood: -12016.386341 EM: Round [210] log likelihood: -12016.384593 EM: Round [211] log likelihood: -12016.382858 EM: Round [212] log likelihood: -12016.381136 EM: Round [213] log likelihood: -12016.379427 EM: Round [214] log likelihood: -12016.377731 EM: Round [215] log likelihood: -12016.376047 EM: Round [216] log likelihood: -12016.374376 EM: Round [217] log likelihood: -12016.372717 EM: Round [218] log likelihood: -12016.371071 EM: Round [219] log likelihood: -12016.369437 EM: Round [220] log likelihood: -12016.367815 EM: Round [221] log likelihood: -12016.366205 EM: Round [222] log likelihood: -12016.364607 EM: Round [223] log likelihood: -12016.363021 EM: Round [224] log likelihood: -12016.361447 EM: Round [225] log likelihood: -12016.359884 EM: Round [226] log likelihood: -12016.358333 EM: Round [227] log likelihood: -12016.356794 EM: Round [228] log likelihood: -12016.355265 EM: Round [229] log likelihood: -12016.353749 EM: Round [230] log likelihood: -12016.352243 EM: Round [231] log likelihood: -12016.350748 EM: Round [232] log likelihood: -12016.349265 EM: Round [233] log likelihood: -12016.347793 EM: Round [234] log likelihood: -12016.346331 EM: Round [235] log likelihood: -12016.344880 EM: Round [236] log likelihood: -12016.343440 EM: Round [237] log likelihood: -12016.342011 EM: Round [238] log likelihood: -12016.340592 EM: Round [239] log likelihood: -12016.339183 EM: Round [240] log likelihood: -12016.337785 EM: Round [241] log likelihood: -12016.336397 EM: Round [242] log likelihood: -12016.335020 EM: Round [243] log likelihood: -12016.333652 EM: Round [244] log likelihood: -12016.332295 EM: Round [245] log likelihood: -12016.330947 EM: Round [246] log likelihood: -12016.329609 EM: Round [247] log likelihood: -12016.328282 EM: Round [248] log likelihood: -12016.326964 EM: Round [249] log likelihood: -12016.325655 EM: Round [250] log likelihood: -12016.324356 EM: Round [251] log likelihood: -12016.323067 EM: Round [252] log likelihood: -12016.321787 EM: Round [253] log likelihood: -12016.320517 EM: Round [254] log likelihood: -12016.319256 EM: Round [255] log likelihood: -12016.318004 EM: Round [256] log likelihood: -12016.316761 EM: Round [257] log likelihood: -12016.315527 EM: Round [258] log likelihood: -12016.314303 EM: Round [259] log likelihood: -12016.313087 EM: Round [260] log likelihood: -12016.311880 EM: Round [261] log likelihood: -12016.310682 EM: Round [262] log likelihood: -12016.309493 EM: Round [263] log likelihood: -12016.308312 EM: Round [264] log likelihood: -12016.307140 EM: Round [265] log likelihood: -12016.305976 EM: Round [266] log likelihood: -12016.304821 EM: Round [267] log likelihood: -12016.303674 EM: Round [268] log likelihood: -12016.302536 EM: Round [269] log likelihood: -12016.301406 EM: Round [270] log likelihood: -12016.300284 EM: Round [271] log likelihood: -12016.299171 EM: Round [272] log likelihood: -12016.298065 EM: Round [273] log likelihood: -12016.296968 EM: Round [274] log likelihood: -12016.295878 EM: Round [275] log likelihood: -12016.294796 EM: Round [276] log likelihood: -12016.293722 EM: Round [277] log likelihood: -12016.292656 EM: Round [278] log likelihood: -12016.291598 EM: Round [279] log likelihood: -12016.290547 EM: Round [280] log likelihood: -12016.289504 EM: Round [281] log likelihood: -12016.288469 EM: Round [282] log likelihood: -12016.287441 EM: Round [283] log likelihood: -12016.286420 EM: Round [284] log likelihood: -12016.285407 EM: Round [285] log likelihood: -12016.284401 EM: Round [286] log likelihood: -12016.283403 EM: Round [287] log likelihood: -12016.282411 EM: Round [288] log likelihood: -12016.281427 EM: Round [289] log likelihood: -12016.280450 EM: Round [290] log likelihood: -12016.279480 EM: Round [291] log likelihood: -12016.278517 EM: Round [292] log likelihood: -12016.277561 EM: Round [293] log likelihood: -12016.276612 EM: Round [294] log likelihood: -12016.275670 EM: Round [295] log likelihood: -12016.274734 EM: Round [296] log likelihood: -12016.273805 EM: Round [297] log likelihood: -12016.272883 EM: Round [298] log likelihood: -12016.271968 EM: Round [299] log likelihood: -12016.271059 EM: Round [300] log likelihood: -12016.270156 EM: Round [301] log likelihood: -12016.269261 EM: Round [302] log likelihood: -12016.268371 EM: Round [303] log likelihood: -12016.267488 EM: Round [304] log likelihood: -12016.266612 EM: Round [305] log likelihood: -12016.265741 EM: Round [306] log likelihood: -12016.264877 EM: Round [307] log likelihood: -12016.264019 EM: Round [308] log likelihood: -12016.263167 EM: Round [309] log likelihood: -12016.262322 EM: Round [310] log likelihood: -12016.261482 EM: Round [311] log likelihood: -12016.260649 EM: Round [312] log likelihood: -12016.259821 EM: Round [313] log likelihood: -12016.259000 EM: Round [314] log likelihood: -12016.258184 EM: Round [315] log likelihood: -12016.257374 EM: Round [316] log likelihood: -12016.256570 EM: Round [317] log likelihood: -12016.255772 EM: Round [318] log likelihood: -12016.254979 EM: Round [319] log likelihood: -12016.254192 EM: Round [320] log likelihood: -12016.253411 EM: Round [321] log likelihood: -12016.252635 EM: Round [322] log likelihood: -12016.251865 EM: Round [323] log likelihood: -12016.251100 EM: Round [324] log likelihood: -12016.250341 EM: Round [325] log likelihood: -12016.249587 EM: Round [326] log likelihood: -12016.248839 EM: Round [327] log likelihood: -12016.248096 EM: Round [328] log likelihood: -12016.247358 EM: Round [329] log likelihood: -12016.246626 EM: Round [330] log likelihood: -12016.245898 EM: Round [331] log likelihood: -12016.245176 EM: Round [332] log likelihood: -12016.244459 EM: Round [333] log likelihood: -12016.243748 EM: Round [334] log likelihood: -12016.243041 EM: Round [335] log likelihood: -12016.242339 EM: Round [336] log likelihood: -12016.241643 EM: Round [337] log likelihood: -12016.240951 EM: Round [338] log likelihood: -12016.240264 EM: Round [339] log likelihood: -12016.239582 EM: Round [340] log likelihood: -12016.238905 EM: Round [341] log likelihood: -12016.238233 EM: Round [342] log likelihood: -12016.237566 EM: Round [343] log likelihood: -12016.236903 EM: Round [344] log likelihood: -12016.236245 EM: Round [345] log likelihood: -12016.235592 EM: Round [346] log likelihood: -12016.234943 EM: Round [347] log likelihood: -12016.234299 EM: Round [348] log likelihood: -12016.233660 EM: Round [349] log likelihood: -12016.233025 EM: Round [350] log likelihood: -12016.232395 EM: Round [351] log likelihood: -12016.231769 EM: Round [352] log likelihood: -12016.231147 EM: Round [353] log likelihood: -12016.230530 EM: Round [354] log likelihood: -12016.229918 EM: Round [355] log likelihood: -12016.229309 EM: Round [356] log likelihood: -12016.228705 EM: Round [357] log likelihood: -12016.228106 EM: Round [358] log likelihood: -12016.227510 EM: Round [359] log likelihood: -12016.226919 EM: Round [360] log likelihood: -12016.226332 EM: Round [361] log likelihood: -12016.225749 EM: Round [362] log likelihood: -12016.225171 EM: Round [363] log likelihood: -12016.224596 EM: Round [364] log likelihood: -12016.224025 EM: Round [365] log likelihood: -12016.223459 EM: Round [366] log likelihood: -12016.222896 EM: Round [367] log likelihood: -12016.222338 EM: Round [368] log likelihood: -12016.221783 EM: Round [369] log likelihood: -12016.221233 EM: Round [370] log likelihood: -12016.220686 EM: Round [371] log likelihood: -12016.220143 EM: Round [372] log likelihood: -12016.219604 EM: Round [373] log likelihood: -12016.219069 EM: Round [374] log likelihood: -12016.218538 EM: Round [375] log likelihood: -12016.218010 EM: Round [376] log likelihood: -12016.217486 EM: Round [377] log likelihood: -12016.216966 EM: Round [378] log likelihood: -12016.216449 EM: Round [379] log likelihood: -12016.215936 EM: Round [380] log likelihood: -12016.215427 EM: Round [381] log likelihood: -12016.214921 EM: Round [382] log likelihood: -12016.214419 EM: Round [383] log likelihood: -12016.213921 EM: Round [384] log likelihood: -12016.213426 EM: Round [385] log likelihood: -12016.212934 EM: Round [386] log likelihood: -12016.212446 EM: Round [387] log likelihood: -12016.211961 EM: Round [388] log likelihood: -12016.211480 EM: Round [389] log likelihood: -12016.211002 EM: Round [390] log likelihood: -12016.210528 EM: Round [391] log likelihood: -12016.210057 EM: Round [392] log likelihood: -12016.209589 EM: Round [393] log likelihood: -12016.209125 EM: Round [394] log likelihood: -12016.208664 EM: Round [395] log likelihood: -12016.208206 EM: Round [396] log likelihood: -12016.207751 EM: Round [397] log likelihood: -12016.207299 EM: Round [398] log likelihood: -12016.206851 EM: Round [399] log likelihood: -12016.206406 EM: Round [400] log likelihood: -12016.205964 EM: Round [401] log likelihood: -12016.205525 EM: Round [402] log likelihood: -12016.205089 EM: Round [403] log likelihood: -12016.204656 EM: Round [404] log likelihood: -12016.204227 EM: Round [405] log likelihood: -12016.203800 EM: Round [406] log likelihood: -12016.203376 EM: Round [407] log likelihood: -12016.202956 EM: Round [408] log likelihood: -12016.202538 EM: Round [409] log likelihood: -12016.202123 EM: Round [410] log likelihood: -12016.201711 EM: Round [411] log likelihood: -12016.201302 EM: Round [412] log likelihood: -12016.200896 EM: Round [413] log likelihood: -12016.200493 EM: Round [414] log likelihood: -12016.200092 EM: Round [415] log likelihood: -12016.199695 EM: Round [416] log likelihood: -12016.199300 EM: Round [417] log likelihood: -12016.198908 EM: Round [418] log likelihood: -12016.198519 EM: Round [419] log likelihood: -12016.198132 EM: Round [420] log likelihood: -12016.197748 EM: Round [421] log likelihood: -12016.197367 EM: Round [422] log likelihood: -12016.196989 EM: Round [423] log likelihood: -12016.196613 EM: Round [424] log likelihood: -12016.196240 EM: Round [425] log likelihood: -12016.195869 EM: Round [426] log likelihood: -12016.195501 EM: Round [427] log likelihood: -12016.195136 EM: Round [428] log likelihood: -12016.194773 EM: Round [429] log likelihood: -12016.194413 EM: Round [430] log likelihood: -12016.194055 EM: Round [431] log likelihood: -12016.193700 EM: Round [432] log likelihood: -12016.193347 EM: Round [433] log likelihood: -12016.192997 EM: Round [434] log likelihood: -12016.192649 EM: Round [435] log likelihood: -12016.192304 EM: Round [436] log likelihood: -12016.191961 EM: Round [437] log likelihood: -12016.191620 EM: Round [438] log likelihood: -12016.191282 EM: Round [439] log likelihood: -12016.190946 EM: Round [440] log likelihood: -12016.190613 EM: Round [441] log likelihood: -12016.190282 EM: Round [442] log likelihood: -12016.189953 EM: Round [443] log likelihood: -12016.189627 EM: Round [444] log likelihood: -12016.189302 EM: Round [445] log likelihood: -12016.188981 EM: Round [446] log likelihood: -12016.188661 EM: Round [447] log likelihood: -12016.188343 EM: Round [448] log likelihood: -12016.188028 EM: Round [449] log likelihood: -12016.187715 EM: Round [450] log likelihood: -12016.187405 EM: Round [451] log likelihood: -12016.187096 EM: Round [452] log likelihood: -12016.186789 EM: Round [453] log likelihood: -12016.186485 EM: Round [454] log likelihood: -12016.186183 EM: Round [455] log likelihood: -12016.185883 EM: Round [456] log likelihood: -12016.185585 EM: Round [457] log likelihood: -12016.185289 EM: Round [458] log likelihood: -12016.184995 EM: Round [459] log likelihood: -12016.184703 EM: Round [460] log likelihood: -12016.184414 EM: Round [461] log likelihood: -12016.184126 EM: Round [462] log likelihood: -12016.183840 EM: Round [463] log likelihood: -12016.183557 EM: Round [464] log likelihood: -12016.183275 EM: Round [465] log likelihood: -12016.182995 EM: Round [466] log likelihood: -12016.182718 EM: Round [467] log likelihood: -12016.182442 EM: Round [468] log likelihood: -12016.182168 EM: Round [469] log likelihood: -12016.181896 EM: Round [470] log likelihood: -12016.181626 EM: Round [471] log likelihood: -12016.181358 EM: Round [472] log likelihood: -12016.181091 EM: Round [473] log likelihood: -12016.180827 EM: Round [474] log likelihood: -12016.180564 EM: Round [475] log likelihood: -12016.180303 EM: Round [476] log likelihood: -12016.180044 EM: Round [477] log likelihood: -12016.179787 EM: Round [478] log likelihood: -12016.179532 EM: Round [479] log likelihood: -12016.179278 EM: Round [480] log likelihood: -12016.179026 EM: Round [481] log likelihood: -12016.178776 EM: Round [482] log likelihood: -12016.178528 EM: Round [483] log likelihood: -12016.178282 EM: Round [484] log likelihood: -12016.178037 EM: Round [485] log likelihood: -12016.177794 EM: Round [486] log likelihood: -12016.177552 EM: Round [487] log likelihood: -12016.177312 EM: Round [488] log likelihood: -12016.177074 EM: Round [489] log likelihood: -12016.176838 EM: Round [490] log likelihood: -12016.176603 EM: Round [491] log likelihood: -12016.176370 EM: Round [492] log likelihood: -12016.176138 EM: Round [493] log likelihood: -12016.175908 EM: Round [494] log likelihood: -12016.175680 EM: Round [495] log likelihood: -12016.175453 EM: Round [496] log likelihood: -12016.175228 EM: Round [497] log likelihood: -12016.175005 EM: Round [498] log likelihood: -12016.174783 EM: Round [499] log likelihood: -12016.174562 EM: Round [500] log likelihood: -12016.174343 EM: Round [501] log likelihood: -12016.174126 EM: Round [502] log likelihood: -12016.173910 EM: Round [503] log likelihood: -12016.173696 EM: Round [504] log likelihood: -12016.173483 EM: Round [505] log likelihood: -12016.173272 EM: Round [506] log likelihood: -12016.173062 EM: Round [507] log likelihood: -12016.172853 EM: Round [508] log likelihood: -12016.172646 EM: Round [509] log likelihood: -12016.172441 EM: Round [510] log likelihood: -12016.172236 EM: Round [511] log likelihood: -12016.172034 EM: Round [512] log likelihood: -12016.171832 EM: Round [513] log likelihood: -12016.171633 EM: Round [514] log likelihood: -12016.171434 EM: Round [515] log likelihood: -12016.171237 EM: Round [516] log likelihood: -12016.171041 EM: Round [517] log likelihood: -12016.170847 EM: Round [518] log likelihood: -12016.170654 EM: Round [519] log likelihood: -12016.170462 EM: Round [520] log likelihood: -12016.170272 EM: Round [521] log likelihood: -12016.170083 EM: Round [522] log likelihood: -12016.169895 EM: Round [523] log likelihood: -12016.169709 EM: Round [524] log likelihood: -12016.169523 EM: Round [525] log likelihood: -12016.169340 EM: Round [526] log likelihood: -12016.169157 EM: Round [527] log likelihood: -12016.168976 EM: Round [528] log likelihood: -12016.168796 EM: Round [529] log likelihood: -12016.168617 EM: Round [530] log likelihood: -12016.168440 EM: Round [531] log likelihood: -12016.168263 EM: Round [532] log likelihood: -12016.168088 EM: Round [533] log likelihood: -12016.167914 EM: Round [534] log likelihood: -12016.167742 EM: Round [535] log likelihood: -12016.167570 EM: Round [536] log likelihood: -12016.167400 EM: Round [537] log likelihood: -12016.167231 EM: Round [538] log likelihood: -12016.167063 EM: Round [539] log likelihood: -12016.166896 EM: Round [540] log likelihood: -12016.166731 EM: Round [541] log likelihood: -12016.166567 EM: Round [542] log likelihood: -12016.166403 EM: Round [543] log likelihood: -12016.166241 EM: Round [544] log likelihood: -12016.166080 EM: Round [545] log likelihood: -12016.165920 EM: Round [546] log likelihood: -12016.165762 EM: Round [547] log likelihood: -12016.165604 EM: Round [548] log likelihood: -12016.165447 EM: Round [549] log likelihood: -12016.165292 EM: Round [550] log likelihood: -12016.165137 EM: Round [551] log likelihood: -12016.164984 EM: Round [552] log likelihood: -12016.164832 EM: Round [553] log likelihood: -12016.164681 EM: Round [554] log likelihood: -12016.164530 EM: Round [555] log likelihood: -12016.164381 EM: Round [556] log likelihood: -12016.164233 EM: Round [557] log likelihood: -12016.164086 EM: Round [558] log likelihood: -12016.163940 EM: Round [559] log likelihood: -12016.163795 EM: Round [560] log likelihood: -12016.163651 EM: Round [561] log likelihood: -12016.163508 EM: Round [562] log likelihood: -12016.163366 EM: Round [563] log likelihood: -12016.163225 EM: Round [564] log likelihood: -12016.163085 EM: Round [565] log likelihood: -12016.162946 EM: Round [566] log likelihood: -12016.162808 EM: Round [567] log likelihood: -12016.162671 EM: Round [568] log likelihood: -12016.162535 EM: Round [569] log likelihood: -12016.162399 EM: Round [570] log likelihood: -12016.162265 EM: Round [571] log likelihood: -12016.162132 EM: Round [572] log likelihood: -12016.161999 EM: Round [573] log likelihood: -12016.161868 EM: Round [574] log likelihood: -12016.161737 EM: Round [575] log likelihood: -12016.161607 EM: Round [576] log likelihood: -12016.161479 EM: Round [577] log likelihood: -12016.161351 EM: Round [578] log likelihood: -12016.161224 EM: Round [579] log likelihood: -12016.161097 EM: Round [580] log likelihood: -12016.160972 EM: Round [581] log likelihood: -12016.160848 EM: Round [582] log likelihood: -12016.160724 EM: Round [583] log likelihood: -12016.160602 EM: Round [584] log likelihood: -12016.160480 EM: Round [585] log likelihood: -12016.160359 EM: Round [586] log likelihood: -12016.160239 EM: Round [587] log likelihood: -12016.160119 EM: Round [588] log likelihood: -12016.160001 EM: Round [589] log likelihood: -12016.159883 EM: Round [590] log likelihood: -12016.159766 EM: Round [591] log likelihood: -12016.159650 EM: Round [592] log likelihood: -12016.159535 EM: Round [593] log likelihood: -12016.159421 EM: Round [594] log likelihood: -12016.159307 EM: Round [595] log likelihood: -12016.159194 EM: Round [596] log likelihood: -12016.159082 EM: Round [597] log likelihood: -12016.158971 EM: Round [598] log likelihood: -12016.158860 EM: Round [599] log likelihood: -12016.158750 EM: Round [600] log likelihood: -12016.158641 EM: Round [601] log likelihood: -12016.158533 EM: Round [602] log likelihood: -12016.158426 EM: Round [603] log likelihood: -12016.158319 EM: Round [604] log likelihood: -12016.158213 EM: Round [605] log likelihood: -12016.158108 EM: Round [606] log likelihood: -12016.158003 EM: Round [607] log likelihood: -12016.157899 EM: Round [608] log likelihood: -12016.157796 EM: Round [609] log likelihood: -12016.157694 EM: Round [610] log likelihood: -12016.157592 EM: Round [611] log likelihood: -12016.157491 EM: Round [612] log likelihood: -12016.157391 EM: Round [613] log likelihood: -12016.157291 EM: Stopping iterations at round 613 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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam" Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/tih_rna_sample_00650_B23MVV7LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.69 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.FusionJuncSpan Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa > /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/tih_rna_sample_00650_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir -done, see /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -11533.090684 EM: Round [1] log likelihood: -11532.630869 EM: Round [2] log likelihood: -11532.630623 EM: Round [3] log likelihood: -11532.630622 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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz: 296362499 Execution Time = 5.85 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa --gtf /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fa --gtf /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gtf > /tmp/nxf.HJZ3GQTWH8/fi_workdir/microH.dat Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.HJZ3GQTWH8/fi_workdir/microH.dat /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_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.HJZ3GQTWH8/fi_workdir/microH.dat /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.HJZ3GQTWH8 --json_outfile /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00650_B23MVV7LT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.HJZ3GQTWH8 --json_outfile /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00650_B23MVV7LT4_1 Running: touch /tmp/nxf.HJZ3GQTWH8/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.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00650_B23MVV7LT4_1 --html_output /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00650_B23MVV7LT4_1 --html_output /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000265018.6] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000174384.9] WARNING, no entry stored in dbm for [ENSG00000174384.9] WARNING, no entry stored in dbm for [ENSG00000174384.9] WARNING, no entry stored in dbm for [ENSG00000174384.9] WARNING, no entry stored in dbm for [ENSG00000174384.9] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000228327.3] WARNING, no entry stored in dbm for [ENSG00000228327.3] WARNING, no entry stored in dbm for [ENSG00000228327.3] WARNING, no entry stored in dbm for [ENSG00000228327.3] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] WARNING, no entry stored in dbm for [ENSG00000254633.2] 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 [ENSG00000242193.11] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.HJZ3GQTWH8/ctat_genome_lib_build_dir > /tmp/nxf.HJZ3GQTWH8/tih_rna_sample_00650_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.HJZ3GQTWH8/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory