Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4fd190dad4046b9da18af76c592fcb/tih_rna_sample_00479_B23WHTKLT4_1_1.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/a8/88caaae735347dd57d014e6bb2151b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/88caaae735347dd57d014e6bb2151b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/30ed0f4b1d94ae2e648234fc84a2be/tih_rna_sample_00479_B23WHTKLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4fd190dad4046b9da18af76c592fcb/tih_rna_sample_00479_B23WHTKLT4_1_2.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_00479_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00479_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/cytoBand.txt Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed -parsing GTF file: /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00479_B23WHTKLT4_1.star --out_dir /tmp/nxf.3KRbpDehHe/fi_workdir --reads "/tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:17:49 ..... started STAR run Jun 08 10:17:49 ..... loading genome Jun 08 10:19:36 ... generating Suffix Array index Jun 08 10:23:27 ... completed Suffix Array index Jun 08 10:23:27 ..... processing annotations GTF Jun 08 10:23:27 ..... inserting junctions into the genome indices Jun 08 10:24:29 ..... started mapping Jun 08 11:44:43 ..... finished mapping Jun 08 11:44:45 ..... started sorting BAM Jun 08 11:44:47 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00479_B23WHTKLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00479_B23WHTKLT4_1.star.sortedByCoord.out.bam Execution Time = 87.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00479_B23WHTKLT4_1.star --out_dir /tmp/nxf.3KRbpDehHe/fi_workdir --reads "/tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:45:16 : INFO : Done. Execution Time = 0.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf -parsing /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] 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[4270000] [4280000] [4290000] [4300000] [4310000] [4320000] [4330000] [4340000] [4350000] [4360000] [4370000] [4380000] [4390000] [4400000] [4410000] [4420000] [4430000] [4440000] [4450000] [4460000] [4470000] [4480000] [4490000] [4500000] [4510000] -done parsing /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 20, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4, ' ** passed ** ' => 15697, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1218, 'num genes matched < 2' => 320, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 398, 'exons hit < 2' => 17, 'low complexity anchor region' => 31, 'per_id < 96' => 21589, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 143, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 12, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 28, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 45, 'small anchor length' => 14, 'seq-similar region overlap' => 347, 'excessive soft clipping' => 31621, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 20, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 45, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 286 }; -writing fusion junction support info. Execution Time = 2.53 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: AC092666.2--ACTR3B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 -fusion SPANNING read extraction for scaff: AC105021.1--AC011474.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] -fusion SPANNING read extraction for scaff: ARHGDIA--FAAP100 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -fusion SPANNING read extraction for scaff: ASCC2--LARGE1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: AVL9--AC011592.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: AVL9--LARP7P4 [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: CCN4--TG [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: CENPBD1P1--ZNF780B -fusion SPANNING read extraction for scaff: CENPBD1P1--NTNG2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: CEP112--UTP6 [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] 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[13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] -fusion SPANNING read extraction for scaff: CREBBP--C19orf12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] -fusion SPANNING read extraction for scaff: CREBBP--AC008798.3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] -fusion SPANNING read extraction for scaff: CRYBB2P1--MYO18B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: CTC1--MYBPC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: DENND6B--PHF21B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] -fusion SPANNING read extraction for scaff: DIP2C--IL9RP2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] -fusion SPANNING read extraction for scaff: EIF2B3--PUM1 [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] -fusion SPANNING read extraction for scaff: EIF2S1--GPHN [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: EIF3H--TMEM211 [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] -fusion SPANNING read extraction for scaff: EIF4G3--AL445231.1 [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] -fusion SPANNING read extraction for scaff: EXT2--PLS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: FAM86C1P--RNF121 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] -fusion SPANNING read extraction for scaff: GBF1--BORCS7 [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] -fusion SPANNING read extraction for scaff: GK5--GOLGB1 [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: GK5--IQCB1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: GNAQ--GNA14 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] -fusion SPANNING read extraction for scaff: GNPTAB--RN7SL88P [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] -fusion SPANNING read extraction for scaff: GNPTAB--LINC02452 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] -fusion SPANNING read extraction for scaff: HIF1A--PRKCH [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: HMGB3P23--ACO1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: IQCB1--LINC00882 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: KIAA2026--AC025254.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: KIAA2026--AC090049.2 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: LDLRAD3--DMD-AS3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: LDLRAD3--DMD [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: LMNB2--AC004490.1 [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] -fusion SPANNING read extraction for scaff: MAP3K1--AC244502.1 [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] -fusion SPANNING read extraction for scaff: MCM5--LINC01643 [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] -fusion SPANNING read extraction for scaff: MCM5--AL021877.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] -fusion SPANNING read extraction for scaff: MECOM--PHC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: MGAT3--PHF21B [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] -fusion SPANNING read extraction for scaff: MORF4L1--VAT1L [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] -fusion SPANNING read extraction for scaff: NELFB--EHMT1 [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] -fusion SPANNING read extraction for scaff: NF2--WWTR1 [1000] -fusion SPANNING read extraction for scaff: NXPH2--LINC01832 [1000] -fusion SPANNING read extraction for scaff: NXPH2--RPL15P5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: OSBP2--LRRC8C [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: OTUD3--TTF2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHA2--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] -fusion SPANNING read extraction for scaff: PCDHA3--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] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1 [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: PCDHA3--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] -fusion SPANNING read extraction for scaff: 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] [43000] [44000] -fusion SPANNING read extraction for scaff: PEPD--AC011474.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] -fusion SPANNING read extraction for scaff: PER1--CELSR1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PHF21B--Z99755.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] -fusion SPANNING read extraction for scaff: PHTF2--PTPN12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PITPNM2--CSMD3 [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] -fusion SPANNING read extraction for scaff: PKD1--NPIPB2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] -fusion SPANNING read extraction for scaff: RBM19--YPEL5P3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] -fusion SPANNING read extraction for scaff: RBM19--RN7SL88P [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: REL--AHSA2P [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: RNA5SP281--ACO1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -fusion SPANNING read extraction for scaff: SBF2--GRK7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: SGF29--NPHS1 [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] -fusion SPANNING read extraction for scaff: TANC2--GAS7 [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] -fusion SPANNING read extraction for scaff: TIMM44--GRAMD1A [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: TIMM44--AC020907.4 [1000] [2000] [3000] [4000] -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] -fusion SPANNING read extraction for scaff: TNIK--NAALADL2 [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: TOMM70--DCBLD2 [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: TP53--LINC02071 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] -fusion SPANNING read extraction for scaff: TTC17--SLC9A9 [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] -fusion SPANNING read extraction for scaff: TTC28--ZNRF3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] -fusion SPANNING read extraction for scaff: URI1--LIN37 [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] -fusion SPANNING read extraction for scaff: URI1--PROSER3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: ZFPM2--DPYS [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: ZFPM2--AP002847.1 [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] -fusion SPANNING read extraction for scaff: ZNF146--ZNF568 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: ZNF536--COX7A1 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 33743, 'seq similar region alignment' => 112104 }; Execution Time = 7.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -23945.220698 EM: Round [1] log likelihood: -23942.726877 EM: Round [2] log likelihood: -23942.570152 EM: Round [3] log likelihood: -23942.436429 EM: Round [4] log likelihood: -23942.319356 EM: Round [5] log likelihood: -23942.216408 EM: Round [6] log likelihood: -23942.125540 EM: Round [7] log likelihood: -23942.045068 EM: Round [8] log likelihood: -23941.973590 EM: Round [9] log likelihood: -23941.909928 EM: Round [10] log likelihood: -23941.853086 EM: Round [11] log likelihood: -23941.802216 EM: Round [12] log likelihood: -23941.756592 EM: Round [13] log likelihood: -23941.715588 EM: Round [14] log likelihood: -23941.678663 EM: Round [15] log likelihood: -23941.645347 EM: Round [16] log likelihood: -23941.615230 EM: Round [17] log likelihood: -23941.587955 EM: Round [18] log likelihood: -23941.563208 EM: Round [19] log likelihood: -23941.540712 EM: Round [20] log likelihood: -23941.520225 EM: Round [21] log likelihood: -23941.501533 EM: Round [22] log likelihood: -23941.484445 EM: Round [23] log likelihood: -23941.468793 EM: Round [24] log likelihood: -23941.454428 EM: Round [25] log likelihood: -23941.441217 EM: Round [26] log likelihood: -23941.429043 EM: Round [27] log likelihood: -23941.417801 EM: Round [28] log likelihood: -23941.407396 EM: Round [29] log likelihood: -23941.397747 EM: Round [30] log likelihood: -23941.388777 EM: Round [31] log likelihood: -23941.380421 EM: Round [32] log likelihood: -23941.372619 EM: Round [33] log likelihood: -23941.365317 EM: Round [34] log likelihood: -23941.358468 EM: Round [35] log likelihood: -23941.352030 EM: Round [36] log likelihood: -23941.345963 EM: Round [37] log likelihood: -23941.340234 EM: Round [38] log likelihood: -23941.334812 EM: Round [39] log likelihood: -23941.329669 EM: Round [40] log likelihood: -23941.324780 EM: Round [41] log likelihood: -23941.320123 EM: Round [42] log likelihood: -23941.315678 EM: Round [43] log likelihood: -23941.311426 EM: Round [44] log likelihood: -23941.307353 EM: Round [45] log likelihood: -23941.303442 EM: Round [46] log likelihood: -23941.299681 EM: Round [47] log likelihood: -23941.296058 EM: Round [48] log likelihood: -23941.292562 EM: Round [49] log likelihood: -23941.289184 EM: Round [50] log likelihood: -23941.285914 EM: Round [51] log likelihood: -23941.282746 EM: Round [52] log likelihood: -23941.279672 EM: Round [53] log likelihood: -23941.276685 EM: Round [54] log likelihood: -23941.273779 EM: Round [55] log likelihood: -23941.270951 EM: Round [56] log likelihood: -23941.268193 EM: Round [57] log likelihood: -23941.265503 EM: Round [58] log likelihood: -23941.262877 EM: Round [59] log likelihood: -23941.260310 EM: Round [60] log likelihood: -23941.257800 EM: Round [61] log likelihood: -23941.255343 EM: Round [62] log likelihood: -23941.252937 EM: Round [63] log likelihood: -23941.250580 EM: Round [64] log likelihood: -23941.248268 EM: Round [65] log likelihood: -23941.246001 EM: Round [66] log likelihood: -23941.243776 EM: Round [67] log likelihood: -23941.241591 EM: Round [68] log likelihood: -23941.239445 EM: Round [69] log likelihood: -23941.237337 EM: Round [70] log likelihood: -23941.235264 EM: Round [71] log likelihood: -23941.233226 EM: Round [72] log likelihood: -23941.231221 EM: Round [73] log likelihood: -23941.229249 EM: Round [74] log likelihood: -23941.227309 EM: Round [75] log likelihood: -23941.225398 EM: Round [76] log likelihood: -23941.223518 EM: Round [77] log likelihood: -23941.221666 EM: Round [78] log likelihood: -23941.219842 EM: Round [79] log likelihood: -23941.218046 EM: Round [80] log likelihood: -23941.216276 EM: Round [81] log likelihood: -23941.214532 EM: Round [82] log likelihood: -23941.212814 EM: Round [83] log likelihood: -23941.211120 EM: Round [84] log likelihood: -23941.209451 EM: Round [85] log likelihood: -23941.207805 EM: Round [86] log likelihood: -23941.206182 EM: Round [87] log likelihood: -23941.204583 EM: Round [88] log likelihood: -23941.203005 EM: Round [89] log likelihood: -23941.201450 EM: Round [90] log likelihood: -23941.199915 EM: Round [91] log likelihood: -23941.198402 EM: Round [92] log likelihood: -23941.196910 EM: Round [93] log likelihood: -23941.195438 EM: Round [94] log likelihood: -23941.193986 EM: Round [95] log likelihood: -23941.192553 EM: Round [96] log likelihood: -23941.191140 EM: Round [97] log likelihood: -23941.189746 EM: Round [98] log likelihood: -23941.188370 EM: Round [99] log likelihood: -23941.187013 EM: Round [100] log likelihood: -23941.185674 EM: Round [101] log likelihood: -23941.184352 EM: Round [102] log likelihood: -23941.183049 EM: Round [103] log likelihood: -23941.181762 EM: Round [104] log likelihood: -23941.180492 EM: Round [105] log likelihood: -23941.179239 EM: Round [106] log likelihood: -23941.178002 EM: Round [107] log likelihood: -23941.176781 EM: Round [108] log likelihood: -23941.175577 EM: Round [109] log likelihood: -23941.174388 EM: Round [110] log likelihood: -23941.173214 EM: Round [111] log likelihood: -23941.172056 EM: Round [112] log likelihood: -23941.170913 EM: Round [113] log likelihood: -23941.169785 EM: Round [114] log likelihood: -23941.168671 EM: Round [115] log likelihood: -23941.167571 EM: Round [116] log likelihood: -23941.166486 EM: Round [117] log likelihood: -23941.165415 EM: Round [118] log likelihood: -23941.164357 EM: Round [119] log likelihood: -23941.163313 EM: Round [120] log likelihood: -23941.162282 EM: Round [121] log likelihood: -23941.161265 EM: Round [122] log likelihood: -23941.160261 EM: Round [123] log likelihood: -23941.159269 EM: Round [124] log likelihood: -23941.158290 EM: Round [125] log likelihood: -23941.157324 EM: Round [126] log likelihood: -23941.156370 EM: Round [127] log likelihood: -23941.155428 EM: Round [128] log likelihood: -23941.154498 EM: Round [129] log likelihood: -23941.153579 EM: Round [130] log likelihood: -23941.152673 EM: Round [131] log likelihood: -23941.151778 EM: Round [132] log likelihood: -23941.150894 EM: Round [133] log likelihood: -23941.150021 EM: Round [134] log likelihood: -23941.149160 EM: Round [135] log likelihood: -23941.148309 EM: Round [136] log likelihood: -23941.147469 EM: Round [137] log likelihood: -23941.146640 EM: Round [138] log likelihood: -23941.145821 EM: Round [139] log likelihood: -23941.145012 EM: Round [140] log likelihood: -23941.144213 EM: Round [141] log likelihood: -23941.143425 EM: Round [142] log likelihood: -23941.142646 EM: Round [143] log likelihood: -23941.141877 EM: Round [144] log likelihood: -23941.141118 EM: Round [145] log likelihood: -23941.140368 EM: Round [146] log likelihood: -23941.139628 EM: Round [147] log likelihood: -23941.138897 EM: Round [148] log likelihood: -23941.138175 EM: Round [149] log likelihood: -23941.137462 EM: Round [150] log likelihood: -23941.136758 EM: Round [151] log likelihood: -23941.136063 EM: Round [152] log likelihood: -23941.135376 EM: Round [153] log likelihood: -23941.134698 EM: Round [154] log likelihood: -23941.134028 EM: Round [155] log likelihood: -23941.133367 EM: Round [156] log likelihood: -23941.132714 EM: Round [157] log likelihood: -23941.132069 EM: Round [158] log likelihood: -23941.131432 EM: Round [159] log likelihood: -23941.130803 EM: Round [160] log likelihood: -23941.130181 EM: Round [161] log likelihood: -23941.129568 EM: Round [162] log likelihood: -23941.128961 EM: Round [163] log likelihood: -23941.128363 EM: Round [164] log likelihood: -23941.127772 EM: Round [165] log likelihood: -23941.127188 EM: Round [166] log likelihood: -23941.126611 EM: Round [167] log likelihood: -23941.126041 EM: Round [168] log likelihood: -23941.125479 EM: Round [169] log likelihood: -23941.124923 EM: Round [170] log likelihood: -23941.124374 EM: Round [171] log likelihood: -23941.123832 EM: Round [172] log likelihood: -23941.123297 EM: Round [173] log likelihood: -23941.122768 EM: Round [174] log likelihood: -23941.122246 EM: Round [175] log likelihood: -23941.121730 EM: Round [176] log likelihood: -23941.121221 EM: Round [177] log likelihood: -23941.120717 EM: Round [178] log likelihood: -23941.120220 EM: Round [179] log likelihood: -23941.119729 EM: Round [180] log likelihood: -23941.119244 EM: Round [181] log likelihood: -23941.118765 EM: Round [182] log likelihood: -23941.118292 EM: Round [183] log likelihood: -23941.117824 EM: Round [184] log likelihood: -23941.117363 EM: Round [185] log likelihood: -23941.116906 EM: Round [186] log likelihood: -23941.116456 EM: Round [187] log likelihood: -23941.116011 EM: Round [188] log likelihood: -23941.115571 EM: Round [189] log likelihood: -23941.115137 EM: Round [190] log likelihood: -23941.114708 EM: Round [191] log likelihood: -23941.114284 EM: Round [192] log likelihood: -23941.113866 EM: Round [193] log likelihood: -23941.113452 EM: Round [194] log likelihood: -23941.113044 EM: Round [195] log likelihood: -23941.112641 EM: Round [196] log likelihood: -23941.112242 EM: Round [197] log likelihood: -23941.111848 EM: Round [198] log likelihood: -23941.111459 EM: Round [199] log likelihood: -23941.111075 EM: Round [200] log likelihood: -23941.110696 EM: Round [201] log likelihood: -23941.110321 EM: Round [202] log likelihood: -23941.109950 EM: Round [203] log likelihood: -23941.109585 EM: Round [204] log likelihood: -23941.109223 EM: Round [205] log likelihood: -23941.108866 EM: Round [206] log likelihood: -23941.108513 EM: Round [207] log likelihood: -23941.108165 EM: Round [208] log likelihood: -23941.107821 EM: Round [209] log likelihood: -23941.107480 EM: Round [210] log likelihood: -23941.107145 EM: Round [211] log likelihood: -23941.106813 EM: Round [212] log likelihood: -23941.106485 EM: Round [213] log likelihood: -23941.106161 EM: Round [214] log likelihood: -23941.105841 EM: Round [215] log likelihood: -23941.105525 EM: Round [216] log likelihood: -23941.105212 EM: Round [217] log likelihood: -23941.104904 EM: Round [218] log likelihood: -23941.104599 EM: Round [219] log likelihood: -23941.104298 EM: Round [220] log likelihood: -23941.104000 EM: Round [221] log likelihood: -23941.103706 EM: Round [222] log likelihood: -23941.103416 EM: Round [223] log likelihood: -23941.103129 EM: Round [224] log likelihood: -23941.102846 EM: Round [225] log likelihood: -23941.102566 EM: Round [226] log likelihood: -23941.102289 EM: Round [227] log likelihood: -23941.102016 EM: Round [228] log likelihood: -23941.101746 EM: Round [229] log likelihood: -23941.101479 EM: Round [230] log likelihood: -23941.101215 EM: Round [231] log likelihood: -23941.100955 EM: Round [232] log likelihood: -23941.100697 EM: Round [233] log likelihood: -23941.100443 EM: Round [234] log likelihood: -23941.100192 EM: Round [235] log likelihood: -23941.099944 EM: Round [236] log likelihood: -23941.099699 EM: Round [237] log likelihood: -23941.099457 EM: Round [238] log likelihood: -23941.099217 EM: Round [239] log likelihood: -23941.098981 EM: Round [240] log likelihood: -23941.098747 EM: Round [241] log likelihood: -23941.098517 EM: Round [242] log likelihood: -23941.098289 EM: Round [243] log likelihood: -23941.098063 EM: Round [244] log likelihood: -23941.097841 EM: Round [245] log likelihood: -23941.097621 EM: Round [246] log likelihood: -23941.097404 EM: Round [247] log likelihood: -23941.097189 EM: Round [248] log likelihood: -23941.096977 EM: Round [249] log likelihood: -23941.096767 EM: Round [250] log likelihood: -23941.096560 EM: Round [251] log likelihood: -23941.096356 EM: Round [252] log likelihood: -23941.096154 EM: Round [253] log likelihood: -23941.095954 EM: Round [254] log likelihood: -23941.095756 EM: Round [255] log likelihood: -23941.095562 EM: Round [256] log likelihood: -23941.095369 EM: Round [257] log likelihood: -23941.095179 EM: Round [258] log likelihood: -23941.094991 EM: Round [259] log likelihood: -23941.094805 EM: Round [260] log likelihood: -23941.094621 EM: Round [261] log likelihood: -23941.094440 EM: Round [262] log likelihood: -23941.094261 EM: Round [263] log likelihood: -23941.094083 EM: Round [264] log likelihood: -23941.093908 EM: Round [265] log likelihood: -23941.093736 EM: Round [266] log likelihood: -23941.093565 EM: Round [267] log likelihood: -23941.093396 EM: Round [268] log likelihood: -23941.093229 EM: Round [269] log likelihood: -23941.093064 EM: Round [270] log likelihood: -23941.092902 EM: Round [271] log likelihood: -23941.092741 EM: Round [272] log likelihood: -23941.092582 EM: Round [273] log likelihood: -23941.092425 EM: Round [274] log likelihood: -23941.092270 EM: Round [275] log likelihood: -23941.092116 EM: Round [276] log likelihood: -23941.091965 EM: Round [277] log likelihood: -23941.091815 EM: Round [278] log likelihood: -23941.091667 EM: Round [279] log likelihood: -23941.091521 EM: Round [280] log likelihood: -23941.091376 EM: Round [281] log likelihood: -23941.091234 EM: Round [282] log likelihood: -23941.091093 EM: Round [283] log likelihood: -23941.090953 EM: Round [284] log likelihood: -23941.090816 EM: Round [285] log likelihood: -23941.090680 EM: Round [286] log likelihood: -23941.090545 EM: Round [287] log likelihood: -23941.090413 EM: Round [288] log likelihood: -23941.090281 EM: Round [289] log likelihood: -23941.090152 EM: Round [290] log likelihood: -23941.090024 EM: Round [291] log likelihood: -23941.089897 EM: Round [292] log likelihood: -23941.089772 EM: Round [293] log likelihood: -23941.089648 EM: Round [294] log likelihood: -23941.089526 EM: Round [295] log likelihood: -23941.089405 EM: Round [296] log likelihood: -23941.089286 EM: Round [297] log likelihood: -23941.089168 EM: Round [298] log likelihood: -23941.089052 EM: Round [299] log likelihood: -23941.088937 EM: Round [300] log likelihood: -23941.088823 EM: Round [301] log likelihood: -23941.088711 EM: Round [302] log likelihood: -23941.088600 EM: Round [303] log likelihood: -23941.088490 EM: Round [304] log likelihood: -23941.088382 EM: Round [305] log likelihood: -23941.088275 EM: Round [306] log likelihood: -23941.088169 EM: Round [307] log likelihood: -23941.088064 EM: Round [308] log likelihood: -23941.087961 EM: Round [309] log likelihood: -23941.087859 EM: Round [310] log likelihood: -23941.087758 EM: Round [311] log likelihood: -23941.087658 EM: Stopping iterations at round 311 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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam" Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/tih_rna_sample_00479_B23WHTKLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.gff3 Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa > /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/tih_rna_sample_00479_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir -done, see /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -20962.486294 EM: Round [1] log likelihood: -20961.615385 EM: Round [2] log likelihood: -20961.614366 EM: Round [3] log likelihood: -20961.614364 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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz: 295851949 Execution Time = 6.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa --gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/fi_workdir/microH.dat Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fa --gtf /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gtf > /tmp/nxf.3KRbpDehHe/fi_workdir/microH.dat Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.3KRbpDehHe/fi_workdir/microH.dat /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_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.3KRbpDehHe/fi_workdir/microH.dat /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.3KRbpDehHe --json_outfile /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00479_B23WHTKLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.3KRbpDehHe --json_outfile /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00479_B23WHTKLT4_1 Running: touch /tmp/nxf.3KRbpDehHe/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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00479_B23WHTKLT4_1 --html_output /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.04 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.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00479_B23WHTKLT4_1 --html_output /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000249383.2] WARNING, no entry stored in dbm for [ENSG00000249383.2] WARNING, no entry stored in dbm for [ENSG00000249383.2] WARNING, no entry stored in dbm for [ENSG00000249383.2] WARNING, no entry stored in dbm for [ENSG00000249383.2] WARNING, no entry stored in dbm for [ENSG00000249383.2] WARNING, no entry stored in dbm for [ENSG00000249383.2] WARNING, no entry stored in dbm for [ENSG00000264515.6] WARNING, no entry stored in dbm for [ENSG00000264515.6] WARNING, no entry stored in dbm for [ENSG00000273068.1] WARNING, no entry stored in dbm for [ENSG00000273068.1] WARNING, no entry stored in dbm for [ENSG00000236137.1] WARNING, no entry stored in dbm for [ENSG00000236137.1] WARNING, no entry stored in dbm for [ENSG00000236137.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000232420.2] WARNING, no entry stored in dbm for [ENSG00000232420.2] WARNING, no entry stored in dbm for [ENSG00000232420.2] WARNING, no entry stored in dbm for [ENSG00000232420.2] WARNING, no entry stored in dbm for [ENSG00000232420.2] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000267122.1] WARNING, no entry stored in dbm for [ENSG00000267122.1] WARNING, no entry stored in dbm for [ENSG00000267122.1] WARNING, no entry stored in dbm for [ENSG00000267122.1] WARNING, no entry stored in dbm for [ENSG00000267122.1] WARNING, no entry stored in dbm for [ENSG00000236828.1] WARNING, no entry stored in dbm for [ENSG00000100058.12] WARNING, no entry stored in dbm for [ENSG00000100058.12] WARNING, no entry stored in dbm for [ENSG00000100058.12] WARNING, no entry stored in dbm for [ENSG00000158483.17] WARNING, no entry stored in dbm for [ENSG00000158483.17] WARNING, no entry stored in dbm for [ENSG00000173209.23] WARNING, no entry stored in dbm for [ENSG00000173209.23] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000242759.8] WARNING, no entry stored in dbm for [ENSG00000242759.8] WARNING, no entry stored in dbm for [ENSG00000213753.11] WARNING, no entry stored in dbm for [ENSG00000213753.11] WARNING, no entry stored in dbm for [ENSG00000213753.11] WARNING, no entry stored in dbm for [ENSG00000213753.11] WARNING, no entry stored in dbm for [ENSG00000213753.11] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.3KRbpDehHe/ctat_genome_lib_build_dir > /tmp/nxf.3KRbpDehHe/tih_rna_sample_00479_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.3KRbpDehHe/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory