Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/c5d7d7640683d33a105ba43900bc8e/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/c5d7d7640683d33a105ba43900bc8e/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/0f41ade7ea9d60193fd1578fcacf2f/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/0cf7431a571ab0d34505f1edf4d8a2/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/0f41ade7ea9d60193fd1578fcacf2f/.command.run ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf > /tmp/nxf.2Wcw9EE4nh/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf > /tmp/nxf.2Wcw9EE4nh/cytoBand.txt Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.2Wcw9EE4nh/fi_workdir --reads "/tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 09:53:55 ..... started STAR run Jun 08 09:53:55 ..... loading genome Jun 08 09:55:38 ... generating Suffix Array index Jun 08 09:59:30 ... completed Suffix Array index Jun 08 09:59:30 ..... processing annotations GTF Jun 08 09:59:31 ..... inserting junctions into the genome indices Jun 08 10:00:32 ..... started mapping Jun 08 11:03:16 ..... finished mapping Jun 08 11:03:18 ..... started sorting BAM Jun 08 11:03:20 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 69.50 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.2Wcw9EE4nh/fi_workdir --reads "/tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:03:49 : INFO : Done. Execution Time = 0.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] 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Extracting junction info. junction read elimination tally: $VAR1 = { 'seq-similar region overlap' => 247, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 78, 'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 12, 'per_id < 96' => 19488, 'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 10, 'small anchor length' => 81, ' ** passed ** ' => 15917, 'num genes matched < 2' => 40, 'low complexity anchor region' => 20, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 18, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 10, 'exons hit < 2' => 24, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 21, 'excessive soft clipping' => 39177, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 330, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 34 }; -writing fusion junction support info. Execution Time = 2.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: AGAP12P--FRMPD2 [1000] [2000] -fusion SPANNING read extraction for scaff: AL669831.4--SEPTIN14 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: ANKRD42--AC139365.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: ANKRD42--AC118650.1 [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] 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[164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] -fusion SPANNING read extraction for scaff: AP000487.1--ADGRA2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: BMS1P7--AGAP14P [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] -fusion SPANNING read extraction for scaff: CLPTM1L--TERT [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] -fusion SPANNING read extraction for scaff: CPT1A--FBXO25 [1000] -fusion SPANNING read extraction for scaff: CST9--CST9L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] 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[157000] [158000] [159000] -fusion SPANNING read extraction for scaff: CTTN--DLG2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: CYP7B1--ADAM32 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: DLG2--AC091182.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: DLG2--AC091182.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: DLGAP2--ANKRD42 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: FBXO25--DLGAP2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1 [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] -fusion SPANNING read extraction for scaff: KAT6A--AC105999.1 [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] -fusion SPANNING read extraction for scaff: KAT6A--AC010857.1 [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] -fusion SPANNING read extraction for scaff: KAT6A--SIRLNT [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] -fusion SPANNING read extraction for scaff: LRP5--FBXO25 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] -fusion SPANNING read extraction for scaff: LSM1--ADAM2 [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: MIR4457--TERT [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: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [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: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [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] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: PCDHA6--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] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [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] -fusion SPANNING read extraction for scaff: PLEKHA2--ANK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] 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[636000] [637000] [638000] [639000] [640000] [641000] [642000] [643000] [644000] [645000] [646000] [647000] [648000] [649000] [650000] [651000] [652000] [653000] [654000] [655000] [656000] [657000] [658000] [659000] [660000] [661000] [662000] [663000] [664000] [665000] [666000] [667000] [668000] [669000] [670000] [671000] [672000] [673000] [674000] [675000] [676000] [677000] [678000] [679000] [680000] [681000] [682000] [683000] [684000] [685000] [686000] [687000] [688000] [689000] [690000] [691000] [692000] [693000] [694000] [695000] [696000] [697000] [698000] [699000] [700000] [701000] [702000] [703000] [704000] [705000] [706000] [707000] [708000] [709000] [710000] [711000] [712000] [713000] [714000] [715000] [716000] [717000] [718000] [719000] [720000] [721000] [722000] [723000] [724000] [725000] [726000] [727000] [728000] [729000] [730000] [731000] [732000] [733000] [734000] [735000] [736000] [737000] [738000] [739000] [740000] [741000] [742000] [743000] [744000] [745000] [746000] 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[858000] [859000] [860000] [861000] [862000] [863000] [864000] [865000] [866000] [867000] [868000] [869000] [870000] [871000] [872000] [873000] [874000] [875000] [876000] [877000] [878000] [879000] [880000] [881000] [882000] [883000] [884000] [885000] [886000] [887000] [888000] [889000] [890000] [891000] [892000] [893000] [894000] [895000] [896000] [897000] [898000] [899000] [900000] [901000] [902000] [903000] [904000] [905000] [906000] [907000] [908000] [909000] [910000] [911000] [912000] [913000] [914000] [915000] [916000] [917000] [918000] [919000] [920000] [921000] [922000] [923000] [924000] [925000] [926000] [927000] [928000] [929000] [930000] [931000] [932000] [933000] [934000] [935000] [936000] [937000] [938000] [939000] [940000] [941000] [942000] [943000] [944000] [945000] [946000] [947000] [948000] [949000] [950000] [951000] [952000] [953000] [954000] [955000] [956000] [957000] [958000] [959000] [960000] [961000] [962000] [963000] [964000] [965000] [966000] [967000] [968000] [969000] [970000] [971000] [972000] [973000] [974000] [975000] [976000] [977000] [978000] [979000] [980000] [981000] [982000] [983000] [984000] [985000] [986000] [987000] [988000] [989000] [990000] [991000] [992000] [993000] [994000] [995000] [996000] [997000] [998000] [999000] [1000000] [1001000] [1002000] [1003000] [1004000] [1005000] [1006000] [1007000] [1008000] [1009000] [1010000] [1011000] [1012000] [1013000] [1014000] [1015000] [1016000] [1017000] [1018000] [1019000] [1020000] [1021000] [1022000] [1023000] [1024000] [1025000] [1026000] [1027000] [1028000] [1029000] [1030000] [1031000] [1032000] [1033000] [1034000] [1035000] [1036000] [1037000] [1038000] [1039000] [1040000] [1041000] [1042000] [1043000] [1044000] [1045000] [1046000] [1047000] [1048000] [1049000] [1050000] [1051000] [1052000] [1053000] [1054000] [1055000] [1056000] [1057000] [1058000] [1059000] [1060000] [1061000] [1062000] [1063000] [1064000] [1065000] [1066000] [1067000] [1068000] [1069000] [1070000] [1071000] [1072000] [1073000] [1074000] [1075000] [1076000] [1077000] [1078000] [1079000] [1080000] [1081000] [1082000] [1083000] [1084000] [1085000] [1086000] [1087000] [1088000] [1089000] [1090000] [1091000] [1092000] [1093000] [1094000] [1095000] [1096000] [1097000] [1098000] [1099000] [1100000] [1101000] [1102000] [1103000] [1104000] [1105000] [1106000] [1107000] [1108000] [1109000] [1110000] [1111000] [1112000] [1113000] [1114000] [1115000] [1116000] [1117000] [1118000] [1119000] [1120000] [1121000] [1122000] [1123000] [1124000] [1125000] [1126000] [1127000] [1128000] [1129000] [1130000] [1131000] [1132000] [1133000] [1134000] [1135000] [1136000] [1137000] [1138000] [1139000] [1140000] [1141000] [1142000] [1143000] [1144000] [1145000] [1146000] [1147000] [1148000] [1149000] [1150000] [1151000] [1152000] [1153000] [1154000] [1155000] [1156000] [1157000] [1158000] [1159000] [1160000] [1161000] [1162000] [1163000] [1164000] [1165000] [1166000] [1167000] [1168000] [1169000] [1170000] [1171000] [1172000] [1173000] [1174000] [1175000] [1176000] [1177000] [1178000] [1179000] [1180000] [1181000] [1182000] [1183000] [1184000] [1185000] [1186000] [1187000] [1188000] [1189000] [1190000] [1191000] [1192000] [1193000] [1194000] [1195000] [1196000] [1197000] [1198000] [1199000] [1200000] [1201000] [1202000] [1203000] [1204000] [1205000] [1206000] [1207000] [1208000] [1209000] [1210000] [1211000] [1212000] [1213000] [1214000] [1215000] [1216000] [1217000] [1218000] [1219000] [1220000] [1221000] [1222000] [1223000] [1224000] [1225000] [1226000] [1227000] [1228000] [1229000] [1230000] [1231000] [1232000] [1233000] [1234000] [1235000] [1236000] [1237000] [1238000] [1239000] [1240000] [1241000] [1242000] [1243000] [1244000] [1245000] [1246000] [1247000] [1248000] [1249000] [1250000] [1251000] [1252000] [1253000] [1254000] [1255000] [1256000] [1257000] [1258000] [1259000] [1260000] [1261000] [1262000] [1263000] [1264000] [1265000] [1266000] [1267000] [1268000] [1269000] [1270000] [1271000] 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[1372000] [1373000] [1374000] [1375000] [1376000] [1377000] [1378000] [1379000] [1380000] [1381000] [1382000] [1383000] [1384000] [1385000] [1386000] [1387000] [1388000] [1389000] [1390000] [1391000] [1392000] [1393000] [1394000] [1395000] [1396000] [1397000] [1398000] [1399000] [1400000] [1401000] [1402000] [1403000] [1404000] [1405000] [1406000] [1407000] [1408000] [1409000] [1410000] [1411000] [1412000] [1413000] [1414000] [1415000] [1416000] [1417000] [1418000] [1419000] [1420000] [1421000] [1422000] [1423000] [1424000] [1425000] [1426000] [1427000] [1428000] [1429000] [1430000] [1431000] [1432000] [1433000] [1434000] [1435000] [1436000] [1437000] [1438000] [1439000] [1440000] [1441000] [1442000] [1443000] [1444000] [1445000] [1446000] [1447000] [1448000] [1449000] [1450000] [1451000] [1452000] [1453000] [1454000] [1455000] [1456000] [1457000] [1458000] [1459000] [1460000] [1461000] [1462000] [1463000] [1464000] [1465000] [1466000] [1467000] [1468000] [1469000] [1470000] [1471000] [1472000] [1473000] [1474000] [1475000] [1476000] [1477000] [1478000] [1479000] [1480000] [1481000] [1482000] [1483000] [1484000] [1485000] [1486000] [1487000] [1488000] [1489000] [1490000] [1491000] [1492000] [1493000] [1494000] [1495000] [1496000] [1497000] [1498000] [1499000] [1500000] [1501000] [1502000] [1503000] [1504000] [1505000] [1506000] [1507000] [1508000] [1509000] [1510000] [1511000] [1512000] [1513000] [1514000] [1515000] [1516000] [1517000] [1518000] [1519000] [1520000] [1521000] [1522000] [1523000] [1524000] [1525000] [1526000] [1527000] [1528000] [1529000] [1530000] [1531000] [1532000] [1533000] [1534000] [1535000] [1536000] [1537000] [1538000] [1539000] [1540000] [1541000] [1542000] [1543000] [1544000] [1545000] [1546000] [1547000] [1548000] [1549000] [1550000] [1551000] [1552000] [1553000] [1554000] [1555000] [1556000] [1557000] [1558000] [1559000] [1560000] [1561000] [1562000] [1563000] [1564000] [1565000] [1566000] [1567000] [1568000] [1569000] [1570000] [1571000] [1572000] [1573000] [1574000] [1575000] [1576000] [1577000] [1578000] [1579000] [1580000] [1581000] [1582000] [1583000] [1584000] [1585000] [1586000] [1587000] [1588000] [1589000] [1590000] [1591000] [1592000] [1593000] [1594000] [1595000] [1596000] [1597000] [1598000] [1599000] [1600000] [1601000] [1602000] [1603000] [1604000] [1605000] [1606000] [1607000] [1608000] [1609000] [1610000] [1611000] [1612000] [1613000] [1614000] [1615000] [1616000] [1617000] [1618000] [1619000] [1620000] [1621000] [1622000] [1623000] [1624000] [1625000] [1626000] [1627000] [1628000] [1629000] [1630000] [1631000] [1632000] [1633000] [1634000] [1635000] [1636000] [1637000] [1638000] [1639000] [1640000] [1641000] [1642000] [1643000] [1644000] [1645000] [1646000] [1647000] [1648000] [1649000] [1650000] [1651000] [1652000] [1653000] [1654000] [1655000] [1656000] [1657000] [1658000] [1659000] [1660000] [1661000] [1662000] [1663000] [1664000] [1665000] [1666000] [1667000] [1668000] [1669000] [1670000] [1671000] [1672000] [1673000] [1674000] [1675000] [1676000] [1677000] [1678000] [1679000] [1680000] [1681000] [1682000] [1683000] [1684000] [1685000] [1686000] [1687000] [1688000] [1689000] [1690000] [1691000] [1692000] [1693000] [1694000] [1695000] [1696000] [1697000] [1698000] [1699000] [1700000] [1701000] [1702000] [1703000] [1704000] [1705000] [1706000] [1707000] [1708000] [1709000] [1710000] [1711000] [1712000] [1713000] [1714000] [1715000] [1716000] [1717000] [1718000] [1719000] [1720000] [1721000] [1722000] [1723000] [1724000] [1725000] [1726000] [1727000] [1728000] [1729000] [1730000] [1731000] [1732000] [1733000] [1734000] [1735000] [1736000] [1737000] [1738000] [1739000] [1740000] [1741000] [1742000] [1743000] [1744000] [1745000] [1746000] [1747000] [1748000] [1749000] [1750000] [1751000] [1752000] [1753000] [1754000] [1755000] [1756000] [1757000] [1758000] [1759000] [1760000] [1761000] [1762000] [1763000] [1764000] [1765000] [1766000] [1767000] [1768000] [1769000] [1770000] [1771000] [1772000] [1773000] [1774000] [1775000] [1776000] [1777000] [1778000] [1779000] [1780000] [1781000] [1782000] [1783000] [1784000] [1785000] [1786000] [1787000] [1788000] [1789000] [1790000] [1791000] [1792000] [1793000] [1794000] [1795000] [1796000] [1797000] [1798000] [1799000] [1800000] [1801000] [1802000] [1803000] [1804000] [1805000] [1806000] [1807000] [1808000] [1809000] [1810000] [1811000] [1812000] [1813000] [1814000] [1815000] [1816000] [1817000] [1818000] [1819000] [1820000] [1821000] [1822000] [1823000] [1824000] [1825000] [1826000] [1827000] [1828000] [1829000] [1830000] [1831000] [1832000] [1833000] [1834000] [1835000] [1836000] [1837000] [1838000] [1839000] [1840000] [1841000] [1842000] [1843000] [1844000] [1845000] [1846000] [1847000] [1848000] [1849000] [1850000] [1851000] [1852000] [1853000] [1854000] [1855000] [1856000] [1857000] [1858000] [1859000] [1860000] [1861000] [1862000] [1863000] [1864000] [1865000] [1866000] [1867000] [1868000] -fusion SPANNING read extraction for scaff: PLPBP--NSD3 [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] -fusion SPANNING read extraction for scaff: PLPBP--ASH2L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] -fusion SPANNING read extraction for scaff: PPP6R3--C11orf24 [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: PPP6R3--AP002813.1 [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] [113000] -fusion SPANNING read extraction for scaff: PPP6R3--LRP5 [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] -fusion SPANNING read extraction for scaff: PRR12--PPP5C [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] -fusion SPANNING read extraction for scaff: PRR12--CCDC8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PSG8--CD177 [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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -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] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 34110, 'lacks exon overlap' => 160182 }; Execution Time = 6.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -17941.052741 EM: Round [1] log likelihood: -17937.084232 EM: Round [2] log likelihood: -17935.958867 EM: Round [3] log likelihood: -17934.995829 EM: Round [4] log likelihood: -17934.164702 EM: Round [5] log likelihood: -17933.444394 EM: Round [6] log likelihood: -17932.817924 EM: Round [7] log likelihood: -17932.271432 EM: Round [8] log likelihood: -17931.793487 EM: Round [9] log likelihood: -17931.374570 EM: Round [10] log likelihood: -17931.006695 EM: Round [11] log likelihood: -17930.683110 EM: Round [12] log likelihood: -17930.398077 EM: Round [13] log likelihood: -17930.146690 EM: Round [14] log likelihood: -17929.924736 EM: Round [15] log likelihood: -17929.728582 EM: Round [16] log likelihood: -17929.555085 EM: Round [17] log likelihood: -17929.401515 EM: Round [18] log likelihood: -17929.265495 EM: Round [19] log likelihood: -17929.144951 EM: Round [20] log likelihood: -17929.038068 EM: Round [21] log likelihood: -17928.943256 EM: Round [22] log likelihood: -17928.859120 EM: Round [23] log likelihood: -17928.784430 EM: Round [24] log likelihood: -17928.718107 EM: Round [25] log likelihood: -17928.659196 EM: Round [26] log likelihood: -17928.606857 EM: Round [27] log likelihood: -17928.560347 EM: Round [28] log likelihood: -17928.519008 EM: Round [29] log likelihood: -17928.482260 EM: Round [30] log likelihood: -17928.449588 EM: Round [31] log likelihood: -17928.420536 EM: Round [32] log likelihood: -17928.394699 EM: Round [33] log likelihood: -17928.371720 EM: Round [34] log likelihood: -17928.351281 EM: Round [35] log likelihood: -17928.333099 EM: Round [36] log likelihood: -17928.316924 EM: Round [37] log likelihood: -17928.302533 EM: Round [38] log likelihood: -17928.289729 EM: Round [39] log likelihood: -17928.278336 EM: Round [40] log likelihood: -17928.268198 EM: Round [41] log likelihood: -17928.259177 EM: Round [42] log likelihood: -17928.251150 EM: Round [43] log likelihood: -17928.244006 EM: Round [44] log likelihood: -17928.237648 EM: Round [45] log likelihood: -17928.231990 EM: Round [46] log likelihood: -17928.226954 EM: Round [47] log likelihood: -17928.222472 EM: Round [48] log likelihood: -17928.218483 EM: Round [49] log likelihood: -17928.214933 EM: Round [50] log likelihood: -17928.211773 EM: Round [51] log likelihood: -17928.208961 EM: Round [52] log likelihood: -17928.206457 EM: Round [53] log likelihood: -17928.204229 EM: Round [54] log likelihood: -17928.202246 EM: Round [55] log likelihood: -17928.200481 EM: Round [56] log likelihood: -17928.198909 EM: Round [57] log likelihood: -17928.197511 EM: Round [58] log likelihood: -17928.196266 EM: Round [59] log likelihood: -17928.195158 EM: Round [60] log likelihood: -17928.194171 EM: Round [61] log likelihood: -17928.193293 EM: Round [62] log likelihood: -17928.192512 EM: Round [63] log likelihood: -17928.191816 EM: Round [64] log likelihood: -17928.191197 EM: Round [65] log likelihood: -17928.190646 EM: Round [66] log likelihood: -17928.190155 EM: Round [67] log likelihood: -17928.189719 EM: Round [68] log likelihood: -17928.189330 EM: Round [69] log likelihood: -17928.188984 EM: Round [70] log likelihood: -17928.188676 EM: Round [71] log likelihood: -17928.188402 EM: Round [72] log likelihood: -17928.188157 EM: Round [73] log likelihood: -17928.187940 EM: Round [74] log likelihood: -17928.187747 EM: Round [75] log likelihood: -17928.187575 EM: Round [76] log likelihood: -17928.187421 EM: Round [77] log likelihood: -17928.187285 EM: Round [78] log likelihood: -17928.187164 EM: Round [79] log likelihood: -17928.187056 EM: Round [80] log likelihood: -17928.186959 EM: Stopping iterations at round 80 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.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_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.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam || : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.27 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.Pfam.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa > /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.2Wcw9EE4nh/fi_workdir/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir -done, see /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -14812.153272 EM: Round [1] log likelihood: -14811.682131 EM: Round [2] log likelihood: -14811.681989 EM: Round [3] log likelihood: -14811.681987 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.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296573757 Execution Time = 5.64 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf > /tmp/nxf.2Wcw9EE4nh/fi_workdir/microH.dat Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gtf > /tmp/nxf.2Wcw9EE4nh/fi_workdir/microH.dat Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.2Wcw9EE4nh/fi_workdir/microH.dat /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.2Wcw9EE4nh/fi_workdir/microH.dat /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.2Wcw9EE4nh --json_outfile /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-9b89b4-R1_A23YTGFLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.2Wcw9EE4nh --json_outfile /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-9b89b4-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.2Wcw9EE4nh/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.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-9b89b4-R1_A23YTGFLT4_1 --html_output /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.02 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.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-9b89b4-R1_A23YTGFLT4_1 --html_output /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000230092.7] 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 [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000265018.6] WARNING, no entry stored in dbm for [ENSG00000265018.6] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000246889.2] WARNING, no entry stored in dbm for [ENSG00000246889.2] WARNING, no entry stored in dbm for [ENSG00000246889.2] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000279058.2] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000279058.2] WARNING, no entry stored in dbm for [ENSG00000253354.2] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.2Wcw9EE4nh/ctat_genome_lib_build_dir > /tmp/nxf.2Wcw9EE4nh/aih-tih-sc-9b89b4-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.2Wcw9EE4nh/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory