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/df/8cce9acd6b906a1647cde72c28b3eb/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/93202e58d5142714636fd130154445/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/8cce9acd6b906a1647cde72c28b3eb/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/93202e58d5142714636fd130154445/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/03e54c7e16b62c6ced84bdcdaa52ac/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/cytoBand.txt Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed -parsing GTF file: /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.atNtBlHYmi/fi_workdir --reads "/tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 13:58:56 ..... started STAR run Jun 08 13:58:56 ..... loading genome Jun 08 14:00:38 ... generating Suffix Array index Jun 08 14:04:29 ... completed Suffix Array index Jun 08 14:04:29 ..... processing annotations GTF Jun 08 14:04:30 ..... inserting junctions into the genome indices Jun 08 14:05:30 ..... started mapping Jun 08 14:46:09 ..... finished mapping Jun 08 14:46:10 ..... started sorting BAM Jun 08 14:46:12 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam Execution Time = 47.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.atNtBlHYmi/fi_workdir --reads "/tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 14:46:38 : INFO : Done. Execution Time = 0.37 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf -parsing /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] 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[4260000] [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] [4520000] [4530000] [4540000] [4550000] [4560000] [4570000] [4580000] [4590000] [4600000] [4610000] [4620000] [4630000] [4640000] [4650000] [4660000] [4670000] [4680000] [4690000] [4700000] [4710000] [4720000] [4730000] [4740000] [4750000] [4760000] [4770000] [4780000] [4790000] [4800000] [4810000] [4820000] [4830000] [4840000] [4850000] [4860000] [4870000] [4880000] -done parsing /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { ' ** passed ** ' => 9170, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6, 'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5, 'num genes matched < 2' => 48, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 72, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 62, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 27, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 75, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 92, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 24, 'small anchor length' => 168, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8, 'low complexity anchor region' => 19, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 2, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 32, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 154, 'per_id < 96' => 229729, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1024, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 2, 'exons hit < 2' => 21, 'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 2, 'excessive soft clipping' => 130892, 'seq-similar region overlap' => 359 }; -writing fusion junction support info. Execution Time = 2.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: AC134878.2--AK6 [1000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: CROT--DEFB123 [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: DHX40--SKA2 [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] -fusion SPANNING read extraction for scaff: GUSBP13--NAIP [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] -fusion SPANNING read extraction for scaff: NBAS--EFEMP1 [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: 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] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] -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] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] -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] -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] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -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] [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: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [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: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [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: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] -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] [45000] [46000] [47000] [48000] -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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] -fusion SPANNING read extraction for scaff: POLR2F--HMGB1 [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] -fusion SPANNING read extraction for scaff: POLR2F--MXI1 [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] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] [489000] [490000] [491000] [492000] [493000] [494000] [495000] [496000] [497000] [498000] [499000] [500000] [501000] [502000] [503000] [504000] [505000] [506000] [507000] [508000] [509000] [510000] [511000] [512000] [513000] [514000] [515000] [516000] [517000] [518000] [519000] [520000] [521000] [522000] [523000] [524000] [525000] [526000] [527000] [528000] [529000] [530000] [531000] [532000] [533000] [534000] [535000] [536000] [537000] [538000] [539000] [540000] [541000] [542000] [543000] [544000] [545000] [546000] [547000] [548000] [549000] [550000] [551000] [552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] [573000] [574000] [575000] [576000] [577000] [578000] [579000] [580000] [581000] [582000] [583000] [584000] [585000] [586000] [587000] [588000] [589000] [590000] [591000] [592000] [593000] [594000] [595000] [596000] [597000] [598000] [599000] [600000] [601000] [602000] [603000] [604000] [605000] [606000] [607000] [608000] [609000] [610000] [611000] [612000] [613000] [614000] [615000] [616000] [617000] [618000] [619000] [620000] [621000] [622000] [623000] [624000] [625000] [626000] [627000] [628000] [629000] [630000] [631000] [632000] [633000] [634000] [635000] [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] [747000] [748000] [749000] [750000] [751000] [752000] [753000] [754000] [755000] [756000] [757000] [758000] [759000] [760000] [761000] [762000] [763000] [764000] [765000] [766000] [767000] [768000] [769000] [770000] [771000] [772000] [773000] [774000] [775000] [776000] [777000] [778000] [779000] [780000] [781000] [782000] [783000] [784000] [785000] [786000] [787000] [788000] [789000] [790000] [791000] [792000] [793000] [794000] [795000] [796000] [797000] [798000] [799000] [800000] [801000] [802000] [803000] [804000] [805000] [806000] [807000] [808000] [809000] [810000] [811000] [812000] [813000] [814000] [815000] [816000] [817000] [818000] [819000] [820000] [821000] [822000] [823000] [824000] -fusion SPANNING read extraction for scaff: POLR2F--GNAS [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] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] [489000] [490000] [491000] [492000] [493000] [494000] [495000] [496000] [497000] [498000] [499000] [500000] [501000] [502000] [503000] [504000] -fusion SPANNING read extraction for scaff: RPL14--MAML2 [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] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] -fusion SPANNING read extraction for scaff: RPL14--ATN1 [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] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] -fusion SPANNING read extraction for scaff: RPL14--EP400 [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] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] -fusion SPANNING read extraction for scaff: RPL14--MPRIP [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] -fusion SPANNING read extraction for scaff: RPL14--E2F4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: SKA2--RNFT1-DT [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: TAS2R14--PRR4 [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] -fusion SPANNING read extraction for scaff: TCEAL4--MTRNR2L12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] -fusion SPANNING read extraction for scaff: TTC26--HIPK2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] -fusion SPANNING read extraction for scaff: WDR91--AC008163.1 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 7305, 'seq similar region alignment' => 89484 }; Execution Time = 6.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -6038.855409 EM: Round [1] log likelihood: -6038.155514 EM: Round [2] log likelihood: -6037.805726 EM: Round [3] log likelihood: -6037.493492 EM: Round [4] log likelihood: -6037.213398 EM: Round [5] log likelihood: -6036.961260 EM: Round [6] log likelihood: -6036.733581 EM: Round [7] log likelihood: -6036.527408 EM: Round [8] log likelihood: -6036.340229 EM: Round [9] log likelihood: -6036.169890 EM: Round [10] log likelihood: -6036.014531 EM: Round [11] log likelihood: -6035.872542 EM: Round [12] log likelihood: -6035.742516 EM: Round [13] log likelihood: -6035.623224 EM: Round [14] log likelihood: -6035.513584 EM: Round [15] log likelihood: -6035.412639 EM: Round [16] log likelihood: -6035.319545 EM: Round [17] log likelihood: -6035.233552 EM: Round [18] log likelihood: -6035.153989 EM: Round [19] log likelihood: -6035.080260 EM: Round [20] log likelihood: -6035.011830 EM: Round [21] log likelihood: -6034.948222 EM: Round [22] log likelihood: -6034.889003 EM: Round [23] log likelihood: -6034.833787 EM: Round [24] log likelihood: -6034.782226 EM: Round [25] log likelihood: -6034.734002 EM: Round [26] log likelihood: -6034.688833 EM: Round [27] log likelihood: -6034.646461 EM: Round [28] log likelihood: -6034.606651 EM: Round [29] log likelihood: -6034.569193 EM: Round [30] log likelihood: -6034.533893 EM: Round [31] log likelihood: -6034.500578 EM: Round [32] log likelihood: -6034.469088 EM: Round [33] log likelihood: -6034.439279 EM: Round [34] log likelihood: -6034.411020 EM: Round [35] log likelihood: -6034.384190 EM: Round [36] log likelihood: -6034.358680 EM: Round [37] log likelihood: -6034.334389 EM: Round [38] log likelihood: -6034.311228 EM: Round [39] log likelihood: -6034.289112 EM: Round [40] log likelihood: -6034.267965 EM: Round [41] log likelihood: -6034.247717 EM: Round [42] log likelihood: -6034.228305 EM: Round [43] log likelihood: -6034.209670 EM: Round [44] log likelihood: -6034.191759 EM: Round [45] log likelihood: -6034.174523 EM: Round [46] log likelihood: -6034.157916 EM: Round [47] log likelihood: -6034.141897 EM: Round [48] log likelihood: -6034.126428 EM: Round [49] log likelihood: -6034.111474 EM: Round [50] log likelihood: -6034.097004 EM: Round [51] log likelihood: -6034.082987 EM: Round [52] log likelihood: -6034.069397 EM: Round [53] log likelihood: -6034.056208 EM: Round [54] log likelihood: -6034.043397 EM: Round [55] log likelihood: -6034.030944 EM: Round [56] log likelihood: -6034.018828 EM: Round [57] log likelihood: -6034.007032 EM: Round [58] log likelihood: -6033.995538 EM: Round [59] log likelihood: -6033.984331 EM: Round [60] log likelihood: -6033.973398 EM: Round [61] log likelihood: -6033.962723 EM: Round [62] log likelihood: -6033.952296 EM: Round [63] log likelihood: -6033.942105 EM: Round [64] log likelihood: -6033.932139 EM: Round [65] log likelihood: -6033.922388 EM: Round [66] log likelihood: -6033.912844 EM: Round [67] log likelihood: -6033.903497 EM: Round [68] log likelihood: -6033.894339 EM: Round [69] log likelihood: -6033.885364 EM: Round [70] log likelihood: -6033.876564 EM: Round [71] log likelihood: -6033.867933 EM: Round [72] log likelihood: -6033.859464 EM: Round [73] log likelihood: -6033.851153 EM: Round [74] log likelihood: -6033.842993 EM: Round [75] log likelihood: -6033.834980 EM: Round [76] log likelihood: -6033.827108 EM: Round [77] log likelihood: -6033.819374 EM: Round [78] log likelihood: -6033.811774 EM: Round [79] log likelihood: -6033.804302 EM: Round [80] log likelihood: -6033.796956 EM: Round [81] log likelihood: -6033.789733 EM: Round [82] log likelihood: -6033.782627 EM: Round [83] log likelihood: -6033.775638 EM: Round [84] log likelihood: -6033.768761 EM: Round [85] log likelihood: -6033.761993 EM: Round [86] log likelihood: -6033.755333 EM: Round [87] log likelihood: -6033.748776 EM: Round [88] log likelihood: -6033.742322 EM: Round [89] log likelihood: -6033.735967 EM: Round [90] log likelihood: -6033.729709 EM: Round [91] log likelihood: -6033.723546 EM: Round [92] log likelihood: -6033.717476 EM: Round [93] log likelihood: -6033.711497 EM: Round [94] log likelihood: -6033.705607 EM: Round [95] log likelihood: -6033.699804 EM: Round [96] log likelihood: -6033.694086 EM: Round [97] log likelihood: -6033.688452 EM: Round [98] log likelihood: -6033.682900 EM: Round [99] log likelihood: -6033.677429 EM: Round [100] log likelihood: -6033.672037 EM: Round [101] log likelihood: -6033.666721 EM: Round [102] log likelihood: -6033.661482 EM: Round [103] log likelihood: -6033.656318 EM: Round [104] log likelihood: -6033.651227 EM: Round [105] log likelihood: -6033.646207 EM: Round [106] log likelihood: -6033.641258 EM: Round [107] log likelihood: -6033.636379 EM: Round [108] log likelihood: -6033.631568 EM: Round [109] log likelihood: -6033.626824 EM: Round [110] log likelihood: -6033.622146 EM: Round [111] log likelihood: -6033.617533 EM: Round [112] log likelihood: -6033.612983 EM: Round [113] log likelihood: -6033.608496 EM: Round [114] log likelihood: -6033.604071 EM: Round [115] log likelihood: -6033.599706 EM: Round [116] log likelihood: -6033.595401 EM: Round [117] log likelihood: -6033.591155 EM: Round [118] log likelihood: -6033.586966 EM: Round [119] log likelihood: -6033.582835 EM: Round [120] log likelihood: -6033.578759 EM: Round [121] log likelihood: -6033.574738 EM: Round [122] log likelihood: -6033.570772 EM: Round [123] log likelihood: -6033.566859 EM: Round [124] log likelihood: -6033.562999 EM: Round [125] log likelihood: -6033.559190 EM: Round [126] log likelihood: -6033.555433 EM: Round [127] log likelihood: -6033.551726 EM: Round [128] log likelihood: -6033.548068 EM: Round [129] log likelihood: -6033.544459 EM: Round [130] log likelihood: -6033.540898 EM: Round [131] log likelihood: -6033.537384 EM: Round [132] log likelihood: -6033.533917 EM: Round [133] log likelihood: -6033.530496 EM: Round [134] log likelihood: -6033.527120 EM: Round [135] log likelihood: -6033.523789 EM: Round [136] log likelihood: -6033.520501 EM: Round [137] log likelihood: -6033.517257 EM: Round [138] log likelihood: -6033.514056 EM: Round [139] log likelihood: -6033.510897 EM: Round [140] log likelihood: -6033.507779 EM: Round [141] log likelihood: -6033.504702 EM: Round [142] log likelihood: -6033.501665 EM: Round [143] log likelihood: -6033.498668 EM: Round [144] log likelihood: -6033.495711 EM: Round [145] log likelihood: -6033.492792 EM: Round [146] log likelihood: -6033.489910 EM: Round [147] log likelihood: -6033.487067 EM: Round [148] log likelihood: -6033.484260 EM: Round [149] log likelihood: -6033.481490 EM: Round [150] log likelihood: -6033.478756 EM: Round [151] log likelihood: -6033.476057 EM: Round [152] log likelihood: -6033.473394 EM: Round [153] log likelihood: -6033.470764 EM: Round [154] log likelihood: -6033.468169 EM: Round [155] log likelihood: -6033.465608 EM: Round [156] log likelihood: -6033.463079 EM: Round [157] log likelihood: -6033.460583 EM: Round [158] log likelihood: -6033.458119 EM: Round [159] log likelihood: -6033.455687 EM: Round [160] log likelihood: -6033.453287 EM: Round [161] log likelihood: -6033.450917 EM: Round [162] log likelihood: -6033.448577 EM: Round [163] log likelihood: -6033.446268 EM: Round [164] log likelihood: -6033.443988 EM: Round [165] log likelihood: -6033.441738 EM: Round [166] log likelihood: -6033.439516 EM: Round [167] log likelihood: -6033.437323 EM: Round [168] log likelihood: -6033.435158 EM: Round [169] log likelihood: -6033.433020 EM: Round [170] log likelihood: -6033.430910 EM: Round [171] log likelihood: -6033.428827 EM: Round [172] log likelihood: -6033.426770 EM: Round [173] log likelihood: -6033.424740 EM: Round [174] log likelihood: -6033.422735 EM: Round [175] log likelihood: -6033.420756 EM: Round [176] log likelihood: -6033.418803 EM: Round [177] log likelihood: -6033.416874 EM: Round [178] log likelihood: -6033.414969 EM: Round [179] log likelihood: -6033.413089 EM: Round [180] log likelihood: -6033.411233 EM: Round [181] log likelihood: -6033.409400 EM: Round [182] log likelihood: -6033.407590 EM: Round [183] log likelihood: -6033.405804 EM: Round [184] log likelihood: -6033.404040 EM: Round [185] log likelihood: -6033.402298 EM: Round [186] log likelihood: -6033.400579 EM: Round [187] log likelihood: -6033.398881 EM: Round [188] log likelihood: -6033.397205 EM: Round [189] log likelihood: -6033.395549 EM: Round [190] log likelihood: -6033.393915 EM: Round [191] log likelihood: -6033.392302 EM: Round [192] log likelihood: -6033.390708 EM: Round [193] log likelihood: -6033.389135 EM: Round [194] log likelihood: -6033.387582 EM: Round [195] log likelihood: -6033.386048 EM: Round [196] log likelihood: -6033.384534 EM: Round [197] log likelihood: -6033.383038 EM: Round [198] log likelihood: -6033.381562 EM: Round [199] log likelihood: -6033.380104 EM: Round [200] log likelihood: -6033.378664 EM: Round [201] log likelihood: -6033.377243 EM: Round [202] log likelihood: -6033.375839 EM: Round [203] log likelihood: -6033.374453 EM: Round [204] log likelihood: -6033.373084 EM: Round [205] log likelihood: -6033.371733 EM: Round [206] log likelihood: -6033.370399 EM: Round [207] log likelihood: -6033.369081 EM: Round [208] log likelihood: -6033.367780 EM: Round [209] log likelihood: -6033.366495 EM: Round [210] log likelihood: -6033.365226 EM: Round [211] log likelihood: -6033.363973 EM: Round [212] log likelihood: -6033.362736 EM: Round [213] log likelihood: -6033.361514 EM: Round [214] log likelihood: -6033.360307 EM: Round [215] log likelihood: -6033.359116 EM: Round [216] log likelihood: -6033.357939 EM: Round [217] log likelihood: -6033.356778 EM: Round [218] log likelihood: -6033.355630 EM: Round [219] log likelihood: -6033.354497 EM: Round [220] log likelihood: -6033.353379 EM: Round [221] log likelihood: -6033.352274 EM: Round [222] log likelihood: -6033.351183 EM: Round [223] log likelihood: -6033.350105 EM: Round [224] log likelihood: -6033.349041 EM: Round [225] log likelihood: -6033.347991 EM: Round [226] log likelihood: -6033.346953 EM: Round [227] log likelihood: -6033.345928 EM: Round [228] log likelihood: -6033.344916 EM: Round [229] log likelihood: -6033.343917 EM: Round [230] log likelihood: -6033.342930 EM: Round [231] log likelihood: -6033.341955 EM: Round [232] log likelihood: -6033.340993 EM: Round [233] log likelihood: -6033.340042 EM: Round [234] log likelihood: -6033.339104 EM: Round [235] log likelihood: -6033.338177 EM: Round [236] log likelihood: -6033.337261 EM: Round [237] log likelihood: -6033.336357 EM: Round [238] log likelihood: -6033.335464 EM: Round [239] log likelihood: -6033.334582 EM: Round [240] log likelihood: -6033.333712 EM: Round [241] log likelihood: -6033.332851 EM: Round [242] log likelihood: -6033.332002 EM: Round [243] log likelihood: -6033.331163 EM: Round [244] log likelihood: -6033.330335 EM: Round [245] log likelihood: -6033.329517 EM: Round [246] log likelihood: -6033.328709 EM: Round [247] log likelihood: -6033.327911 EM: Round [248] log likelihood: -6033.327123 EM: Round [249] log likelihood: -6033.326344 EM: Round [250] log likelihood: -6033.325576 EM: Round [251] log likelihood: -6033.324817 EM: Round [252] log likelihood: -6033.324067 EM: Round [253] log likelihood: -6033.323326 EM: Round [254] log likelihood: -6033.322595 EM: Round [255] log likelihood: -6033.321873 EM: Round [256] log likelihood: -6033.321160 EM: Round [257] log likelihood: -6033.320455 EM: Round [258] log likelihood: -6033.319759 EM: Round [259] log likelihood: -6033.319072 EM: Round [260] log likelihood: -6033.318393 EM: Round [261] log likelihood: -6033.317723 EM: Round [262] log likelihood: -6033.317061 EM: Round [263] log likelihood: -6033.316407 EM: Round [264] log likelihood: -6033.315762 EM: Round [265] log likelihood: -6033.315124 EM: Round [266] log likelihood: -6033.314494 EM: Round [267] log likelihood: -6033.313872 EM: Round [268] log likelihood: -6033.313258 EM: Round [269] log likelihood: -6033.312651 EM: Round [270] log likelihood: -6033.312052 EM: Round [271] log likelihood: -6033.311460 EM: Round [272] log likelihood: -6033.310875 EM: Round [273] log likelihood: -6033.310298 EM: Round [274] log likelihood: -6033.309727 EM: Round [275] log likelihood: -6033.309164 EM: Round [276] log likelihood: -6033.308608 EM: Round [277] log likelihood: -6033.308058 EM: Round [278] log likelihood: -6033.307516 EM: Round [279] log likelihood: -6033.306980 EM: Round [280] log likelihood: -6033.306451 EM: Round [281] log likelihood: -6033.305928 EM: Round [282] log likelihood: -6033.305411 EM: Round [283] log likelihood: -6033.304901 EM: Round [284] log likelihood: -6033.304398 EM: Round [285] log likelihood: -6033.303900 EM: Round [286] log likelihood: -6033.303409 EM: Round [287] log likelihood: -6033.302923 EM: Round [288] log likelihood: -6033.302444 EM: Round [289] log likelihood: -6033.301970 EM: Round [290] log likelihood: -6033.301503 EM: Round [291] log likelihood: -6033.301041 EM: Round [292] log likelihood: -6033.300585 EM: Round [293] log likelihood: -6033.300134 EM: Round [294] log likelihood: -6033.299689 EM: Round [295] log likelihood: -6033.299250 EM: Round [296] log likelihood: -6033.298815 EM: Round [297] log likelihood: -6033.298387 EM: Round [298] log likelihood: -6033.297963 EM: Round [299] log likelihood: -6033.297545 EM: Round [300] log likelihood: -6033.297132 EM: Round [301] log likelihood: -6033.296724 EM: Round [302] log likelihood: -6033.296320 EM: Round [303] log likelihood: -6033.295922 EM: Round [304] log likelihood: -6033.295529 EM: Round [305] log likelihood: -6033.295141 EM: Round [306] log likelihood: -6033.294757 EM: Round [307] log likelihood: -6033.294378 EM: Round [308] log likelihood: -6033.294004 EM: Round [309] log likelihood: -6033.293634 EM: Round [310] log likelihood: -6033.293269 EM: Round [311] log likelihood: -6033.292909 EM: Round [312] log likelihood: -6033.292552 EM: Round [313] log likelihood: -6033.292201 EM: Round [314] log likelihood: -6033.291853 EM: Round [315] log likelihood: -6033.291510 EM: Round [316] log likelihood: -6033.291171 EM: Round [317] log likelihood: -6033.290836 EM: Round [318] log likelihood: -6033.290505 EM: Round [319] log likelihood: -6033.290179 EM: Round [320] log likelihood: -6033.289856 EM: Round [321] log likelihood: -6033.289537 EM: Round [322] log likelihood: -6033.289222 EM: Round [323] log likelihood: -6033.288912 EM: Round [324] log likelihood: -6033.288604 EM: Round [325] log likelihood: -6033.288301 EM: Round [326] log likelihood: -6033.288001 EM: Round [327] log likelihood: -6033.287706 EM: Round [328] log likelihood: -6033.287413 EM: Round [329] log likelihood: -6033.287124 EM: Round [330] log likelihood: -6033.286839 EM: Round [331] log likelihood: -6033.286558 EM: Round [332] log likelihood: -6033.286279 EM: Round [333] log likelihood: -6033.286005 EM: Round [334] log likelihood: -6033.285733 EM: Round [335] log likelihood: -6033.285465 EM: Round [336] log likelihood: -6033.285200 EM: Round [337] log likelihood: -6033.284939 EM: Round [338] log likelihood: -6033.284680 EM: Round [339] log likelihood: -6033.284425 EM: Round [340] log likelihood: -6033.284173 EM: Round [341] log likelihood: -6033.283924 EM: Round [342] log likelihood: -6033.283678 EM: Round [343] log likelihood: -6033.283435 EM: Round [344] log likelihood: -6033.283195 EM: Round [345] log likelihood: -6033.282958 EM: Round [346] log likelihood: -6033.282724 EM: Round [347] log likelihood: -6033.282493 EM: Round [348] log likelihood: -6033.282264 EM: Round [349] log likelihood: -6033.282039 EM: Round [350] log likelihood: -6033.281816 EM: Round [351] log likelihood: -6033.281596 EM: Round [352] log likelihood: -6033.281378 EM: Round [353] log likelihood: -6033.281163 EM: Round [354] log likelihood: -6033.280951 EM: Round [355] log likelihood: -6033.280742 EM: Round [356] log likelihood: -6033.280535 EM: Round [357] log likelihood: -6033.280330 EM: Round [358] log likelihood: -6033.280129 EM: Round [359] log likelihood: -6033.279929 EM: Round [360] log likelihood: -6033.279732 EM: Round [361] log likelihood: -6033.279537 EM: Round [362] log likelihood: -6033.279345 EM: Round [363] log likelihood: -6033.279155 EM: Round [364] log likelihood: -6033.278968 EM: Round [365] log likelihood: -6033.278783 EM: Round [366] log likelihood: -6033.278600 EM: Round [367] log likelihood: -6033.278419 EM: Round [368] log likelihood: -6033.278240 EM: Round [369] log likelihood: -6033.278064 EM: Round [370] log likelihood: -6033.277890 EM: Round [371] log likelihood: -6033.277718 EM: Round [372] log likelihood: -6033.277548 EM: Round [373] log likelihood: -6033.277380 EM: Round [374] log likelihood: -6033.277214 EM: Round [375] log likelihood: -6033.277050 EM: Round [376] log likelihood: -6033.276889 EM: Round [377] log likelihood: -6033.276729 EM: Round [378] log likelihood: -6033.276571 EM: Round [379] log likelihood: -6033.276415 EM: Round [380] log likelihood: -6033.276261 EM: Round [381] log likelihood: -6033.276109 EM: Round [382] log likelihood: -6033.275959 EM: Round [383] log likelihood: -6033.275810 EM: Round [384] log likelihood: -6033.275664 EM: Round [385] log likelihood: -6033.275519 EM: Round [386] log likelihood: -6033.275376 EM: Round [387] log likelihood: -6033.275235 EM: Round [388] log likelihood: -6033.275095 EM: Round [389] log likelihood: -6033.274957 EM: Round [390] log likelihood: -6033.274821 EM: Round [391] log likelihood: -6033.274686 EM: Round [392] log likelihood: -6033.274554 EM: Round [393] log likelihood: -6033.274422 EM: Round [394] log likelihood: -6033.274293 EM: Round [395] log likelihood: -6033.274165 EM: Round [396] log likelihood: -6033.274038 EM: Round [397] log likelihood: -6033.273913 EM: Round [398] log likelihood: -6033.273790 EM: Round [399] log likelihood: -6033.273668 EM: Round [400] log likelihood: -6033.273548 EM: Round [401] log likelihood: -6033.273429 EM: Round [402] log likelihood: -6033.273311 EM: Round [403] log likelihood: -6033.273195 EM: Round [404] log likelihood: -6033.273080 EM: Round [405] log likelihood: -6033.272967 EM: Round [406] log likelihood: -6033.272855 EM: Round [407] log likelihood: -6033.272745 EM: Round [408] log likelihood: -6033.272636 EM: Round [409] log likelihood: -6033.272528 EM: Round [410] log likelihood: -6033.272421 EM: Round [411] log likelihood: -6033.272316 EM: Round [412] log likelihood: -6033.272212 EM: Round [413] log likelihood: -6033.272110 EM: Round [414] log likelihood: -6033.272008 EM: Round [415] log likelihood: -6033.271908 EM: Round [416] log likelihood: -6033.271809 EM: Stopping iterations at round 416 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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir -done, see /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -4709.957846 EM: Round [1] log likelihood: -4709.947075 EM: Round [2] log likelihood: -4709.947056 EM: Stopping iterations at round 2 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 265946703 Execution Time = 4.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.atNtBlHYmi/fi_workdir/microH.dat Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.atNtBlHYmi/fi_workdir/microH.dat /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_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.atNtBlHYmi/fi_workdir/microH.dat /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.atNtBlHYmi --json_outfile /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.atNtBlHYmi --json_outfile /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 Running: touch /tmp/nxf.atNtBlHYmi/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.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000198237.8] 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 [ENSG00000267302.5] WARNING, no entry stored in dbm for [ENSG00000267302.5] 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 [ENSG00000278212.2] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.atNtBlHYmi/ctat_genome_lib_build_dir > /tmp/nxf.atNtBlHYmi/1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.atNtBlHYmi/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory