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/e0/41a4413ff86c381a2c1fe39d3f8080/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/8d3634cd695171888017f8cc392a8f/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/dc427eb79239bd5125c1ca74fe1ba8/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/dc427eb79239bd5125c1ca74fe1ba8/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/8d3634cd695171888017f8cc392a8f/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.cqmxTZ3giy/1173_PCB_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_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/cytoBand.txt Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed -parsing GTF file: /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.cqmxTZ3giy/fi_workdir --reads "/tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 08:24:07 ..... started STAR run Jun 08 08:24:07 ..... loading genome Jun 08 08:25:48 ... generating Suffix Array index Jun 08 08:29:39 ... completed Suffix Array index Jun 08 08:29:40 ..... processing annotations GTF Jun 08 08:29:40 ..... inserting junctions into the genome indices Jun 08 08:30:43 ..... started mapping Jun 08 08:51:37 ..... finished mapping Jun 08 08:51:38 ..... started sorting BAM Jun 08 08:51:39 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam Execution Time = 27.53 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.cqmxTZ3giy/fi_workdir --reads "/tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 08:51:42 : INFO : Done. Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf -parsing /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] -done parsing /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 20, ' ** passed ** ' => 4863, 'exons hit < 2' => 7, 'excessive soft clipping' => 2980, 'seq-similar region overlap' => 60, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4, 'per_id < 96' => 2623 }; -writing fusion junction support info. Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] -fusion SPANNING read extraction for scaff: ARHGAP27--PKD1P6 [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] -fusion SPANNING read extraction for scaff: ARHGAP27--PDXDC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: FAM91A1--ANXA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: FGFR3--TACC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: GDF11--RDH5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: GPATCH1--ASCC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] -fusion SPANNING read extraction for scaff: INTS1--VMP1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [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: PCDHGA6--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA6--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] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3 [1000] -fusion SPANNING read extraction for scaff: PPM1J--AL157944.1 [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: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -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] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 16394, 'lacks exon overlap' => 6446 }; Execution Time = 0.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -1818.307133 EM: Round [1] log likelihood: -1818.013887 EM: Round [2] log likelihood: -1817.913627 EM: Round [3] log likelihood: -1817.831643 EM: Round [4] log likelihood: -1817.755042 EM: Round [5] log likelihood: -1817.682579 EM: Round [6] log likelihood: -1817.613870 EM: Round [7] log likelihood: -1817.548622 EM: Round [8] log likelihood: -1817.486577 EM: Round [9] log likelihood: -1817.427503 EM: Round [10] log likelihood: -1817.371191 EM: Round [11] log likelihood: -1817.317452 EM: Round [12] log likelihood: -1817.266112 EM: Round [13] log likelihood: -1817.217016 EM: Round [14] log likelihood: -1817.170021 EM: Round [15] log likelihood: -1817.124995 EM: Round [16] log likelihood: -1817.081818 EM: Round [17] log likelihood: -1817.040381 EM: Round [18] log likelihood: -1817.000580 EM: Round [19] log likelihood: -1816.962322 EM: Round [20] log likelihood: -1816.925520 EM: Round [21] log likelihood: -1816.890093 EM: Round [22] log likelihood: -1816.855967 EM: Round [23] log likelihood: -1816.823072 EM: Round [24] log likelihood: -1816.791343 EM: Round [25] log likelihood: -1816.760720 EM: Round [26] log likelihood: -1816.731147 EM: Round [27] log likelihood: -1816.702570 EM: Round [28] log likelihood: -1816.674941 EM: Round [29] log likelihood: -1816.648214 EM: Round [30] log likelihood: -1816.622344 EM: Round [31] log likelihood: -1816.597293 EM: Round [32] log likelihood: -1816.573020 EM: Round [33] log likelihood: -1816.549490 EM: Round [34] log likelihood: -1816.526671 EM: Round [35] log likelihood: -1816.504528 EM: Round [36] log likelihood: -1816.483034 EM: Round [37] log likelihood: -1816.462158 EM: Round [38] log likelihood: -1816.441875 EM: Round [39] log likelihood: -1816.422158 EM: Round [40] log likelihood: -1816.402985 EM: Round [41] log likelihood: -1816.384332 EM: Round [42] log likelihood: -1816.366177 EM: Round [43] log likelihood: -1816.348501 EM: Round [44] log likelihood: -1816.331285 EM: Round [45] log likelihood: -1816.314508 EM: Round [46] log likelihood: -1816.298156 EM: Round [47] log likelihood: -1816.282210 EM: Round [48] log likelihood: -1816.266655 EM: Round [49] log likelihood: -1816.251476 EM: Round [50] log likelihood: -1816.236659 EM: Round [51] log likelihood: -1816.222190 EM: Round [52] log likelihood: -1816.208057 EM: Round [53] log likelihood: -1816.194247 EM: Round [54] log likelihood: -1816.180748 EM: Round [55] log likelihood: -1816.167549 EM: Round [56] log likelihood: -1816.154640 EM: Round [57] log likelihood: -1816.142011 EM: Round [58] log likelihood: -1816.129651 EM: Round [59] log likelihood: -1816.117551 EM: Round [60] log likelihood: -1816.105703 EM: Round [61] log likelihood: -1816.094098 EM: Round [62] log likelihood: -1816.082729 EM: Round [63] log likelihood: -1816.071586 EM: Round [64] log likelihood: -1816.060663 EM: Round [65] log likelihood: -1816.049952 EM: Round [66] log likelihood: -1816.039448 EM: Round [67] log likelihood: -1816.029143 EM: Round [68] log likelihood: -1816.019031 EM: Round [69] log likelihood: -1816.009106 EM: Round [70] log likelihood: -1815.999362 EM: Round [71] log likelihood: -1815.989795 EM: Round [72] log likelihood: -1815.980398 EM: Round [73] log likelihood: -1815.971166 EM: Round [74] log likelihood: -1815.962095 EM: Round [75] log likelihood: -1815.953180 EM: Round [76] log likelihood: -1815.944417 EM: Round [77] log likelihood: -1815.935800 EM: Round [78] log likelihood: -1815.927327 EM: Round [79] log likelihood: -1815.918993 EM: Round [80] log likelihood: -1815.910793 EM: Round [81] log likelihood: -1815.902726 EM: Round [82] log likelihood: -1815.894786 EM: Round [83] log likelihood: -1815.886971 EM: Round [84] log likelihood: -1815.879277 EM: Round [85] log likelihood: -1815.871701 EM: Round [86] log likelihood: -1815.864240 EM: Round [87] log likelihood: -1815.856892 EM: Round [88] log likelihood: -1815.849652 EM: Round [89] log likelihood: -1815.842519 EM: Round [90] log likelihood: -1815.835490 EM: Round [91] log likelihood: -1815.828562 EM: Round [92] log likelihood: -1815.821733 EM: Round [93] log likelihood: -1815.815000 EM: Round [94] log likelihood: -1815.808362 EM: Round [95] log likelihood: -1815.801815 EM: Round [96] log likelihood: -1815.795358 EM: Round [97] log likelihood: -1815.788989 EM: Round [98] log likelihood: -1815.782706 EM: Round [99] log likelihood: -1815.776507 EM: Round [100] log likelihood: -1815.770390 EM: Round [101] log likelihood: -1815.764352 EM: Round [102] log likelihood: -1815.758394 EM: Round [103] log likelihood: -1815.752511 EM: Round [104] log likelihood: -1815.746704 EM: Round [105] log likelihood: -1815.740971 EM: Round [106] log likelihood: -1815.735309 EM: Round [107] log likelihood: -1815.729718 EM: Round [108] log likelihood: -1815.724196 EM: Round [109] log likelihood: -1815.718742 EM: Round [110] log likelihood: -1815.713354 EM: Round [111] log likelihood: -1815.708030 EM: Round [112] log likelihood: -1815.702771 EM: Round [113] log likelihood: -1815.697574 EM: Round [114] log likelihood: -1815.692438 EM: Round [115] log likelihood: -1815.687362 EM: Round [116] log likelihood: -1815.682345 EM: Round [117] log likelihood: -1815.677386 EM: Round [118] log likelihood: -1815.672484 EM: Round [119] log likelihood: -1815.667637 EM: Round [120] log likelihood: -1815.662845 EM: Round [121] log likelihood: -1815.658107 EM: Round [122] log likelihood: -1815.653422 EM: Round [123] log likelihood: -1815.648788 EM: Round [124] log likelihood: -1815.644206 EM: Round [125] log likelihood: -1815.639673 EM: Round [126] log likelihood: -1815.635190 EM: Round [127] log likelihood: -1815.630755 EM: Round [128] log likelihood: -1815.626367 EM: Round [129] log likelihood: -1815.622027 EM: Round [130] log likelihood: -1815.617732 EM: Round [131] log likelihood: -1815.613483 EM: Round [132] log likelihood: -1815.609278 EM: Round [133] log likelihood: -1815.605116 EM: Round [134] log likelihood: -1815.600998 EM: Round [135] log likelihood: -1815.596923 EM: Round [136] log likelihood: -1815.592889 EM: Round [137] log likelihood: -1815.588896 EM: Round [138] log likelihood: -1815.584943 EM: Round [139] log likelihood: -1815.581031 EM: Round [140] log likelihood: -1815.577157 EM: Round [141] log likelihood: -1815.573323 EM: Round [142] log likelihood: -1815.569526 EM: Round [143] log likelihood: -1815.565767 EM: Round [144] log likelihood: -1815.562044 EM: Round [145] log likelihood: -1815.558359 EM: Round [146] log likelihood: -1815.554709 EM: Round [147] log likelihood: -1815.551094 EM: Round [148] log likelihood: -1815.547514 EM: Round [149] log likelihood: -1815.543969 EM: Round [150] log likelihood: -1815.540458 EM: Round [151] log likelihood: -1815.536980 EM: Round [152] log likelihood: -1815.533535 EM: Round [153] log likelihood: -1815.530122 EM: Round [154] log likelihood: -1815.526742 EM: Round [155] log likelihood: -1815.523393 EM: Round [156] log likelihood: -1815.520075 EM: Round [157] log likelihood: -1815.516789 EM: Round [158] log likelihood: -1815.513532 EM: Round [159] log likelihood: -1815.510306 EM: Round [160] log likelihood: -1815.507109 EM: Round [161] log likelihood: -1815.503941 EM: Round [162] log likelihood: -1815.500802 EM: Round [163] log likelihood: -1815.497692 EM: Round [164] log likelihood: -1815.494610 EM: Round [165] log likelihood: -1815.491555 EM: Round [166] log likelihood: -1815.488528 EM: Round [167] log likelihood: -1815.485528 EM: Round [168] log likelihood: -1815.482555 EM: Round [169] log likelihood: -1815.479608 EM: Round [170] log likelihood: -1815.476687 EM: Round [171] log likelihood: -1815.473792 EM: Round [172] log likelihood: -1815.470922 EM: Round [173] log likelihood: -1815.468077 EM: Round [174] log likelihood: -1815.465258 EM: Round [175] log likelihood: -1815.462462 EM: Round [176] log likelihood: -1815.459691 EM: Round [177] log likelihood: -1815.456944 EM: Round [178] log likelihood: -1815.454221 EM: Round [179] log likelihood: -1815.451521 EM: Round [180] log likelihood: -1815.448844 EM: Round [181] log likelihood: -1815.446190 EM: Round [182] log likelihood: -1815.443559 EM: Round [183] log likelihood: -1815.440950 EM: Round [184] log likelihood: -1815.438363 EM: Round [185] log likelihood: -1815.435797 EM: Round [186] log likelihood: -1815.433254 EM: Round [187] log likelihood: -1815.430732 EM: Round [188] log likelihood: -1815.428230 EM: Round [189] log likelihood: -1815.425750 EM: Round [190] log likelihood: -1815.423291 EM: Round [191] log likelihood: -1815.420851 EM: Round [192] log likelihood: -1815.418432 EM: Round [193] log likelihood: -1815.416033 EM: Round [194] log likelihood: -1815.413654 EM: Round [195] log likelihood: -1815.411294 EM: Round [196] log likelihood: -1815.408954 EM: Round [197] log likelihood: -1815.406632 EM: Round [198] log likelihood: -1815.404330 EM: Round [199] log likelihood: -1815.402046 EM: Round [200] log likelihood: -1815.399781 EM: Round [201] log likelihood: -1815.397534 EM: Round [202] log likelihood: -1815.395306 EM: Round [203] log likelihood: -1815.393095 EM: Round [204] log likelihood: -1815.390902 EM: Round [205] log likelihood: -1815.388727 EM: Round [206] log likelihood: -1815.386569 EM: Round [207] log likelihood: -1815.384428 EM: Round [208] log likelihood: -1815.382304 EM: Round [209] log likelihood: -1815.380197 EM: Round [210] log likelihood: -1815.378107 EM: Round [211] log likelihood: -1815.376033 EM: Round [212] log likelihood: -1815.373976 EM: Round [213] log likelihood: -1815.371935 EM: Round [214] log likelihood: -1815.369910 EM: Round [215] log likelihood: -1815.367900 EM: Round [216] log likelihood: -1815.365907 EM: Round [217] log likelihood: -1815.363929 EM: Round [218] log likelihood: -1815.361966 EM: Round [219] log likelihood: -1815.360019 EM: Round [220] log likelihood: -1815.358087 EM: Round [221] log likelihood: -1815.356170 EM: Round [222] log likelihood: -1815.354267 EM: Round [223] log likelihood: -1815.352380 EM: Round [224] log likelihood: -1815.350506 EM: Round [225] log likelihood: -1815.348648 EM: Round [226] log likelihood: -1815.346803 EM: Round [227] log likelihood: -1815.344973 EM: Round [228] log likelihood: -1815.343156 EM: Round [229] log likelihood: -1815.341354 EM: Round [230] log likelihood: -1815.339565 EM: Round [231] log likelihood: -1815.337789 EM: Round [232] log likelihood: -1815.336028 EM: Round [233] log likelihood: -1815.334279 EM: Round [234] log likelihood: -1815.332544 EM: Round [235] log likelihood: -1815.330821 EM: Round [236] log likelihood: -1815.329112 EM: Round [237] log likelihood: -1815.327416 EM: Round [238] log likelihood: -1815.325732 EM: Round [239] log likelihood: -1815.324061 EM: Round [240] log likelihood: -1815.322402 EM: Round [241] log likelihood: -1815.320756 EM: Round [242] log likelihood: -1815.319122 EM: Round [243] log likelihood: -1815.317501 EM: Round [244] log likelihood: -1815.315891 EM: Round [245] log likelihood: -1815.314293 EM: Round [246] log likelihood: -1815.312707 EM: Round [247] log likelihood: -1815.311133 EM: Round [248] log likelihood: -1815.309570 EM: Round [249] log likelihood: -1815.308019 EM: Round [250] log likelihood: -1815.306479 EM: Round [251] log likelihood: -1815.304951 EM: Round [252] log likelihood: -1815.303434 EM: Round [253] log likelihood: -1815.301927 EM: Round [254] log likelihood: -1815.300432 EM: Round [255] log likelihood: -1815.298948 EM: Round [256] log likelihood: -1815.297475 EM: Round [257] log likelihood: -1815.296012 EM: Round [258] log likelihood: -1815.294560 EM: Round [259] log likelihood: -1815.293119 EM: Round [260] log likelihood: -1815.291687 EM: Round [261] log likelihood: -1815.290267 EM: Round [262] log likelihood: -1815.288856 EM: Round [263] log likelihood: -1815.287456 EM: Round [264] log likelihood: -1815.286066 EM: Round [265] log likelihood: -1815.284686 EM: Round [266] log likelihood: -1815.283315 EM: Round [267] log likelihood: -1815.281955 EM: Round [268] log likelihood: -1815.280604 EM: Round [269] log likelihood: -1815.279263 EM: Round [270] log likelihood: -1815.277932 EM: Round [271] log likelihood: -1815.276610 EM: Round [272] log likelihood: -1815.275297 EM: Round [273] log likelihood: -1815.273994 EM: Round [274] log likelihood: -1815.272700 EM: Round [275] log likelihood: -1815.271415 EM: Round [276] log likelihood: -1815.270140 EM: Round [277] log likelihood: -1815.268873 EM: Round [278] log likelihood: -1815.267616 EM: Round [279] log likelihood: -1815.266367 EM: Round [280] log likelihood: -1815.265127 EM: Round [281] log likelihood: -1815.263896 EM: Round [282] log likelihood: -1815.262673 EM: Round [283] log likelihood: -1815.261459 EM: Round [284] log likelihood: -1815.260254 EM: Round [285] log likelihood: -1815.259057 EM: Round [286] log likelihood: -1815.257868 EM: Round [287] log likelihood: -1815.256688 EM: Round [288] log likelihood: -1815.255515 EM: Round [289] log likelihood: -1815.254352 EM: Round [290] log likelihood: -1815.253196 EM: Round [291] log likelihood: -1815.252048 EM: Round [292] log likelihood: -1815.250908 EM: Round [293] log likelihood: -1815.249776 EM: Round [294] log likelihood: -1815.248652 EM: Round [295] log likelihood: -1815.247536 EM: Round [296] log likelihood: -1815.246428 EM: Round [297] log likelihood: -1815.245327 EM: Round [298] log likelihood: -1815.244234 EM: Round [299] log likelihood: -1815.243148 EM: Round [300] log likelihood: -1815.242070 EM: Round [301] log likelihood: -1815.240999 EM: Round [302] log likelihood: -1815.239935 EM: Round [303] log likelihood: -1815.238879 EM: Round [304] log likelihood: -1815.237830 EM: Round [305] log likelihood: -1815.236789 EM: Round [306] log likelihood: -1815.235754 EM: Round [307] log likelihood: -1815.234727 EM: Round [308] log likelihood: -1815.233706 EM: Round [309] log likelihood: -1815.232693 EM: Round [310] log likelihood: -1815.231686 EM: Round [311] log likelihood: -1815.230686 EM: Round [312] log likelihood: -1815.229693 EM: Round [313] log likelihood: -1815.228707 EM: Round [314] log likelihood: -1815.227728 EM: Round [315] log likelihood: -1815.226755 EM: Round [316] log likelihood: -1815.225789 EM: Round [317] log likelihood: -1815.224829 EM: Round [318] log likelihood: -1815.223876 EM: Round [319] log likelihood: -1815.222929 EM: Round [320] log likelihood: -1815.221989 EM: Round [321] log likelihood: -1815.221054 EM: Round [322] log likelihood: -1815.220127 EM: Round [323] log likelihood: -1815.219205 EM: Round [324] log likelihood: -1815.218290 EM: Round [325] log likelihood: -1815.217381 EM: Round [326] log likelihood: -1815.216478 EM: Round [327] log likelihood: -1815.215581 EM: Round [328] log likelihood: -1815.214690 EM: Round [329] log likelihood: -1815.213805 EM: Round [330] log likelihood: -1815.212926 EM: Round [331] log likelihood: -1815.212052 EM: Round [332] log likelihood: -1815.211185 EM: Round [333] log likelihood: -1815.210324 EM: Round [334] log likelihood: -1815.209468 EM: Round [335] log likelihood: -1815.208618 EM: Round [336] log likelihood: -1815.207773 EM: Round [337] log likelihood: -1815.206934 EM: Round [338] log likelihood: -1815.206101 EM: Round [339] log likelihood: -1815.205273 EM: Round [340] log likelihood: -1815.204451 EM: Round [341] log likelihood: -1815.203634 EM: Round [342] log likelihood: -1815.202823 EM: Round [343] log likelihood: -1815.202017 EM: Round [344] log likelihood: -1815.201216 EM: Round [345] log likelihood: -1815.200420 EM: Round [346] log likelihood: -1815.199630 EM: Round [347] log likelihood: -1815.198845 EM: Round [348] log likelihood: -1815.198066 EM: Round [349] log likelihood: -1815.197291 EM: Round [350] log likelihood: -1815.196521 EM: Round [351] log likelihood: -1815.195757 EM: Round [352] log likelihood: -1815.194997 EM: Round [353] log likelihood: -1815.194243 EM: Round [354] log likelihood: -1815.193493 EM: Round [355] log likelihood: -1815.192749 EM: Round [356] log likelihood: -1815.192009 EM: Round [357] log likelihood: -1815.191274 EM: Round [358] log likelihood: -1815.190544 EM: Round [359] log likelihood: -1815.189819 EM: Round [360] log likelihood: -1815.189098 EM: Round [361] log likelihood: -1815.188382 EM: Round [362] log likelihood: -1815.187671 EM: Round [363] log likelihood: -1815.186965 EM: Round [364] log likelihood: -1815.186263 EM: Round [365] log likelihood: -1815.185565 EM: Round [366] log likelihood: -1815.184872 EM: Round [367] log likelihood: -1815.184184 EM: Round [368] log likelihood: -1815.183500 EM: Round [369] log likelihood: -1815.182821 EM: Round [370] log likelihood: -1815.182146 EM: Round [371] log likelihood: -1815.181475 EM: Round [372] log likelihood: -1815.180809 EM: Round [373] log likelihood: -1815.180147 EM: Round [374] log likelihood: -1815.179489 EM: Round [375] log likelihood: -1815.178836 EM: Round [376] log likelihood: -1815.178186 EM: Round [377] log likelihood: -1815.177541 EM: Round [378] log likelihood: -1815.176900 EM: Round [379] log likelihood: -1815.176264 EM: Round [380] log likelihood: -1815.175631 EM: Round [381] log likelihood: -1815.175002 EM: Round [382] log likelihood: -1815.174378 EM: Round [383] log likelihood: -1815.173757 EM: Round [384] log likelihood: -1815.173141 EM: Round [385] log likelihood: -1815.172528 EM: Round [386] log likelihood: -1815.171920 EM: Round [387] log likelihood: -1815.171315 EM: Round [388] log likelihood: -1815.170714 EM: Round [389] log likelihood: -1815.170117 EM: Round [390] log likelihood: -1815.169524 EM: Round [391] log likelihood: -1815.168935 EM: Round [392] log likelihood: -1815.168349 EM: Round [393] log likelihood: -1815.167767 EM: Round [394] log likelihood: -1815.167189 EM: Round [395] log likelihood: -1815.166615 EM: Round [396] log likelihood: -1815.166044 EM: Round [397] log likelihood: -1815.165477 EM: Round [398] log likelihood: -1815.164913 EM: Round [399] log likelihood: -1815.164353 EM: Round [400] log likelihood: -1815.163797 EM: Round [401] log likelihood: -1815.163244 EM: Round [402] log likelihood: -1815.162695 EM: Round [403] log likelihood: -1815.162149 EM: Round [404] log likelihood: -1815.161607 EM: Round [405] log likelihood: -1815.161068 EM: Round [406] log likelihood: -1815.160532 EM: Round [407] log likelihood: -1815.160000 EM: Round [408] log likelihood: -1815.159471 EM: Round [409] log likelihood: -1815.158946 EM: Round [410] log likelihood: -1815.158424 EM: Round [411] log likelihood: -1815.157905 EM: Round [412] log likelihood: -1815.157390 EM: Round [413] log likelihood: -1815.156878 EM: Round [414] log likelihood: -1815.156369 EM: Round [415] log likelihood: -1815.155863 EM: Round [416] log likelihood: -1815.155360 EM: Round [417] log likelihood: -1815.154861 EM: Round [418] log likelihood: -1815.154365 EM: Round [419] log likelihood: -1815.153872 EM: Round [420] log likelihood: -1815.153382 EM: Round [421] log likelihood: -1815.152895 EM: Round [422] log likelihood: -1815.152411 EM: Round [423] log likelihood: -1815.151930 EM: Round [424] log likelihood: -1815.151453 EM: Round [425] log likelihood: -1815.150978 EM: Round [426] log likelihood: -1815.150506 EM: Round [427] log likelihood: -1815.150037 EM: Round [428] log likelihood: -1815.149571 EM: Round [429] log likelihood: -1815.149108 EM: Round [430] log likelihood: -1815.148648 EM: Round [431] log likelihood: -1815.148191 EM: Round [432] log likelihood: -1815.147737 EM: Round [433] log likelihood: -1815.147286 EM: Round [434] log likelihood: -1815.146837 EM: Round [435] log likelihood: -1815.146391 EM: Round [436] log likelihood: -1815.145948 EM: Round [437] log likelihood: -1815.145508 EM: Round [438] log likelihood: -1815.145070 EM: Round [439] log likelihood: -1815.144636 EM: Round [440] log likelihood: -1815.144204 EM: Round [441] log likelihood: -1815.143774 EM: Round [442] log likelihood: -1815.143348 EM: Round [443] log likelihood: -1815.142924 EM: Round [444] log likelihood: -1815.142502 EM: Round [445] log likelihood: -1815.142083 EM: Round [446] log likelihood: -1815.141667 EM: Round [447] log likelihood: -1815.141254 EM: Round [448] log likelihood: -1815.140843 EM: Round [449] log likelihood: -1815.140434 EM: Round [450] log likelihood: -1815.140029 EM: Round [451] log likelihood: -1815.139625 EM: Round [452] log likelihood: -1815.139224 EM: Round [453] log likelihood: -1815.138826 EM: Round [454] log likelihood: -1815.138430 EM: Round [455] log likelihood: -1815.138037 EM: Round [456] log likelihood: -1815.137646 EM: Round [457] log likelihood: -1815.137257 EM: Round [458] log likelihood: -1815.136871 EM: Round [459] log likelihood: -1815.136487 EM: Round [460] log likelihood: -1815.136106 EM: Round [461] log likelihood: -1815.135727 EM: Round [462] log likelihood: -1815.135350 EM: Round [463] log likelihood: -1815.134976 EM: Round [464] log likelihood: -1815.134604 EM: Round [465] log likelihood: -1815.134234 EM: Round [466] log likelihood: -1815.133867 EM: Round [467] log likelihood: -1815.133501 EM: Round [468] log likelihood: -1815.133139 EM: Round [469] log likelihood: -1815.132778 EM: Round [470] log likelihood: -1815.132419 EM: Round [471] log likelihood: -1815.132063 EM: Round [472] log likelihood: -1815.131709 EM: Round [473] log likelihood: -1815.131357 EM: Round [474] log likelihood: -1815.131008 EM: Round [475] log likelihood: -1815.130660 EM: Round [476] log likelihood: -1815.130315 EM: Round [477] log likelihood: -1815.129971 EM: Round [478] log likelihood: -1815.129630 EM: Round [479] log likelihood: -1815.129291 EM: Round [480] log likelihood: -1815.128954 EM: Round [481] log likelihood: -1815.128619 EM: Round [482] log likelihood: -1815.128287 EM: Round [483] log likelihood: -1815.127956 EM: Round [484] log likelihood: -1815.127627 EM: Round [485] log likelihood: -1815.127300 EM: Round [486] log likelihood: -1815.126975 EM: Round [487] log likelihood: -1815.126653 EM: Round [488] log likelihood: -1815.126332 EM: Round [489] log likelihood: -1815.126013 EM: Round [490] log likelihood: -1815.125696 EM: Round [491] log likelihood: -1815.125381 EM: Round [492] log likelihood: -1815.125068 EM: Round [493] log likelihood: -1815.124757 EM: Round [494] log likelihood: -1815.124448 EM: Round [495] log likelihood: -1815.124141 EM: Round [496] log likelihood: -1815.123836 EM: Round [497] log likelihood: -1815.123532 EM: Round [498] log likelihood: -1815.123230 EM: Round [499] log likelihood: -1815.122931 EM: Round [500] log likelihood: -1815.122633 EM: Round [501] log likelihood: -1815.122336 EM: Round [502] log likelihood: -1815.122042 EM: Round [503] log likelihood: -1815.121750 EM: Round [504] log likelihood: -1815.121459 EM: Round [505] log likelihood: -1815.121170 EM: Round [506] log likelihood: -1815.120883 EM: Round [507] log likelihood: -1815.120597 EM: Round [508] log likelihood: -1815.120313 EM: Round [509] log likelihood: -1815.120031 EM: Round [510] log likelihood: -1815.119751 EM: Round [511] log likelihood: -1815.119472 EM: Round [512] log likelihood: -1815.119196 EM: Round [513] log likelihood: -1815.118920 EM: Round [514] log likelihood: -1815.118647 EM: Round [515] log likelihood: -1815.118375 EM: Round [516] log likelihood: -1815.118105 EM: Round [517] log likelihood: -1815.117836 EM: Round [518] log likelihood: -1815.117569 EM: Round [519] log likelihood: -1815.117304 EM: Round [520] log likelihood: -1815.117040 EM: Round [521] log likelihood: -1815.116778 EM: Round [522] log likelihood: -1815.116518 EM: Round [523] log likelihood: -1815.116259 EM: Round [524] log likelihood: -1815.116001 EM: Round [525] log likelihood: -1815.115746 EM: Round [526] log likelihood: -1815.115491 EM: Round [527] log likelihood: -1815.115239 EM: Round [528] log likelihood: -1815.114987 EM: Round [529] log likelihood: -1815.114738 EM: Round [530] log likelihood: -1815.114490 EM: Round [531] log likelihood: -1815.114243 EM: Round [532] log likelihood: -1815.113998 EM: Round [533] log likelihood: -1815.113754 EM: Round [534] log likelihood: -1815.113512 EM: Round [535] log likelihood: -1815.113271 EM: Round [536] log likelihood: -1815.113032 EM: Round [537] log likelihood: -1815.112794 EM: Round [538] log likelihood: -1815.112558 EM: Round [539] log likelihood: -1815.112323 EM: Round [540] log likelihood: -1815.112090 EM: Round [541] log likelihood: -1815.111857 EM: Round [542] log likelihood: -1815.111627 EM: Round [543] log likelihood: -1815.111397 EM: Round [544] log likelihood: -1815.111170 EM: Round [545] log likelihood: -1815.110943 EM: Round [546] log likelihood: -1815.110718 EM: Round [547] log likelihood: -1815.110494 EM: Round [548] log likelihood: -1815.110272 EM: Round [549] log likelihood: -1815.110050 EM: Round [550] log likelihood: -1815.109831 EM: Round [551] log likelihood: -1815.109612 EM: Round [552] log likelihood: -1815.109395 EM: Round [553] log likelihood: -1815.109179 EM: Round [554] log likelihood: -1815.108965 EM: Round [555] log likelihood: -1815.108751 EM: Round [556] log likelihood: -1815.108539 EM: Round [557] log likelihood: -1815.108329 EM: Round [558] log likelihood: -1815.108119 EM: Round [559] log likelihood: -1815.107911 EM: Round [560] log likelihood: -1815.107704 EM: Round [561] log likelihood: -1815.107499 EM: Round [562] log likelihood: -1815.107294 EM: Round [563] log likelihood: -1815.107091 EM: Round [564] log likelihood: -1815.106889 EM: Round [565] log likelihood: -1815.106688 EM: Round [566] log likelihood: -1815.106489 EM: Round [567] log likelihood: -1815.106291 EM: Round [568] log likelihood: -1815.106093 EM: Round [569] log likelihood: -1815.105897 EM: Round [570] log likelihood: -1815.105703 EM: Round [571] log likelihood: -1815.105509 EM: Round [572] log likelihood: -1815.105317 EM: Round [573] log likelihood: -1815.105125 EM: Round [574] log likelihood: -1815.104935 EM: Round [575] log likelihood: -1815.104746 EM: Round [576] log likelihood: -1815.104558 EM: Round [577] log likelihood: -1815.104372 EM: Round [578] log likelihood: -1815.104186 EM: Round [579] log likelihood: -1815.104001 EM: Round [580] log likelihood: -1815.103818 EM: Round [581] log likelihood: -1815.103636 EM: Round [582] log likelihood: -1815.103454 EM: Round [583] log likelihood: -1815.103274 EM: Round [584] log likelihood: -1815.103095 EM: Round [585] log likelihood: -1815.102917 EM: Round [586] log likelihood: -1815.102740 EM: Round [587] log likelihood: -1815.102565 EM: Round [588] log likelihood: -1815.102390 EM: Round [589] log likelihood: -1815.102216 EM: Round [590] log likelihood: -1815.102043 EM: Round [591] log likelihood: -1815.101872 EM: Round [592] log likelihood: -1815.101701 EM: Round [593] log likelihood: -1815.101531 EM: Round [594] log likelihood: -1815.101363 EM: Round [595] log likelihood: -1815.101195 EM: Round [596] log likelihood: -1815.101029 EM: Round [597] log likelihood: -1815.100863 EM: Round [598] log likelihood: -1815.100698 EM: Round [599] log likelihood: -1815.100535 EM: Round [600] log likelihood: -1815.100372 EM: Round [601] log likelihood: -1815.100210 EM: Round [602] log likelihood: -1815.100050 EM: Round [603] log likelihood: -1815.099890 EM: Round [604] log likelihood: -1815.099731 EM: Round [605] log likelihood: -1815.099573 EM: Round [606] log likelihood: -1815.099416 EM: Round [607] log likelihood: -1815.099260 EM: Round [608] log likelihood: -1815.099105 EM: Round [609] log likelihood: -1815.098951 EM: Round [610] log likelihood: -1815.098798 EM: Round [611] log likelihood: -1815.098646 EM: Round [612] log likelihood: -1815.098494 EM: Round [613] log likelihood: -1815.098344 EM: Round [614] log likelihood: -1815.098194 EM: Round [615] log likelihood: -1815.098046 EM: Round [616] log likelihood: -1815.097898 EM: Round [617] log likelihood: -1815.097751 EM: Round [618] log likelihood: -1815.097605 EM: Round [619] log likelihood: -1815.097460 EM: Round [620] log likelihood: -1815.097315 EM: Round [621] log likelihood: -1815.097172 EM: Round [622] log likelihood: -1815.097029 EM: Round [623] log likelihood: -1815.096888 EM: Round [624] log likelihood: -1815.096747 EM: Round [625] log likelihood: -1815.096607 EM: Round [626] log likelihood: -1815.096467 EM: Round [627] log likelihood: -1815.096329 EM: Round [628] log likelihood: -1815.096191 EM: Round [629] log likelihood: -1815.096055 EM: Round [630] log likelihood: -1815.095919 EM: Round [631] log likelihood: -1815.095784 EM: Round [632] log likelihood: -1815.095649 EM: Round [633] log likelihood: -1815.095516 EM: Round [634] log likelihood: -1815.095383 EM: Round [635] log likelihood: -1815.095251 EM: Round [636] log likelihood: -1815.095120 EM: Round [637] log likelihood: -1815.094990 EM: Round [638] log likelihood: -1815.094860 EM: Round [639] log likelihood: -1815.094731 EM: Round [640] log likelihood: -1815.094603 EM: Round [641] log likelihood: -1815.094476 EM: Round [642] log likelihood: -1815.094349 EM: Round [643] log likelihood: -1815.094223 EM: Round [644] log likelihood: -1815.094098 EM: Round [645] log likelihood: -1815.093974 EM: Round [646] log likelihood: -1815.093850 EM: Round [647] log likelihood: -1815.093728 EM: Round [648] log likelihood: -1815.093605 EM: Round [649] log likelihood: -1815.093484 EM: Round [650] log likelihood: -1815.093363 EM: Round [651] log likelihood: -1815.093243 EM: Round [652] log likelihood: -1815.093124 EM: Round [653] log likelihood: -1815.093006 EM: Round [654] log likelihood: -1815.092888 EM: Round [655] log likelihood: -1815.092771 EM: Round [656] log likelihood: -1815.092654 EM: Round [657] log likelihood: -1815.092539 EM: Round [658] log likelihood: -1815.092423 EM: Round [659] log likelihood: -1815.092309 EM: Round [660] log likelihood: -1815.092195 EM: Round [661] log likelihood: -1815.092082 EM: Round [662] log likelihood: -1815.091970 EM: Round [663] log likelihood: -1815.091858 EM: Round [664] log likelihood: -1815.091747 EM: Round [665] log likelihood: -1815.091637 EM: Round [666] log likelihood: -1815.091527 EM: Round [667] log likelihood: -1815.091418 EM: Round [668] log likelihood: -1815.091310 EM: Round [669] log likelihood: -1815.091202 EM: Round [670] log likelihood: -1815.091095 EM: Round [671] log likelihood: -1815.090988 EM: Round [672] log likelihood: -1815.090882 EM: Round [673] log likelihood: -1815.090777 EM: Round [674] log likelihood: -1815.090673 EM: Round [675] log likelihood: -1815.090569 EM: Round [676] log likelihood: -1815.090465 EM: Round [677] log likelihood: -1815.090362 EM: Round [678] log likelihood: -1815.090260 EM: Round [679] log likelihood: -1815.090159 EM: Round [680] log likelihood: -1815.090058 EM: Round [681] log likelihood: -1815.089957 EM: Round [682] log likelihood: -1815.089857 EM: Stopping iterations at round 682 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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir -done, see /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -1227.026214 EM: Round [1] log likelihood: -1226.824098 EM: Round [2] log likelihood: -1226.809651 EM: Round [3] log likelihood: -1226.808633 EM: Round [4] log likelihood: -1226.808561 EM: Stopping iterations at round 4 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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 105119483 Execution Time = 2.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.cqmxTZ3giy/fi_workdir/microH.dat Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.cqmxTZ3giy/fi_workdir/microH.dat /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/fi_workdir/microH.dat /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.cqmxTZ3giy --json_outfile /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_PCB_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.cqmxTZ3giy --json_outfile /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1 Running: touch /tmp/nxf.cqmxTZ3giy/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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_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.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000280136.2] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.cqmxTZ3giy/ctat_genome_lib_build_dir > /tmp/nxf.cqmxTZ3giy/1173_PCB_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.cqmxTZ3giy/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory