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/5a/421a8a1966fe647f3bcaa370826a0b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/421a8a1966fe647f3bcaa370826a0b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/dfea8092ca59d5e6e90122e6298c87/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/387af25a3a0e5e8d5bad9f24034cd9/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/387af25a3a0e5e8d5bad9f24034cd9/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusionreport.tsv --gtf /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusionreport.tsv --gtf /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/cytoBand.txt Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed -parsing GTF file: /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.bedsort.ok Running: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.sorted.bed.gz Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.bed.tabix.ok Running: samtools faidx /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --CPU 8 --out_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star --out_dir /tmp/nxf.ksoFEZ4fk5/fi_workdir --reads "/tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:26:54 ..... started STAR run Jun 08 10:26:54 ..... loading genome Jun 08 10:28:42 ... generating Suffix Array index Jun 08 10:33:01 ... completed Suffix Array index Jun 08 10:33:01 ..... processing annotations GTF Jun 08 10:33:02 ..... inserting junctions into the genome indices Jun 08 10:34:09 ..... started mapping Jun 08 12:11:04 ..... finished mapping Jun 08 12:11:06 ..... started sorting BAM Jun 08 12:11:06 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam * Running CMD: samtools index 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam Execution Time = 104.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --CPU 8 --out_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2.star --out_dir /tmp/nxf.ksoFEZ4fk5/fi_workdir --reads "/tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz" Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --remove_dups 12:11:09 : INFO : Done. Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf -parsing /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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] -done parsing /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'per_id < 96' => 1786, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 72, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 9, 'seq-similar region overlap' => 65, 'num genes matched < 2' => 20, 'excessive soft clipping' => 2693, 'small anchor length' => 36, ' ** passed ** ' => 3277 }; -writing fusion junction support info. Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] -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] [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] -fusion SPANNING read extraction for scaff: CCDC6--RET [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: DNAJC1--C10orf143 [1000] [2000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: NEBL--CDK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -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] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2 [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: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A [1000] [2000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 4916, 'lacks exon overlap' => 1997 }; Execution Time = 0.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -2892.601368 EM: Round [1] log likelihood: -2890.826180 EM: Round [2] log likelihood: -2890.817047 EM: Round [3] log likelihood: -2890.808458 EM: Round [4] log likelihood: -2890.800020 EM: Round [5] log likelihood: -2890.791728 EM: Round [6] log likelihood: -2890.783579 EM: Round [7] log likelihood: -2890.775569 EM: Round [8] log likelihood: -2890.767695 EM: Round [9] log likelihood: -2890.759953 EM: Round [10] log likelihood: -2890.752341 EM: Round [11] log likelihood: -2890.744854 EM: Round [12] log likelihood: -2890.737490 EM: Round [13] log likelihood: -2890.730247 EM: Round [14] log likelihood: -2890.723121 EM: Round [15] log likelihood: -2890.716109 EM: Round [16] log likelihood: -2890.709210 EM: Round [17] log likelihood: -2890.702420 EM: Round [18] log likelihood: -2890.695737 EM: Round [19] log likelihood: -2890.689158 EM: Round [20] log likelihood: -2890.682682 EM: Round [21] log likelihood: -2890.676306 EM: Round [22] log likelihood: -2890.670028 EM: Round [23] log likelihood: -2890.663845 EM: Round [24] log likelihood: -2890.657757 EM: Round [25] log likelihood: -2890.651760 EM: Round [26] log likelihood: -2890.645853 EM: Round [27] log likelihood: -2890.640034 EM: Round [28] log likelihood: -2890.634301 EM: Round [29] log likelihood: -2890.628652 EM: Round [30] log likelihood: -2890.623087 EM: Round [31] log likelihood: -2890.617602 EM: Round [32] log likelihood: -2890.612197 EM: Round [33] log likelihood: -2890.606869 EM: Round [34] log likelihood: -2890.601618 EM: Round [35] log likelihood: -2890.596442 EM: Round [36] log likelihood: -2890.591339 EM: Round [37] log likelihood: -2890.586309 EM: Round [38] log likelihood: -2890.581349 EM: Round [39] log likelihood: -2890.576458 EM: Round [40] log likelihood: -2890.571635 EM: Round [41] log likelihood: -2890.566879 EM: Round [42] log likelihood: -2890.562188 EM: Round [43] log likelihood: -2890.557562 EM: Round [44] log likelihood: -2890.552999 EM: Round [45] log likelihood: -2890.548498 EM: Round [46] log likelihood: -2890.544058 EM: Round [47] log likelihood: -2890.539677 EM: Round [48] log likelihood: -2890.535356 EM: Round [49] log likelihood: -2890.531091 EM: Round [50] log likelihood: -2890.526884 EM: Round [51] log likelihood: -2890.522732 EM: Round [52] log likelihood: -2890.518635 EM: Round [53] log likelihood: -2890.514592 EM: Round [54] log likelihood: -2890.510602 EM: Round [55] log likelihood: -2890.506664 EM: Round [56] log likelihood: -2890.502776 EM: Round [57] log likelihood: -2890.498939 EM: Round [58] log likelihood: -2890.495152 EM: Round [59] log likelihood: -2890.491413 EM: Round [60] log likelihood: -2890.487721 EM: Round [61] log likelihood: -2890.484077 EM: Round [62] log likelihood: -2890.480479 EM: Round [63] log likelihood: -2890.476927 EM: Round [64] log likelihood: -2890.473419 EM: Round [65] log likelihood: -2890.469955 EM: Round [66] log likelihood: -2890.466535 EM: Round [67] log likelihood: -2890.463157 EM: Round [68] log likelihood: -2890.459821 EM: Round [69] log likelihood: -2890.456526 EM: Round [70] log likelihood: -2890.453273 EM: Round [71] log likelihood: -2890.450059 EM: Round [72] log likelihood: -2890.446884 EM: Round [73] log likelihood: -2890.443749 EM: Round [74] log likelihood: -2890.440651 EM: Round [75] log likelihood: -2890.437592 EM: Round [76] log likelihood: -2890.434569 EM: Round [77] log likelihood: -2890.431583 EM: Round [78] log likelihood: -2890.428632 EM: Round [79] log likelihood: -2890.425718 EM: Round [80] log likelihood: -2890.422838 EM: Round [81] log likelihood: -2890.419992 EM: Round [82] log likelihood: -2890.417180 EM: Round [83] log likelihood: -2890.414402 EM: Round [84] log likelihood: -2890.411657 EM: Round [85] log likelihood: -2890.408944 EM: Round [86] log likelihood: -2890.406262 EM: Round [87] log likelihood: -2890.403613 EM: Round [88] log likelihood: -2890.400994 EM: Round [89] log likelihood: -2890.398406 EM: Round [90] log likelihood: -2890.395848 EM: Round [91] log likelihood: -2890.393320 EM: Round [92] log likelihood: -2890.390821 EM: Round [93] log likelihood: -2890.388352 EM: Round [94] log likelihood: -2890.385910 EM: Round [95] log likelihood: -2890.383497 EM: Round [96] log likelihood: -2890.381111 EM: Round [97] log likelihood: -2890.378753 EM: Round [98] log likelihood: -2890.376421 EM: Round [99] log likelihood: -2890.374117 EM: Round [100] log likelihood: -2890.371838 EM: Round [101] log likelihood: -2890.369585 EM: Round [102] log likelihood: -2890.367358 EM: Round [103] log likelihood: -2890.365156 EM: Round [104] log likelihood: -2890.362979 EM: Round [105] log likelihood: -2890.360826 EM: Round [106] log likelihood: -2890.358697 EM: Round [107] log likelihood: -2890.356592 EM: Round [108] log likelihood: -2890.354511 EM: Round [109] log likelihood: -2890.352453 EM: Round [110] log likelihood: -2890.350418 EM: Round [111] log likelihood: -2890.348405 EM: Round [112] log likelihood: -2890.346415 EM: Round [113] log likelihood: -2890.344447 EM: Round [114] log likelihood: -2890.342500 EM: Round [115] log likelihood: -2890.340575 EM: Round [116] log likelihood: -2890.338672 EM: Round [117] log likelihood: -2890.336789 EM: Round [118] log likelihood: -2890.334926 EM: Round [119] log likelihood: -2890.333084 EM: Round [120] log likelihood: -2890.331262 EM: Round [121] log likelihood: -2890.329460 EM: Round [122] log likelihood: -2890.327678 EM: Round [123] log likelihood: -2890.325915 EM: Round [124] log likelihood: -2890.324171 EM: Round [125] log likelihood: -2890.322446 EM: Round [126] log likelihood: -2890.320740 EM: Round [127] log likelihood: -2890.319052 EM: Round [128] log likelihood: -2890.317382 EM: Round [129] log likelihood: -2890.315730 EM: Round [130] log likelihood: -2890.314096 EM: Round [131] log likelihood: -2890.312479 EM: Round [132] log likelihood: -2890.310880 EM: Round [133] log likelihood: -2890.309297 EM: Round [134] log likelihood: -2890.307732 EM: Round [135] log likelihood: -2890.306183 EM: Round [136] log likelihood: -2890.304651 EM: Round [137] log likelihood: -2890.303135 EM: Round [138] log likelihood: -2890.301635 EM: Round [139] log likelihood: -2890.300151 EM: Round [140] log likelihood: -2890.298682 EM: Round [141] log likelihood: -2890.297229 EM: Round [142] log likelihood: -2890.295792 EM: Round [143] log likelihood: -2890.294369 EM: Round [144] log likelihood: -2890.292962 EM: Round [145] log likelihood: -2890.291569 EM: Round [146] log likelihood: -2890.290191 EM: Round [147] log likelihood: -2890.288827 EM: Round [148] log likelihood: -2890.287477 EM: Round [149] log likelihood: -2890.286142 EM: Round [150] log likelihood: -2890.284820 EM: Round [151] log likelihood: -2890.283513 EM: Round [152] log likelihood: -2890.282218 EM: Round [153] log likelihood: -2890.280938 EM: Round [154] log likelihood: -2890.279670 EM: Round [155] log likelihood: -2890.278416 EM: Round [156] log likelihood: -2890.277174 EM: Round [157] log likelihood: -2890.275946 EM: Round [158] log likelihood: -2890.274730 EM: Round [159] log likelihood: -2890.273526 EM: Round [160] log likelihood: -2890.272335 EM: Round [161] log likelihood: -2890.271157 EM: Round [162] log likelihood: -2890.269990 EM: Round [163] log likelihood: -2890.268835 EM: Round [164] log likelihood: -2890.267692 EM: Round [165] log likelihood: -2890.266561 EM: Round [166] log likelihood: -2890.265442 EM: Round [167] log likelihood: -2890.264333 EM: Round [168] log likelihood: -2890.263237 EM: Round [169] log likelihood: -2890.262151 EM: Round [170] log likelihood: -2890.261076 EM: Round [171] log likelihood: -2890.260012 EM: Round [172] log likelihood: -2890.258959 EM: Round [173] log likelihood: -2890.257917 EM: Round [174] log likelihood: -2890.256885 EM: Round [175] log likelihood: -2890.255864 EM: Round [176] log likelihood: -2890.254853 EM: Round [177] log likelihood: -2890.253852 EM: Round [178] log likelihood: -2890.252862 EM: Round [179] log likelihood: -2890.251881 EM: Round [180] log likelihood: -2890.250910 EM: Round [181] log likelihood: -2890.249949 EM: Round [182] log likelihood: -2890.248998 EM: Round [183] log likelihood: -2890.248056 EM: Round [184] log likelihood: -2890.247124 EM: Round [185] log likelihood: -2890.246201 EM: Round [186] log likelihood: -2890.245287 EM: Round [187] log likelihood: -2890.244382 EM: Round [188] log likelihood: -2890.243487 EM: Round [189] log likelihood: -2890.242600 EM: Round [190] log likelihood: -2890.241722 EM: Round [191] log likelihood: -2890.240853 EM: Round [192] log likelihood: -2890.239993 EM: Round [193] log likelihood: -2890.239141 EM: Round [194] log likelihood: -2890.238298 EM: Round [195] log likelihood: -2890.237463 EM: Round [196] log likelihood: -2890.236636 EM: Round [197] log likelihood: -2890.235817 EM: Round [198] log likelihood: -2890.235007 EM: Round [199] log likelihood: -2890.234205 EM: Round [200] log likelihood: -2890.233410 EM: Round [201] log likelihood: -2890.232624 EM: Round [202] log likelihood: -2890.231845 EM: Round [203] log likelihood: -2890.231074 EM: Round [204] log likelihood: -2890.230310 EM: Round [205] log likelihood: -2890.229554 EM: Round [206] log likelihood: -2890.228806 EM: Round [207] log likelihood: -2890.228065 EM: Round [208] log likelihood: -2890.227331 EM: Round [209] log likelihood: -2890.226604 EM: Round [210] log likelihood: -2890.225885 EM: Round [211] log likelihood: -2890.225172 EM: Round [212] log likelihood: -2890.224467 EM: Round [213] log likelihood: -2890.223768 EM: Round [214] log likelihood: -2890.223076 EM: Round [215] log likelihood: -2890.222391 EM: Round [216] log likelihood: -2890.221713 EM: Round [217] log likelihood: -2890.221041 EM: Round [218] log likelihood: -2890.220376 EM: Round [219] log likelihood: -2890.219718 EM: Round [220] log likelihood: -2890.219066 EM: Round [221] log likelihood: -2890.218420 EM: Round [222] log likelihood: -2890.217780 EM: Round [223] log likelihood: -2890.217147 EM: Round [224] log likelihood: -2890.216520 EM: Round [225] log likelihood: -2890.215899 EM: Round [226] log likelihood: -2890.215284 EM: Round [227] log likelihood: -2890.214675 EM: Round [228] log likelihood: -2890.214072 EM: Round [229] log likelihood: -2890.213474 EM: Round [230] log likelihood: -2890.212883 EM: Round [231] log likelihood: -2890.212297 EM: Round [232] log likelihood: -2890.211717 EM: Round [233] log likelihood: -2890.211143 EM: Round [234] log likelihood: -2890.210574 EM: Round [235] log likelihood: -2890.210010 EM: Round [236] log likelihood: -2890.209452 EM: Round [237] log likelihood: -2890.208900 EM: Round [238] log likelihood: -2890.208353 EM: Round [239] log likelihood: -2890.207811 EM: Round [240] log likelihood: -2890.207274 EM: Round [241] log likelihood: -2890.206742 EM: Round [242] log likelihood: -2890.206216 EM: Round [243] log likelihood: -2890.205694 EM: Round [244] log likelihood: -2890.205178 EM: Round [245] log likelihood: -2890.204667 EM: Round [246] log likelihood: -2890.204160 EM: Round [247] log likelihood: -2890.203658 EM: Round [248] log likelihood: -2890.203162 EM: Round [249] log likelihood: -2890.202669 EM: Round [250] log likelihood: -2890.202182 EM: Round [251] log likelihood: -2890.201699 EM: Round [252] log likelihood: -2890.201221 EM: Round [253] log likelihood: -2890.200748 EM: Round [254] log likelihood: -2890.200279 EM: Round [255] log likelihood: -2890.199815 EM: Round [256] log likelihood: -2890.199355 EM: Round [257] log likelihood: -2890.198899 EM: Round [258] log likelihood: -2890.198448 EM: Round [259] log likelihood: -2890.198001 EM: Round [260] log likelihood: -2890.197558 EM: Round [261] log likelihood: -2890.197120 EM: Round [262] log likelihood: -2890.196685 EM: Round [263] log likelihood: -2890.196255 EM: Round [264] log likelihood: -2890.195829 EM: Round [265] log likelihood: -2890.195407 EM: Round [266] log likelihood: -2890.194989 EM: Round [267] log likelihood: -2890.194575 EM: Round [268] log likelihood: -2890.194165 EM: Round [269] log likelihood: -2890.193759 EM: Round [270] log likelihood: -2890.193357 EM: Round [271] log likelihood: -2890.192958 EM: Round [272] log likelihood: -2890.192563 EM: Round [273] log likelihood: -2890.192173 EM: Round [274] log likelihood: -2890.191785 EM: Round [275] log likelihood: -2890.191402 EM: Round [276] log likelihood: -2890.191022 EM: Round [277] log likelihood: -2890.190645 EM: Round [278] log likelihood: -2890.190273 EM: Round [279] log likelihood: -2890.189903 EM: Round [280] log likelihood: -2890.189538 EM: Round [281] log likelihood: -2890.189175 EM: Round [282] log likelihood: -2890.188817 EM: Round [283] log likelihood: -2890.188461 EM: Round [284] log likelihood: -2890.188109 EM: Round [285] log likelihood: -2890.187760 EM: Round [286] log likelihood: -2890.187415 EM: Round [287] log likelihood: -2890.187073 EM: Round [288] log likelihood: -2890.186734 EM: Round [289] log likelihood: -2890.186398 EM: Round [290] log likelihood: -2890.186065 EM: Round [291] log likelihood: -2890.185736 EM: Round [292] log likelihood: -2890.185409 EM: Round [293] log likelihood: -2890.185086 EM: Round [294] log likelihood: -2890.184766 EM: Round [295] log likelihood: -2890.184449 EM: Round [296] log likelihood: -2890.184134 EM: Round [297] log likelihood: -2890.183823 EM: Round [298] log likelihood: -2890.183515 EM: Round [299] log likelihood: -2890.183209 EM: Round [300] log likelihood: -2890.182907 EM: Round [301] log likelihood: -2890.182607 EM: Round [302] log likelihood: -2890.182310 EM: Round [303] log likelihood: -2890.182016 EM: Round [304] log likelihood: -2890.181725 EM: Round [305] log likelihood: -2890.181436 EM: Round [306] log likelihood: -2890.181150 EM: Round [307] log likelihood: -2890.180867 EM: Round [308] log likelihood: -2890.180586 EM: Round [309] log likelihood: -2890.180308 EM: Round [310] log likelihood: -2890.180033 EM: Round [311] log likelihood: -2890.179760 EM: Round [312] log likelihood: -2890.179490 EM: Round [313] log likelihood: -2890.179222 EM: Round [314] log likelihood: -2890.178957 EM: Round [315] log likelihood: -2890.178695 EM: Round [316] log likelihood: -2890.178434 EM: Round [317] log likelihood: -2890.178177 EM: Round [318] log likelihood: -2890.177921 EM: Round [319] log likelihood: -2890.177668 EM: Round [320] log likelihood: -2890.177418 EM: Round [321] log likelihood: -2890.177169 EM: Round [322] log likelihood: -2890.176923 EM: Round [323] log likelihood: -2890.176680 EM: Round [324] log likelihood: -2890.176438 EM: Round [325] log likelihood: -2890.176199 EM: Round [326] log likelihood: -2890.175962 EM: Round [327] log likelihood: -2890.175728 EM: Round [328] log likelihood: -2890.175495 EM: Round [329] log likelihood: -2890.175265 EM: Round [330] log likelihood: -2890.175037 EM: Round [331] log likelihood: -2890.174811 EM: Round [332] log likelihood: -2890.174587 EM: Round [333] log likelihood: -2890.174365 EM: Round [334] log likelihood: -2890.174145 EM: Round [335] log likelihood: -2890.173927 EM: Round [336] log likelihood: -2890.173712 EM: Round [337] log likelihood: -2890.173498 EM: Round [338] log likelihood: -2890.173286 EM: Round [339] log likelihood: -2890.173077 EM: Round [340] log likelihood: -2890.172869 EM: Round [341] log likelihood: -2890.172663 EM: Round [342] log likelihood: -2890.172459 EM: Round [343] log likelihood: -2890.172257 EM: Round [344] log likelihood: -2890.172057 EM: Round [345] log likelihood: -2890.171859 EM: Round [346] log likelihood: -2890.171662 EM: Round [347] log likelihood: -2890.171468 EM: Round [348] log likelihood: -2890.171275 EM: Round [349] log likelihood: -2890.171084 EM: Round [350] log likelihood: -2890.170895 EM: Round [351] log likelihood: -2890.170707 EM: Round [352] log likelihood: -2890.170521 EM: Round [353] log likelihood: -2890.170337 EM: Round [354] log likelihood: -2890.170155 EM: Round [355] log likelihood: -2890.169974 EM: Round [356] log likelihood: -2890.169796 EM: Round [357] log likelihood: -2890.169618 EM: Round [358] log likelihood: -2890.169443 EM: Round [359] log likelihood: -2890.169269 EM: Round [360] log likelihood: -2890.169096 EM: Round [361] log likelihood: -2890.168925 EM: Round [362] log likelihood: -2890.168756 EM: Round [363] log likelihood: -2890.168589 EM: Round [364] log likelihood: -2890.168423 EM: Round [365] log likelihood: -2890.168258 EM: Round [366] log likelihood: -2890.168095 EM: Round [367] log likelihood: -2890.167933 EM: Round [368] log likelihood: -2890.167773 EM: Round [369] log likelihood: -2890.167615 EM: Round [370] log likelihood: -2890.167458 EM: Round [371] log likelihood: -2890.167302 EM: Round [372] log likelihood: -2890.167148 EM: Round [373] log likelihood: -2890.166995 EM: Round [374] log likelihood: -2890.166844 EM: Round [375] log likelihood: -2890.166694 EM: Round [376] log likelihood: -2890.166546 EM: Round [377] log likelihood: -2890.166398 EM: Round [378] log likelihood: -2890.166253 EM: Round [379] log likelihood: -2890.166108 EM: Round [380] log likelihood: -2890.165965 EM: Round [381] log likelihood: -2890.165823 EM: Round [382] log likelihood: -2890.165683 EM: Round [383] log likelihood: -2890.165544 EM: Round [384] log likelihood: -2890.165406 EM: Round [385] log likelihood: -2890.165269 EM: Round [386] log likelihood: -2890.165134 EM: Round [387] log likelihood: -2890.165000 EM: Round [388] log likelihood: -2890.164867 EM: Round [389] log likelihood: -2890.164735 EM: Round [390] log likelihood: -2890.164605 EM: Round [391] log likelihood: -2890.164475 EM: Round [392] log likelihood: -2890.164347 EM: Round [393] log likelihood: -2890.164220 EM: Round [394] log likelihood: -2890.164095 EM: Round [395] log likelihood: -2890.163970 EM: Round [396] log likelihood: -2890.163847 EM: Round [397] log likelihood: -2890.163725 EM: Round [398] log likelihood: -2890.163604 EM: Round [399] log likelihood: -2890.163484 EM: Round [400] log likelihood: -2890.163365 EM: Round [401] log likelihood: -2890.163247 EM: Round [402] log likelihood: -2890.163130 EM: Round [403] log likelihood: -2890.163015 EM: Round [404] log likelihood: -2890.162900 EM: Round [405] log likelihood: -2890.162786 EM: Round [406] log likelihood: -2890.162674 EM: Round [407] log likelihood: -2890.162563 EM: Round [408] log likelihood: -2890.162452 EM: Round [409] log likelihood: -2890.162343 EM: Round [410] log likelihood: -2890.162234 EM: Round [411] log likelihood: -2890.162127 EM: Round [412] log likelihood: -2890.162021 EM: Round [413] log likelihood: -2890.161915 EM: Round [414] log likelihood: -2890.161811 EM: Round [415] log likelihood: -2890.161707 EM: Round [416] log likelihood: -2890.161605 EM: Round [417] log likelihood: -2890.161503 EM: Round [418] log likelihood: -2890.161403 EM: Round [419] log likelihood: -2890.161303 EM: Stopping iterations at round 419 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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam" Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam || : Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam into /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords CMD: touch /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.FusionJuncSpan Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.FusionJuncSpan Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.gff3 Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.gff3 > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.gff3 > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.Pfam.bed Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.gff3 Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.gff3 > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.gff3 > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.igv.seqsimilar.bed Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa > /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2 --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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir -done, see /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -2645.228701 EM: Round [1] log likelihood: -2645.073177 EM: Round [2] log likelihood: -2645.072982 EM: Round [3] log likelihood: -2645.072982 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz: 295366080 Execution Time = 6.22 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --gtf /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fa --gtf /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.gtf > /tmp/nxf.ksoFEZ4fk5/fi_workdir/microH.dat Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.ksoFEZ4fk5/fi_workdir/microH.dat /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/fi_workdir/microH.dat /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.tsv Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.ksoFEZ4fk5 --json_outfile /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.json --file_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.ksoFEZ4fk5 --json_outfile /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.json --file_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2 Running: touch /tmp/nxf.ksoFEZ4fk5/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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.json --input_file_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2 --html_output /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.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.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.json --input_file_prefix 659_bhK-T1-TRNA-1_A23MVY2LT4_2 --html_output /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.fusion_inspector_web.html Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000236438.7] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [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 [ENSG00000242193.11] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.ksoFEZ4fk5/ctat_genome_lib_build_dir > /tmp/nxf.ksoFEZ4fk5/659_bhK-T1-TRNA-1_A23MVY2LT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.ksoFEZ4fk5/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory