Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/d54225ddd6737e14791fcfb7249325/659_bNS-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/2007b29c08245fae1591d03403d00d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/2007b29c08245fae1591d03403d00d/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/d54225ddd6737e14791fcfb7249325/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/2cb56d52c9912f948e8d67c400308d/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1 --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_bNS-T1-TRNA-1_B23WHTKLT4_1.fusionreport.tsv --gtf /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/cytoBand.txt Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed -parsing GTF file: /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.sA3rneZbym/fi_workdir --reads "/tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.sA3rneZbym/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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:22:41 ..... started STAR run Jun 08 10:22:41 ..... loading genome Jun 08 10:24:33 ... generating Suffix Array index Jun 08 10:28:55 ... completed Suffix Array index Jun 08 10:28:55 ..... processing annotations GTF Jun 08 10:28:55 ..... inserting junctions into the genome indices Jun 08 10:30:06 ..... started mapping Jun 08 11:35:42 ..... finished mapping Jun 08 11:35:44 ..... started sorting BAM Jun 08 11:35:44 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam Execution Time = 73.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --CPU 8 --out_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1.star --out_dir /tmp/nxf.sA3rneZbym/fi_workdir --reads "/tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:35:47 : INFO : Done. Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf -parsing /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_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] -done parsing /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'per_id < 96' => 1247, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2, 'num genes matched < 2' => 4, 'small anchor length' => 14, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 8, 'excessive soft clipping' => 2609, ' ** passed ** ' => 9320, 'exons hit < 2' => 2, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1 }; -writing fusion junction support info. Execution Time = 0.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_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] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] -fusion SPANNING read extraction for scaff: EML4--ALK [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: IGFL1P2--HIF3A [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 906, 'seq similar region alignment' => 17068 }; Execution Time = 0.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -1607.712150 EM: Round [1] log likelihood: -1607.672747 EM: Round [2] log likelihood: -1607.652177 EM: Round [3] log likelihood: -1607.632071 EM: Round [4] log likelihood: -1607.612408 EM: Round [5] log likelihood: -1607.593170 EM: Round [6] log likelihood: -1607.574341 EM: Round [7] log likelihood: -1607.555905 EM: Round [8] log likelihood: -1607.537845 EM: Round [9] log likelihood: -1607.520149 EM: Round [10] log likelihood: -1607.502802 EM: Round [11] log likelihood: -1607.485792 EM: Round [12] log likelihood: -1607.469106 EM: Round [13] log likelihood: -1607.452734 EM: Round [14] log likelihood: -1607.436664 EM: Round [15] log likelihood: -1607.420886 EM: Round [16] log likelihood: -1607.405390 EM: Round [17] log likelihood: -1607.390168 EM: Round [18] log likelihood: -1607.375210 EM: Round [19] log likelihood: -1607.360508 EM: Round [20] log likelihood: -1607.346054 EM: Round [21] log likelihood: -1607.331840 EM: Round [22] log likelihood: -1607.317859 EM: Round [23] log likelihood: -1607.304104 EM: Round [24] log likelihood: -1607.290568 EM: Round [25] log likelihood: -1607.277245 EM: Round [26] log likelihood: -1607.264128 EM: Round [27] log likelihood: -1607.251213 EM: Round [28] log likelihood: -1607.238493 EM: Round [29] log likelihood: -1607.225963 EM: Round [30] log likelihood: -1607.213618 EM: Round [31] log likelihood: -1607.201453 EM: Round [32] log likelihood: -1607.189463 EM: Round [33] log likelihood: -1607.177644 EM: Round [34] log likelihood: -1607.165990 EM: Round [35] log likelihood: -1607.154499 EM: Round [36] log likelihood: -1607.143166 EM: Round [37] log likelihood: -1607.131986 EM: Round [38] log likelihood: -1607.120957 EM: Round [39] log likelihood: -1607.110075 EM: Round [40] log likelihood: -1607.099335 EM: Round [41] log likelihood: -1607.088735 EM: Round [42] log likelihood: -1607.078272 EM: Round [43] log likelihood: -1607.067942 EM: Round [44] log likelihood: -1607.057742 EM: Round [45] log likelihood: -1607.047670 EM: Round [46] log likelihood: -1607.037722 EM: Round [47] log likelihood: -1607.027895 EM: Round [48] log likelihood: -1607.018188 EM: Round [49] log likelihood: -1607.008597 EM: Round [50] log likelihood: -1606.999121 EM: Round [51] log likelihood: -1606.989755 EM: Round [52] log likelihood: -1606.980500 EM: Round [53] log likelihood: -1606.971351 EM: Round [54] log likelihood: -1606.962307 EM: Round [55] log likelihood: -1606.953365 EM: Round [56] log likelihood: -1606.944524 EM: Round [57] log likelihood: -1606.935782 EM: Round [58] log likelihood: -1606.927137 EM: Round [59] log likelihood: -1606.918586 EM: Round [60] log likelihood: -1606.910128 EM: Round [61] log likelihood: -1606.901761 EM: Round [62] log likelihood: -1606.893484 EM: Round [63] log likelihood: -1606.885294 EM: Round [64] log likelihood: -1606.877191 EM: Round [65] log likelihood: -1606.869172 EM: Round [66] log likelihood: -1606.861236 EM: Round [67] log likelihood: -1606.853382 EM: Round [68] log likelihood: -1606.845607 EM: Round [69] log likelihood: -1606.837912 EM: Round [70] log likelihood: -1606.830293 EM: Round [71] log likelihood: -1606.822750 EM: Round [72] log likelihood: -1606.815282 EM: Round [73] log likelihood: -1606.807887 EM: Round [74] log likelihood: -1606.800564 EM: Round [75] log likelihood: -1606.793312 EM: Round [76] log likelihood: -1606.786129 EM: Round [77] log likelihood: -1606.779015 EM: Round [78] log likelihood: -1606.771968 EM: Round [79] log likelihood: -1606.764987 EM: Round [80] log likelihood: -1606.758071 EM: Round [81] log likelihood: -1606.751220 EM: Round [82] log likelihood: -1606.744431 EM: Round [83] log likelihood: -1606.737705 EM: Round [84] log likelihood: -1606.731040 EM: Round [85] log likelihood: -1606.724434 EM: Round [86] log likelihood: -1606.717888 EM: Round [87] log likelihood: -1606.711400 EM: Round [88] log likelihood: -1606.704970 EM: Round [89] log likelihood: -1606.698596 EM: Round [90] log likelihood: -1606.692278 EM: Round [91] log likelihood: -1606.686014 EM: Round [92] log likelihood: -1606.679805 EM: Round [93] log likelihood: -1606.673649 EM: Round [94] log likelihood: -1606.667545 EM: Round [95] log likelihood: -1606.661493 EM: Round [96] log likelihood: -1606.655492 EM: Round [97] log likelihood: -1606.649541 EM: Round [98] log likelihood: -1606.643639 EM: Round [99] log likelihood: -1606.637786 EM: Round [100] log likelihood: -1606.631982 EM: Round [101] log likelihood: -1606.626225 EM: Round [102] log likelihood: -1606.620514 EM: Round [103] log likelihood: -1606.614850 EM: Round [104] log likelihood: -1606.609231 EM: Round [105] log likelihood: -1606.603657 EM: Round [106] log likelihood: -1606.598128 EM: Round [107] log likelihood: -1606.592642 EM: Round [108] log likelihood: -1606.587199 EM: Round [109] log likelihood: -1606.581799 EM: Round [110] log likelihood: -1606.576441 EM: Round [111] log likelihood: -1606.571124 EM: Round [112] log likelihood: -1606.565848 EM: Round [113] log likelihood: -1606.560612 EM: Round [114] log likelihood: -1606.555417 EM: Round [115] log likelihood: -1606.550260 EM: Round [116] log likelihood: -1606.545143 EM: Round [117] log likelihood: -1606.540063 EM: Round [118] log likelihood: -1606.535022 EM: Round [119] log likelihood: -1606.530018 EM: Round [120] log likelihood: -1606.525051 EM: Round [121] log likelihood: -1606.520121 EM: Round [122] log likelihood: -1606.515226 EM: Round [123] log likelihood: -1606.510367 EM: Round [124] log likelihood: -1606.505544 EM: Round [125] log likelihood: -1606.500755 EM: Round [126] log likelihood: -1606.496000 EM: Round [127] log likelihood: -1606.491279 EM: Round [128] log likelihood: -1606.486592 EM: Round [129] log likelihood: -1606.481938 EM: Round [130] log likelihood: -1606.477317 EM: Round [131] log likelihood: -1606.472728 EM: Round [132] log likelihood: -1606.468171 EM: Round [133] log likelihood: -1606.463646 EM: Round [134] log likelihood: -1606.459152 EM: Round [135] log likelihood: -1606.454689 EM: Round [136] log likelihood: -1606.450257 EM: Round [137] log likelihood: -1606.445854 EM: Round [138] log likelihood: -1606.441482 EM: Round [139] log likelihood: -1606.437139 EM: Round [140] log likelihood: -1606.432825 EM: Round [141] log likelihood: -1606.428541 EM: Round [142] log likelihood: -1606.424285 EM: Round [143] log likelihood: -1606.420057 EM: Round [144] log likelihood: -1606.415857 EM: Round [145] log likelihood: -1606.411685 EM: Round [146] log likelihood: -1606.407540 EM: Round [147] log likelihood: -1606.403422 EM: Round [148] log likelihood: -1606.399331 EM: Round [149] log likelihood: -1606.395267 EM: Round [150] log likelihood: -1606.391229 EM: Round [151] log likelihood: -1606.387216 EM: Round [152] log likelihood: -1606.383230 EM: Round [153] log likelihood: -1606.379269 EM: Round [154] log likelihood: -1606.375333 EM: Round [155] log likelihood: -1606.371422 EM: Round [156] log likelihood: -1606.367535 EM: Round [157] log likelihood: -1606.363673 EM: Round [158] log likelihood: -1606.359836 EM: Round [159] log likelihood: -1606.356022 EM: Round [160] log likelihood: -1606.352231 EM: Round [161] log likelihood: -1606.348465 EM: Round [162] log likelihood: -1606.344721 EM: Round [163] log likelihood: -1606.341000 EM: Round [164] log likelihood: -1606.337303 EM: Round [165] log likelihood: -1606.333627 EM: Round [166] log likelihood: -1606.329974 EM: Round [167] log likelihood: -1606.326343 EM: Round [168] log likelihood: -1606.322734 EM: Round [169] log likelihood: -1606.319147 EM: Round [170] log likelihood: -1606.315581 EM: Round [171] log likelihood: -1606.312036 EM: Round [172] log likelihood: -1606.308512 EM: Round [173] log likelihood: -1606.305010 EM: Round [174] log likelihood: -1606.301528 EM: Round [175] log likelihood: -1606.298066 EM: Round [176] log likelihood: -1606.294625 EM: Round [177] log likelihood: -1606.291203 EM: Round [178] log likelihood: -1606.287802 EM: Round [179] log likelihood: -1606.284420 EM: Round [180] log likelihood: -1606.281058 EM: Round [181] log likelihood: -1606.277716 EM: Round [182] log likelihood: -1606.274392 EM: Round [183] log likelihood: -1606.271088 EM: Round [184] log likelihood: -1606.267802 EM: Round [185] log likelihood: -1606.264535 EM: Round [186] log likelihood: -1606.261287 EM: Round [187] log likelihood: -1606.258056 EM: Round [188] log likelihood: -1606.254845 EM: Round [189] log likelihood: -1606.251651 EM: Round [190] log likelihood: -1606.248475 EM: Round [191] log likelihood: -1606.245316 EM: Round [192] log likelihood: -1606.242175 EM: Round [193] log likelihood: -1606.239052 EM: Round [194] log likelihood: -1606.235946 EM: Round [195] log likelihood: -1606.232857 EM: Round [196] log likelihood: -1606.229785 EM: Round [197] log likelihood: -1606.226730 EM: Round [198] log likelihood: -1606.223691 EM: Round [199] log likelihood: -1606.220669 EM: Round [200] log likelihood: -1606.217663 EM: Round [201] log likelihood: -1606.214674 EM: Round [202] log likelihood: -1606.211701 EM: Round [203] log likelihood: -1606.208743 EM: Round [204] log likelihood: -1606.205802 EM: Round [205] log likelihood: -1606.202876 EM: Round [206] log likelihood: -1606.199966 EM: Round [207] log likelihood: -1606.197071 EM: Round [208] log likelihood: -1606.194192 EM: Round [209] log likelihood: -1606.191328 EM: Round [210] log likelihood: -1606.188479 EM: Round [211] log likelihood: -1606.185645 EM: Round [212] log likelihood: -1606.182825 EM: Round [213] log likelihood: -1606.180021 EM: Round [214] log likelihood: -1606.177231 EM: Round [215] log likelihood: -1606.174455 EM: Round [216] log likelihood: -1606.171694 EM: Round [217] log likelihood: -1606.168948 EM: Round [218] log likelihood: -1606.166215 EM: Round [219] log likelihood: -1606.163496 EM: Round [220] log likelihood: -1606.160792 EM: Round [221] log likelihood: -1606.158101 EM: Round [222] log likelihood: -1606.155424 EM: Round [223] log likelihood: -1606.152760 EM: Round [224] log likelihood: -1606.150110 EM: Round [225] log likelihood: -1606.147473 EM: Round [226] log likelihood: -1606.144850 EM: Round [227] log likelihood: -1606.142240 EM: Round [228] log likelihood: -1606.139643 EM: Round [229] log likelihood: -1606.137059 EM: Round [230] log likelihood: -1606.134487 EM: Round [231] log likelihood: -1606.131929 EM: Round [232] log likelihood: -1606.129383 EM: Round [233] log likelihood: -1606.126850 EM: Round [234] log likelihood: -1606.124330 EM: Round [235] log likelihood: -1606.121821 EM: Round [236] log likelihood: -1606.119326 EM: Round [237] log likelihood: -1606.116842 EM: Round [238] log likelihood: -1606.114370 EM: Round [239] log likelihood: -1606.111911 EM: Round [240] log likelihood: -1606.109464 EM: Round [241] log likelihood: -1606.107028 EM: Round [242] log likelihood: -1606.104604 EM: Round [243] log likelihood: -1606.102192 EM: Round [244] log likelihood: -1606.099792 EM: Round [245] log likelihood: -1606.097403 EM: Round [246] log likelihood: -1606.095025 EM: Round [247] log likelihood: -1606.092659 EM: Round [248] log likelihood: -1606.090305 EM: Round [249] log likelihood: -1606.087961 EM: Round [250] log likelihood: -1606.085629 EM: Round [251] log likelihood: -1606.083307 EM: Round [252] log likelihood: -1606.080997 EM: Round [253] log likelihood: -1606.078697 EM: Round [254] log likelihood: -1606.076409 EM: Round [255] log likelihood: -1606.074131 EM: Round [256] log likelihood: -1606.071864 EM: Round [257] log likelihood: -1606.069607 EM: Round [258] log likelihood: -1606.067361 EM: Round [259] log likelihood: -1606.065125 EM: Round [260] log likelihood: -1606.062900 EM: Round [261] log likelihood: -1606.060685 EM: Round [262] log likelihood: -1606.058480 EM: Round [263] log likelihood: -1606.056286 EM: Round [264] log likelihood: -1606.054101 EM: Round [265] log likelihood: -1606.051927 EM: Round [266] log likelihood: -1606.049762 EM: Round [267] log likelihood: -1606.047608 EM: Round [268] log likelihood: -1606.045463 EM: Round [269] log likelihood: -1606.043328 EM: Round [270] log likelihood: -1606.041203 EM: Round [271] log likelihood: -1606.039087 EM: Round [272] log likelihood: -1606.036981 EM: Round [273] log likelihood: -1606.034885 EM: Round [274] log likelihood: -1606.032797 EM: Round [275] log likelihood: -1606.030720 EM: Round [276] log likelihood: -1606.028651 EM: Round [277] log likelihood: -1606.026592 EM: Round [278] log likelihood: -1606.024542 EM: Round [279] log likelihood: -1606.022502 EM: Round [280] log likelihood: -1606.020470 EM: Round [281] log likelihood: -1606.018447 EM: Round [282] log likelihood: -1606.016434 EM: Round [283] log likelihood: -1606.014429 EM: Round [284] log likelihood: -1606.012433 EM: Round [285] log likelihood: -1606.010446 EM: Round [286] log likelihood: -1606.008467 EM: Round [287] log likelihood: -1606.006498 EM: Round [288] log likelihood: -1606.004536 EM: Round [289] log likelihood: -1606.002584 EM: Round [290] log likelihood: -1606.000640 EM: Round [291] log likelihood: -1605.998704 EM: Round [292] log likelihood: -1605.996777 EM: Round [293] log likelihood: -1605.994858 EM: Round [294] log likelihood: 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-1605.567827 EM: Round [757] log likelihood: -1605.567421 EM: Round [758] log likelihood: -1605.567017 EM: Round [759] log likelihood: -1605.566613 EM: Round [760] log likelihood: -1605.566210 EM: Round [761] log likelihood: -1605.565809 EM: Round [762] log likelihood: -1605.565409 EM: Round [763] log likelihood: -1605.565009 EM: Round [764] log likelihood: -1605.564611 EM: Round [765] log likelihood: -1605.564214 EM: Round [766] log likelihood: -1605.563819 EM: Round [767] log likelihood: -1605.563424 EM: Round [768] log likelihood: -1605.563030 EM: Round [769] log likelihood: -1605.562638 EM: Round [770] log likelihood: -1605.562247 EM: Round [771] log likelihood: -1605.561856 EM: Round [772] log likelihood: -1605.561467 EM: Round [773] log likelihood: -1605.561079 EM: Round [774] log likelihood: -1605.560692 EM: Round [775] log likelihood: -1605.560306 EM: Round [776] log likelihood: -1605.559921 EM: Round [777] log likelihood: -1605.559538 EM: Round [778] log likelihood: -1605.559155 EM: Round [779] log likelihood: -1605.558773 EM: Round [780] log likelihood: -1605.558393 EM: Round [781] log likelihood: -1605.558013 EM: Round [782] log likelihood: -1605.557635 EM: Round [783] log likelihood: -1605.557258 EM: Round [784] log likelihood: -1605.556881 EM: Round [785] log likelihood: -1605.556506 EM: Round [786] log likelihood: -1605.556132 EM: Round [787] log likelihood: -1605.555759 EM: Round [788] log likelihood: -1605.555387 EM: Round [789] log likelihood: -1605.555016 EM: Round [790] log likelihood: -1605.554646 EM: Round [791] log likelihood: -1605.554277 EM: Round [792] log likelihood: -1605.553909 EM: Round [793] log likelihood: -1605.553542 EM: Round [794] log likelihood: -1605.553176 EM: Round [795] log likelihood: -1605.552811 EM: Round [796] log likelihood: -1605.552447 EM: Round [797] log likelihood: -1605.552084 EM: Round [798] log likelihood: -1605.551722 EM: Round [799] log likelihood: -1605.551362 EM: Round [800] log likelihood: -1605.551002 EM: Round [801] log likelihood: -1605.550643 EM: Round [802] log likelihood: -1605.550285 EM: Round [803] log likelihood: -1605.549928 EM: Round [804] log likelihood: -1605.549572 EM: Round [805] log likelihood: -1605.549217 EM: Round [806] log likelihood: -1605.548864 EM: Round [807] log likelihood: -1605.548511 EM: Round [808] log likelihood: -1605.548159 EM: Round [809] log likelihood: -1605.547808 EM: Round [810] log likelihood: -1605.547458 EM: Round [811] log likelihood: -1605.547109 EM: Round [812] log likelihood: -1605.546761 EM: Round [813] log likelihood: -1605.546414 EM: Round [814] log likelihood: -1605.546068 EM: Round [815] log likelihood: -1605.545722 EM: Round [816] log likelihood: -1605.545378 EM: Round [817] log likelihood: -1605.545035 EM: Round [818] log likelihood: -1605.544693 EM: Round [819] log likelihood: -1605.544351 EM: Round [820] log likelihood: -1605.544011 EM: Round [821] log likelihood: -1605.543671 EM: Round [822] log likelihood: -1605.543333 EM: Round [823] log likelihood: -1605.542995 EM: Round [824] log likelihood: -1605.542659 EM: Round [825] log likelihood: -1605.542323 EM: Round [826] log likelihood: -1605.541988 EM: Round [827] log likelihood: -1605.541654 EM: Round [828] log likelihood: -1605.541321 EM: Round [829] log likelihood: -1605.540989 EM: Round [830] log likelihood: -1605.540658 EM: Round [831] log likelihood: -1605.540328 EM: Round [832] log likelihood: -1605.539998 EM: Round [833] log likelihood: -1605.539670 EM: Round [834] log likelihood: -1605.539342 EM: Round [835] log likelihood: -1605.539016 EM: Round [836] log likelihood: -1605.538690 EM: Round [837] log likelihood: -1605.538365 EM: Round [838] log likelihood: -1605.538041 EM: Round [839] log likelihood: -1605.537718 EM: Round [840] log likelihood: -1605.537396 EM: Round [841] log likelihood: -1605.537075 EM: Round [842] log likelihood: -1605.536754 EM: Round [843] log likelihood: -1605.536435 EM: Round [844] log likelihood: -1605.536116 EM: Round [845] log likelihood: -1605.535799 EM: Round [846] log likelihood: -1605.535482 EM: Round [847] log likelihood: -1605.535166 EM: Round [848] log likelihood: -1605.534850 EM: Round [849] log likelihood: -1605.534536 EM: Round [850] log likelihood: -1605.534223 EM: Round [851] log likelihood: -1605.533910 EM: Round [852] log likelihood: -1605.533598 EM: Round [853] log likelihood: -1605.533287 EM: Round [854] log likelihood: -1605.532977 EM: Round [855] log likelihood: -1605.532668 EM: Round [856] log likelihood: -1605.532360 EM: Round [857] log likelihood: -1605.532052 EM: Round [858] log likelihood: -1605.531746 EM: Round [859] log likelihood: -1605.531440 EM: Round [860] log likelihood: -1605.531135 EM: Round [861] log likelihood: -1605.530831 EM: Round [862] log likelihood: -1605.530527 EM: Round [863] log likelihood: -1605.530225 EM: Round [864] log likelihood: -1605.529923 EM: Round [865] log likelihood: -1605.529622 EM: Round [866] log likelihood: -1605.529322 EM: Round [867] log likelihood: -1605.529023 EM: Round [868] log likelihood: -1605.528725 EM: Round [869] log likelihood: -1605.528427 EM: Round [870] log likelihood: -1605.528130 EM: Round [871] log likelihood: -1605.527834 EM: Round [872] log likelihood: -1605.527539 EM: Round [873] log likelihood: -1605.527245 EM: Round [874] log likelihood: -1605.526951 EM: Round [875] log likelihood: -1605.526658 EM: Round [876] log likelihood: -1605.526366 EM: Round [877] log likelihood: -1605.526075 EM: Round [878] log likelihood: -1605.525785 EM: Round [879] log likelihood: -1605.525495 EM: Round [880] log likelihood: -1605.525206 EM: Round [881] log likelihood: -1605.524918 EM: Round [882] log likelihood: -1605.524631 EM: Round [883] log likelihood: -1605.524344 EM: Round [884] log likelihood: -1605.524059 EM: Round [885] log likelihood: -1605.523774 EM: Round [886] log likelihood: -1605.523490 EM: Round [887] log likelihood: -1605.523206 EM: Round [888] log likelihood: -1605.522923 EM: Round [889] log likelihood: -1605.522642 EM: Round [890] log likelihood: -1605.522360 EM: Round [891] log likelihood: -1605.522080 EM: Round [892] log likelihood: -1605.521800 EM: Round [893] log likelihood: -1605.521522 EM: Round [894] log likelihood: -1605.521244 EM: Round [895] log likelihood: -1605.520966 EM: Round [896] log likelihood: -1605.520690 EM: Round [897] log likelihood: -1605.520414 EM: Round [898] log likelihood: -1605.520139 EM: Round [899] log likelihood: -1605.519864 EM: Round [900] log likelihood: -1605.519591 EM: Round [901] log likelihood: -1605.519318 EM: Round [902] log likelihood: -1605.519046 EM: Round [903] log likelihood: -1605.518774 EM: Round [904] log likelihood: -1605.518503 EM: Round [905] log likelihood: -1605.518234 EM: Round [906] log likelihood: -1605.517964 EM: Round [907] log likelihood: -1605.517696 EM: Round [908] log likelihood: -1605.517428 EM: Round [909] log likelihood: -1605.517161 EM: Round [910] log likelihood: -1605.516895 EM: Round [911] log likelihood: -1605.516629 EM: Round [912] log likelihood: -1605.516364 EM: Round [913] log likelihood: -1605.516100 EM: Round [914] log likelihood: -1605.515836 EM: Round [915] log likelihood: -1605.515573 EM: Round [916] log likelihood: -1605.515311 EM: Round [917] log likelihood: -1605.515050 EM: Round [918] log likelihood: -1605.514789 EM: Round [919] log likelihood: -1605.514529 EM: Round [920] log likelihood: -1605.514270 EM: Round [921] log likelihood: -1605.514011 EM: Round [922] log likelihood: -1605.513754 EM: Round [923] log likelihood: -1605.513496 EM: Round [924] log likelihood: -1605.513240 EM: Round [925] log likelihood: -1605.512984 EM: Round [926] log likelihood: -1605.512729 EM: Round [927] log likelihood: -1605.512474 EM: Round [928] log likelihood: -1605.512221 EM: Round [929] log likelihood: -1605.511967 EM: Round [930] log likelihood: -1605.511715 EM: Round [931] log likelihood: -1605.511463 EM: Round [932] log likelihood: -1605.511212 EM: Round [933] log likelihood: -1605.510962 EM: Round [934] log likelihood: -1605.510712 EM: Round [935] log likelihood: -1605.510463 EM: Round [936] log likelihood: -1605.510215 EM: Round [937] log likelihood: -1605.509967 EM: Round [938] log likelihood: -1605.509720 EM: Round [939] log likelihood: -1605.509473 EM: Round [940] log likelihood: -1605.509227 EM: Round [941] log likelihood: -1605.508982 EM: Round [942] log likelihood: -1605.508738 EM: Round [943] log likelihood: -1605.508494 EM: Round [944] log likelihood: -1605.508251 EM: Round [945] log likelihood: -1605.508008 EM: Round [946] log likelihood: -1605.507767 EM: Round [947] log likelihood: -1605.507525 EM: Round [948] log likelihood: -1605.507285 EM: Round [949] log likelihood: -1605.507045 EM: Round [950] log likelihood: -1605.506805 EM: Round [951] log likelihood: -1605.506567 EM: Round [952] log likelihood: -1605.506329 EM: Round [953] log likelihood: -1605.506091 EM: Round [954] log likelihood: -1605.505855 EM: Round [955] log likelihood: -1605.505618 EM: Round [956] log likelihood: -1605.505383 EM: Round [957] log likelihood: -1605.505148 EM: Round [958] log likelihood: -1605.504914 EM: Round [959] log likelihood: -1605.504680 EM: Round [960] log likelihood: -1605.504447 EM: Round [961] log likelihood: -1605.504215 EM: Round [962] log likelihood: -1605.503983 EM: Round [963] log likelihood: -1605.503752 EM: Round [964] log likelihood: -1605.503521 EM: Round [965] log likelihood: -1605.503291 EM: Round [966] log likelihood: -1605.503062 EM: Round [967] log likelihood: -1605.502833 EM: Round [968] log likelihood: -1605.502605 EM: Round [969] log likelihood: -1605.502377 EM: Round [970] log likelihood: -1605.502151 EM: Round [971] log likelihood: -1605.501924 EM: Round [972] log likelihood: -1605.501699 EM: Round [973] log likelihood: -1605.501473 EM: Round [974] log likelihood: -1605.501249 EM: Round [975] log likelihood: -1605.501025 EM: Round [976] log likelihood: -1605.500802 EM: Round [977] log likelihood: -1605.500579 EM: Round [978] log likelihood: -1605.500357 EM: Round [979] log likelihood: -1605.500135 EM: Round [980] log likelihood: -1605.499914 EM: Round [981] log likelihood: -1605.499694 EM: Round [982] log likelihood: -1605.499474 EM: Round [983] log likelihood: -1605.499255 EM: Round [984] log likelihood: -1605.499036 EM: Round [985] log likelihood: -1605.498818 EM: Round [986] log likelihood: -1605.498600 EM: Round [987] log likelihood: -1605.498383 EM: Round [988] log likelihood: -1605.498167 EM: Round [989] log likelihood: -1605.497951 EM: Round [990] log likelihood: -1605.497736 EM: Round [991] log likelihood: -1605.497521 EM: Round [992] log likelihood: -1605.497307 EM: Round [993] log likelihood: -1605.497094 EM: Round [994] log likelihood: -1605.496881 EM: Round [995] log likelihood: -1605.496668 EM: Round [996] log likelihood: -1605.496457 EM: Round [997] log likelihood: -1605.496245 EM: Round [998] log likelihood: -1605.496035 EM: Round [999] log likelihood: -1605.495824 EM: Round [1000] log likelihood: -1605.495615 EM: Round [1001] log likelihood: -1605.495406 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam" Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.gff3 > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa > /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.sA3rneZbym/fi_workdir/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir -done, see /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -1358.508098 EM: Round [1] log likelihood: -1358.480125 EM: Round [2] log likelihood: -1358.463942 EM: Round [3] log likelihood: -1358.448054 EM: Round [4] log likelihood: -1358.432453 EM: Round [5] log likelihood: -1358.417129 EM: Round [6] log likelihood: -1358.402072 EM: Round [7] log likelihood: -1358.387274 EM: Round [8] log likelihood: -1358.372727 EM: Round [9] log likelihood: -1358.358423 EM: Round [10] log likelihood: -1358.344354 EM: Round [11] log likelihood: -1358.330514 EM: Round [12] log likelihood: -1358.316896 EM: Round [13] log likelihood: -1358.303493 EM: Round [14] log likelihood: -1358.290299 EM: Round [15] log likelihood: -1358.277309 EM: Round [16] log likelihood: -1358.264516 EM: Round [17] log likelihood: -1358.251914 EM: Round [18] log likelihood: -1358.239500 EM: Round [19] log likelihood: -1358.227267 EM: Round [20] log likelihood: -1358.215211 EM: Round [21] log likelihood: -1358.203328 EM: Round [22] log likelihood: -1358.191612 EM: Round [23] log likelihood: -1358.180060 EM: Round [24] log likelihood: -1358.168667 EM: Round [25] log likelihood: -1358.157430 EM: Round [26] log likelihood: -1358.146345 EM: Round [27] log likelihood: -1358.135407 EM: Round [28] log likelihood: -1358.124614 EM: Round [29] log likelihood: -1358.113961 EM: Round [30] log likelihood: -1358.103447 EM: Round [31] log likelihood: -1358.093067 EM: Round [32] log likelihood: -1358.082818 EM: Round [33] log likelihood: -1358.072697 EM: Round [34] log likelihood: -1358.062703 EM: Round [35] log likelihood: -1358.052831 EM: Round [36] log likelihood: -1358.043079 EM: Round [37] log likelihood: -1358.033444 EM: Round [38] log likelihood: -1358.023924 EM: Round [39] log likelihood: -1358.014517 EM: Round [40] log likelihood: -1358.005220 EM: Round [41] log likelihood: -1357.996031 EM: Round [42] log likelihood: -1357.986948 EM: Round [43] log likelihood: -1357.977967 EM: Round [44] log likelihood: -1357.969089 EM: Round [45] log likelihood: -1357.960309 EM: Round [46] log likelihood: -1357.951627 EM: Round [47] log likelihood: -1357.943041 EM: Round [48] log likelihood: -1357.934548 EM: Round [49] log likelihood: -1357.926147 EM: Round [50] log likelihood: -1357.917836 EM: Round [51] log likelihood: -1357.909614 EM: Round [52] log likelihood: -1357.901478 EM: Round [53] log likelihood: -1357.893427 EM: Round [54] log likelihood: -1357.885460 EM: Round [55] log likelihood: -1357.877575 EM: Round [56] log likelihood: -1357.869770 EM: Round [57] log likelihood: -1357.862045 EM: Round [58] log likelihood: -1357.854397 EM: Round [59] log likelihood: -1357.846826 EM: Round [60] log likelihood: -1357.839329 EM: Round [61] log likelihood: -1357.831907 EM: Round [62] log likelihood: -1357.824557 EM: Round [63] log likelihood: -1357.817278 EM: Round [64] log likelihood: -1357.810069 EM: Round [65] log likelihood: -1357.802929 EM: Round [66] log likelihood: -1357.795856 EM: Round [67] log likelihood: -1357.788851 EM: Round [68] log likelihood: -1357.781910 EM: Round [69] log likelihood: -1357.775035 EM: Round [70] log likelihood: -1357.768223 EM: Round [71] log likelihood: -1357.761473 EM: Round [72] log likelihood: -1357.754784 EM: Round [73] log likelihood: -1357.748156 EM: Round [74] log likelihood: -1357.741588 EM: Round [75] log likelihood: -1357.735078 EM: Round [76] log likelihood: -1357.728626 EM: Round [77] log likelihood: -1357.722231 EM: Round [78] log likelihood: -1357.715891 EM: Round [79] log likelihood: -1357.709607 EM: Round [80] log likelihood: -1357.703377 EM: Round [81] log likelihood: -1357.697201 EM: Round [82] log likelihood: -1357.691078 EM: Round [83] log likelihood: -1357.685006 EM: Round [84] log likelihood: -1357.678986 EM: Round [85] log likelihood: -1357.673016 EM: Round [86] log likelihood: -1357.667095 EM: Round [87] log likelihood: -1357.661224 EM: Round [88] log likelihood: -1357.655402 EM: Round [89] log likelihood: -1357.649627 EM: Round [90] log likelihood: -1357.643898 EM: Round [91] log likelihood: -1357.638217 EM: Round [92] log likelihood: -1357.632581 EM: Round [93] log likelihood: -1357.626990 EM: Round [94] log likelihood: -1357.621444 EM: Round [95] log likelihood: -1357.615941 EM: Round [96] log likelihood: -1357.610482 EM: Round [97] log likelihood: -1357.605066 EM: Round [98] log likelihood: -1357.599692 EM: Round [99] log 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likelihood: -1356.720666 EM: Round [518] log likelihood: -1356.719862 EM: Round [519] log likelihood: -1356.719061 EM: Round [520] log likelihood: -1356.718263 EM: Round [521] log likelihood: -1356.717467 EM: Round [522] log likelihood: -1356.716674 EM: Round [523] log likelihood: -1356.715883 EM: Round [524] log likelihood: -1356.715095 EM: Round [525] log likelihood: -1356.714309 EM: Round [526] log likelihood: -1356.713526 EM: Round [527] log likelihood: -1356.712745 EM: Round [528] log likelihood: -1356.711967 EM: Round [529] log likelihood: -1356.711191 EM: Round [530] log likelihood: -1356.710418 EM: Round [531] log likelihood: -1356.709648 EM: Round [532] log likelihood: -1356.708879 EM: Round [533] log likelihood: -1356.708113 EM: Round [534] log likelihood: -1356.707350 EM: Round [535] log likelihood: -1356.706589 EM: Round [536] log likelihood: -1356.705831 EM: Round [537] log likelihood: -1356.705075 EM: Round [538] log likelihood: -1356.704321 EM: Round [539] log 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likelihood: -1356.687627 EM: Round [562] log likelihood: -1356.686928 EM: Round [563] log likelihood: -1356.686231 EM: Round [564] log likelihood: -1356.685537 EM: Round [565] log likelihood: -1356.684845 EM: Round [566] log likelihood: -1356.684154 EM: Round [567] log likelihood: -1356.683466 EM: Round [568] log likelihood: -1356.682781 EM: Round [569] log likelihood: -1356.682097 EM: Round [570] log likelihood: -1356.681415 EM: Round [571] log likelihood: -1356.680736 EM: Round [572] log likelihood: -1356.680058 EM: Round [573] log likelihood: -1356.679383 EM: Round [574] log likelihood: -1356.678710 EM: Round [575] log likelihood: -1356.678039 EM: Round [576] log likelihood: -1356.677369 EM: Round [577] log likelihood: -1356.676702 EM: Round [578] log likelihood: -1356.676037 EM: Round [579] log likelihood: -1356.675375 EM: Round [580] log likelihood: -1356.674714 EM: Round [581] log likelihood: -1356.674055 EM: Round [582] log likelihood: -1356.673398 EM: Round [583] log likelihood: -1356.672743 EM: Round [584] log likelihood: -1356.672091 EM: Round [585] log likelihood: -1356.671440 EM: Round [586] log likelihood: -1356.670791 EM: Round [587] log likelihood: -1356.670144 EM: Round [588] log likelihood: -1356.669500 EM: Round [589] log likelihood: -1356.668857 EM: Round [590] log likelihood: -1356.668216 EM: Round [591] log likelihood: -1356.667577 EM: Round [592] log likelihood: -1356.666940 EM: Round [593] log likelihood: -1356.666305 EM: Round [594] log likelihood: -1356.665672 EM: Round [595] log likelihood: -1356.665041 EM: Round [596] log likelihood: -1356.664412 EM: Round [597] log likelihood: -1356.663784 EM: Round [598] log likelihood: -1356.663159 EM: Round [599] log likelihood: -1356.662536 EM: Round [600] log likelihood: -1356.661914 EM: Round [601] log likelihood: -1356.661294 EM: Round [602] log likelihood: -1356.660677 EM: Round [603] log likelihood: -1356.660061 EM: Round [604] log likelihood: -1356.659447 EM: Round [605] log likelihood: -1356.658835 EM: Round [606] log likelihood: -1356.658224 EM: Round [607] log likelihood: -1356.657616 EM: Round [608] log likelihood: -1356.657009 EM: Round [609] log likelihood: -1356.656404 EM: Round [610] log likelihood: -1356.655801 EM: Round [611] log likelihood: -1356.655200 EM: Round [612] log likelihood: -1356.654601 EM: Round [613] log likelihood: -1356.654003 EM: Round [614] log likelihood: -1356.653408 EM: Round [615] log likelihood: -1356.652814 EM: Round [616] log likelihood: -1356.652222 EM: Round [617] log likelihood: -1356.651631 EM: Round [618] log likelihood: -1356.651043 EM: Round [619] log likelihood: -1356.650456 EM: Round [620] log likelihood: -1356.649871 EM: Round [621] log likelihood: -1356.649287 EM: Round [622] log likelihood: -1356.648706 EM: Round [623] log likelihood: -1356.648126 EM: Round [624] log likelihood: -1356.647548 EM: Round [625] log likelihood: -1356.646972 EM: Round [626] log likelihood: -1356.646397 EM: Round [627] log likelihood: -1356.645824 EM: Round [628] log likelihood: -1356.645253 EM: Round [629] log likelihood: -1356.644684 EM: Round [630] log likelihood: -1356.644116 EM: Round [631] log likelihood: -1356.643550 EM: Round [632] log likelihood: -1356.642986 EM: Round [633] log likelihood: -1356.642423 EM: Round [634] log likelihood: -1356.641862 EM: Round [635] log likelihood: -1356.641303 EM: Round [636] log likelihood: -1356.640745 EM: Round [637] log likelihood: -1356.640189 EM: Round [638] log likelihood: -1356.639635 EM: Round [639] log likelihood: -1356.639082 EM: Round [640] log likelihood: -1356.638531 EM: Round [641] log likelihood: -1356.637981 EM: Round [642] log likelihood: -1356.637434 EM: Round [643] log likelihood: -1356.636887 EM: Round [644] log likelihood: -1356.636343 EM: Round [645] log likelihood: -1356.635800 EM: Round [646] log likelihood: -1356.635259 EM: Round [647] log likelihood: -1356.634719 EM: Round [648] log likelihood: -1356.634181 EM: Round [649] log likelihood: -1356.633644 EM: Round [650] log likelihood: -1356.633109 EM: Round [651] log likelihood: -1356.632576 EM: Round [652] log likelihood: -1356.632044 EM: Round [653] log likelihood: -1356.631514 EM: Round [654] log likelihood: -1356.630985 EM: Round [655] log likelihood: -1356.630458 EM: Round [656] log likelihood: -1356.629933 EM: Round [657] log likelihood: -1356.629409 EM: Round [658] log likelihood: -1356.628886 EM: Round [659] log likelihood: -1356.628365 EM: Round [660] log likelihood: -1356.627846 EM: Round [661] log likelihood: -1356.627328 EM: Round [662] log likelihood: -1356.626812 EM: Round [663] log likelihood: -1356.626297 EM: Round [664] log likelihood: -1356.625783 EM: Round [665] log likelihood: -1356.625272 EM: Round [666] log likelihood: -1356.624761 EM: Round [667] log likelihood: -1356.624252 EM: Round [668] log likelihood: -1356.623745 EM: Round [669] log likelihood: -1356.623239 EM: Round [670] log likelihood: -1356.622735 EM: Round [671] log likelihood: -1356.622232 EM: Round [672] log likelihood: -1356.621731 EM: Round [673] log likelihood: -1356.621231 EM: Round [674] log likelihood: -1356.620732 EM: Round [675] log likelihood: -1356.620235 EM: Round [676] log likelihood: -1356.619740 EM: Round [677] log likelihood: -1356.619245 EM: Round [678] log likelihood: -1356.618753 EM: Round [679] log likelihood: -1356.618261 EM: Round [680] log likelihood: -1356.617772 EM: Round [681] log likelihood: -1356.617283 EM: Round [682] log likelihood: -1356.616796 EM: Round [683] log likelihood: -1356.616311 EM: Round [684] log likelihood: -1356.615826 EM: Round [685] log likelihood: -1356.615344 EM: Round [686] log likelihood: -1356.614862 EM: Round [687] log likelihood: -1356.614382 EM: Round [688] log likelihood: -1356.613904 EM: Round [689] log likelihood: -1356.613427 EM: Round [690] log likelihood: -1356.612951 EM: Round [691] log likelihood: -1356.612476 EM: Round [692] log likelihood: -1356.612003 EM: Round [693] log likelihood: -1356.611532 EM: Round [694] log likelihood: -1356.611061 EM: Round [695] log likelihood: -1356.610592 EM: Round [696] log likelihood: -1356.610125 EM: Round [697] log likelihood: -1356.609658 EM: Round [698] log likelihood: -1356.609194 EM: Round [699] log likelihood: -1356.608730 EM: Round [700] log likelihood: -1356.608268 EM: Round [701] log likelihood: -1356.607807 EM: Round [702] log likelihood: -1356.607347 EM: Round [703] log likelihood: -1356.606889 EM: Round [704] log likelihood: -1356.606432 EM: Round [705] log likelihood: -1356.605976 EM: Round [706] log likelihood: -1356.605522 EM: Round [707] log likelihood: -1356.605069 EM: Round [708] log likelihood: -1356.604617 EM: Round [709] log likelihood: -1356.604167 EM: Round [710] log likelihood: -1356.603718 EM: Round [711] log likelihood: -1356.603270 EM: Round [712] log likelihood: -1356.602823 EM: Round [713] log likelihood: -1356.602378 EM: Round [714] log likelihood: -1356.601934 EM: Round [715] log likelihood: -1356.601492 EM: Round [716] log likelihood: -1356.601050 EM: Round [717] log likelihood: -1356.600610 EM: Round [718] log likelihood: -1356.600171 EM: Round [719] log likelihood: -1356.599733 EM: Round [720] log likelihood: -1356.599297 EM: Round [721] log likelihood: -1356.598862 EM: Round [722] log likelihood: -1356.598428 EM: Round [723] log likelihood: -1356.597995 EM: Round [724] log likelihood: -1356.597564 EM: Round [725] log likelihood: -1356.597133 EM: Round [726] log likelihood: -1356.596704 EM: Round [727] log likelihood: -1356.596277 EM: Round [728] log likelihood: -1356.595850 EM: Round [729] log likelihood: -1356.595425 EM: Round [730] log likelihood: -1356.595001 EM: Round [731] log likelihood: -1356.594578 EM: Round [732] log likelihood: -1356.594156 EM: Round [733] log likelihood: -1356.593735 EM: Round [734] log likelihood: -1356.593316 EM: Round [735] log likelihood: -1356.592898 EM: Round [736] log likelihood: -1356.592481 EM: Round [737] log likelihood: -1356.592065 EM: Round [738] log likelihood: -1356.591650 EM: Round [739] log likelihood: -1356.591237 EM: Round [740] log likelihood: -1356.590825 EM: Round [741] log likelihood: -1356.590414 EM: Round [742] log likelihood: -1356.590004 EM: Round [743] log likelihood: -1356.589595 EM: Round [744] log likelihood: -1356.589187 EM: Round [745] log likelihood: -1356.588781 EM: Round [746] log likelihood: -1356.588376 EM: Round [747] log likelihood: -1356.587971 EM: Round [748] log likelihood: -1356.587568 EM: Round [749] log likelihood: -1356.587167 EM: Round [750] log likelihood: -1356.586766 EM: Round [751] log likelihood: -1356.586366 EM: Round [752] log likelihood: -1356.585968 EM: Round [753] log likelihood: -1356.585570 EM: Round [754] log likelihood: -1356.585174 EM: Round [755] log likelihood: -1356.584779 EM: Round [756] log likelihood: -1356.584385 EM: Round [757] log likelihood: -1356.583992 EM: Round [758] log likelihood: -1356.583600 EM: Round [759] log likelihood: -1356.583210 EM: Round [760] log likelihood: -1356.582820 EM: Round [761] log likelihood: -1356.582431 EM: Round [762] log likelihood: -1356.582044 EM: Round [763] log likelihood: -1356.581658 EM: Round [764] log likelihood: -1356.581272 EM: Round [765] log likelihood: -1356.580888 EM: Round [766] log likelihood: -1356.580505 EM: Round [767] log likelihood: -1356.580123 EM: Round [768] log likelihood: -1356.579742 EM: Round [769] log likelihood: -1356.579362 EM: Round [770] log likelihood: -1356.578983 EM: Round [771] log likelihood: -1356.578606 EM: Round [772] log likelihood: -1356.578229 EM: Round [773] log likelihood: -1356.577853 EM: Round [774] log likelihood: -1356.577479 EM: Round [775] log likelihood: -1356.577105 EM: Round [776] log likelihood: -1356.576733 EM: Round [777] log likelihood: -1356.576361 EM: Round [778] log likelihood: -1356.575991 EM: Round [779] log likelihood: -1356.575621 EM: Round [780] log likelihood: -1356.575253 EM: Round [781] log likelihood: -1356.574886 EM: Round [782] log likelihood: -1356.574519 EM: Round [783] log likelihood: -1356.574154 EM: Round [784] log likelihood: -1356.573790 EM: Round [785] log likelihood: -1356.573427 EM: Round [786] log likelihood: -1356.573064 EM: Round [787] log likelihood: -1356.572703 EM: Round [788] log likelihood: -1356.572343 EM: Round [789] log likelihood: -1356.571984 EM: Round [790] log likelihood: -1356.571625 EM: Round [791] log likelihood: -1356.571268 EM: Round [792] log likelihood: -1356.570912 EM: Round [793] log likelihood: -1356.570557 EM: Round [794] log likelihood: -1356.570202 EM: Round [795] log likelihood: -1356.569849 EM: Round [796] log likelihood: -1356.569497 EM: Round [797] log likelihood: -1356.569145 EM: Round [798] log likelihood: -1356.568795 EM: Round [799] log likelihood: -1356.568446 EM: Round [800] log likelihood: -1356.568097 EM: Round [801] log likelihood: -1356.567750 EM: Round [802] log likelihood: -1356.567403 EM: Round [803] log likelihood: -1356.567058 EM: Round [804] log likelihood: -1356.566713 EM: Round [805] log likelihood: -1356.566369 EM: Round [806] log likelihood: -1356.566027 EM: Round [807] log likelihood: -1356.565685 EM: Round [808] log likelihood: -1356.565344 EM: Round [809] log likelihood: -1356.565004 EM: Round [810] log likelihood: -1356.564665 EM: Round [811] log likelihood: -1356.564327 EM: Round [812] log likelihood: -1356.563990 EM: Round [813] log likelihood: -1356.563654 EM: Round [814] log likelihood: -1356.563319 EM: Round [815] log likelihood: -1356.562985 EM: Round [816] log likelihood: -1356.562651 EM: Round [817] log likelihood: -1356.562319 EM: Round [818] log likelihood: -1356.561988 EM: Round [819] log likelihood: -1356.561657 EM: Round [820] log likelihood: -1356.561327 EM: Round [821] log likelihood: -1356.560998 EM: Round [822] log likelihood: -1356.560671 EM: Round [823] log likelihood: -1356.560344 EM: Round [824] log likelihood: -1356.560018 EM: Round [825] log likelihood: -1356.559692 EM: Round [826] log likelihood: -1356.559368 EM: Round [827] log likelihood: -1356.559045 EM: Round [828] log likelihood: -1356.558722 EM: Round [829] log likelihood: -1356.558400 EM: Round [830] log likelihood: -1356.558080 EM: Round [831] log likelihood: -1356.557760 EM: Round [832] log likelihood: -1356.557441 EM: Round [833] log likelihood: -1356.557123 EM: Round [834] log likelihood: -1356.556805 EM: Round [835] log likelihood: -1356.556489 EM: Round [836] log likelihood: -1356.556174 EM: Round [837] log likelihood: -1356.555859 EM: Round [838] log likelihood: -1356.555545 EM: Round [839] log likelihood: -1356.555232 EM: Round [840] log likelihood: -1356.554920 EM: Round [841] log likelihood: -1356.554609 EM: Round [842] log likelihood: -1356.554298 EM: Round [843] log likelihood: -1356.553989 EM: Round [844] log likelihood: -1356.553680 EM: Round [845] log likelihood: -1356.553372 EM: Round [846] log likelihood: -1356.553065 EM: Round [847] log likelihood: -1356.552759 EM: Round [848] log likelihood: -1356.552454 EM: Round [849] log likelihood: -1356.552149 EM: Round [850] log likelihood: -1356.551846 EM: Round [851] log likelihood: -1356.551543 EM: Round [852] log likelihood: -1356.551241 EM: Round [853] log likelihood: -1356.550940 EM: Round [854] log likelihood: -1356.550639 EM: Round [855] log likelihood: -1356.550340 EM: Round [856] log likelihood: -1356.550041 EM: Round [857] log likelihood: -1356.549743 EM: Round [858] log likelihood: -1356.549446 EM: Round [859] log likelihood: -1356.549150 EM: Round [860] log likelihood: -1356.548854 EM: Round [861] log likelihood: -1356.548559 EM: Round [862] log likelihood: -1356.548266 EM: Round [863] log likelihood: -1356.547972 EM: Round [864] log likelihood: -1356.547680 EM: Round [865] log likelihood: -1356.547389 EM: Round [866] log likelihood: -1356.547098 EM: Round [867] log likelihood: -1356.546808 EM: Round [868] log likelihood: -1356.546519 EM: Round [869] log likelihood: -1356.546230 EM: Round [870] log likelihood: -1356.545943 EM: Round [871] log likelihood: -1356.545656 EM: Round [872] log likelihood: -1356.545370 EM: Round [873] log likelihood: -1356.545085 EM: Round [874] log likelihood: -1356.544800 EM: Round [875] log likelihood: -1356.544516 EM: Round [876] log likelihood: -1356.544233 EM: Round [877] log likelihood: -1356.543951 EM: Round [878] log likelihood: -1356.543670 EM: Round [879] log likelihood: -1356.543389 EM: Round [880] log likelihood: -1356.543109 EM: Round [881] log likelihood: -1356.542830 EM: Round [882] log likelihood: -1356.542552 EM: Round [883] log likelihood: -1356.542274 EM: Round [884] log likelihood: -1356.541997 EM: Round [885] log likelihood: -1356.541721 EM: Round [886] log likelihood: -1356.541446 EM: Round [887] log likelihood: -1356.541171 EM: Round [888] log likelihood: -1356.540897 EM: Round [889] log likelihood: -1356.540624 EM: Round [890] log likelihood: -1356.540351 EM: Round [891] log likelihood: -1356.540080 EM: Round [892] log likelihood: -1356.539809 EM: Round [893] log likelihood: -1356.539538 EM: Round [894] log likelihood: -1356.539269 EM: Round [895] log likelihood: -1356.539000 EM: Round [896] log likelihood: -1356.538732 EM: Round [897] log likelihood: -1356.538465 EM: Round [898] log likelihood: -1356.538198 EM: Round [899] log likelihood: -1356.537932 EM: Round [900] log likelihood: -1356.537667 EM: Round [901] log likelihood: -1356.537402 EM: Round [902] log likelihood: -1356.537139 EM: Round [903] log likelihood: -1356.536876 EM: Round [904] log likelihood: -1356.536613 EM: Round [905] log likelihood: -1356.536351 EM: Round [906] log likelihood: -1356.536090 EM: Round [907] log likelihood: -1356.535830 EM: Round [908] log likelihood: -1356.535571 EM: Round [909] log likelihood: -1356.535312 EM: Round [910] log likelihood: -1356.535054 EM: Round [911] log likelihood: -1356.534796 EM: Round [912] log likelihood: -1356.534539 EM: Round [913] log likelihood: -1356.534283 EM: Round [914] log likelihood: -1356.534028 EM: Round [915] log likelihood: -1356.533773 EM: Round [916] log likelihood: -1356.533519 EM: Round [917] log likelihood: -1356.533266 EM: Round [918] log likelihood: -1356.533013 EM: Round [919] log likelihood: -1356.532761 EM: Round [920] log likelihood: -1356.532509 EM: Round [921] log likelihood: -1356.532259 EM: Round [922] log likelihood: -1356.532009 EM: Round [923] log likelihood: -1356.531759 EM: Round [924] log likelihood: -1356.531511 EM: Round [925] log likelihood: -1356.531263 EM: Round [926] log likelihood: -1356.531015 EM: Round [927] log likelihood: -1356.530769 EM: Round [928] log likelihood: -1356.530523 EM: Round [929] log likelihood: -1356.530277 EM: Round [930] log likelihood: -1356.530032 EM: Round [931] log likelihood: -1356.529788 EM: Round [932] log likelihood: -1356.529545 EM: Round [933] log likelihood: -1356.529302 EM: Round [934] log likelihood: -1356.529060 EM: Round [935] log likelihood: -1356.528819 EM: Round [936] log likelihood: -1356.528578 EM: Round [937] log likelihood: -1356.528338 EM: Round [938] log likelihood: -1356.528098 EM: Round [939] log likelihood: -1356.527859 EM: Round [940] log likelihood: -1356.527621 EM: Round [941] log likelihood: -1356.527383 EM: Round [942] log likelihood: -1356.527146 EM: Round [943] log likelihood: -1356.526910 EM: Round [944] log likelihood: -1356.526674 EM: Round [945] log likelihood: -1356.526439 EM: Round [946] log likelihood: -1356.526204 EM: Round [947] log likelihood: -1356.525970 EM: Round [948] log likelihood: -1356.525737 EM: Round [949] log likelihood: -1356.525504 EM: Round [950] log likelihood: -1356.525272 EM: Round [951] log likelihood: -1356.525041 EM: Round [952] log likelihood: -1356.524810 EM: Round [953] log likelihood: -1356.524580 EM: Round [954] log likelihood: -1356.524350 EM: Round [955] log likelihood: -1356.524121 EM: Round [956] log likelihood: -1356.523893 EM: Round [957] log likelihood: -1356.523665 EM: Round [958] log likelihood: -1356.523438 EM: Round [959] log likelihood: -1356.523211 EM: Round [960] log likelihood: -1356.522985 EM: Round [961] log likelihood: -1356.522760 EM: Round [962] log likelihood: -1356.522535 EM: Round [963] log likelihood: -1356.522311 EM: Round [964] log likelihood: -1356.522088 EM: Round [965] log likelihood: -1356.521865 EM: Round [966] log likelihood: -1356.521642 EM: Round [967] log likelihood: -1356.521420 EM: Round [968] log likelihood: -1356.521199 EM: Round [969] log likelihood: -1356.520979 EM: Round [970] log likelihood: -1356.520758 EM: Round [971] log likelihood: -1356.520539 EM: Round [972] log likelihood: -1356.520320 EM: Round [973] log likelihood: -1356.520102 EM: Round [974] log likelihood: -1356.519884 EM: Round [975] log likelihood: -1356.519667 EM: Round [976] log likelihood: -1356.519450 EM: Round [977] log likelihood: -1356.519234 EM: Round [978] log likelihood: -1356.519019 EM: Round [979] log likelihood: -1356.518804 EM: Round [980] log likelihood: -1356.518590 EM: Round [981] log likelihood: -1356.518376 EM: Round [982] log likelihood: -1356.518163 EM: Round [983] log likelihood: -1356.517950 EM: Round [984] log likelihood: -1356.517738 EM: Round [985] log likelihood: -1356.517526 EM: Round [986] log likelihood: -1356.517315 EM: Round [987] log likelihood: -1356.517105 EM: Round [988] log likelihood: -1356.516895 EM: Round [989] log likelihood: -1356.516686 EM: Round [990] log likelihood: -1356.516477 EM: Round [991] log likelihood: -1356.516269 EM: Round [992] log likelihood: -1356.516061 EM: Round [993] log likelihood: -1356.515854 EM: Round [994] log likelihood: -1356.515648 EM: Round [995] log likelihood: -1356.515442 EM: Round [996] log likelihood: -1356.515236 EM: Round [997] log likelihood: -1356.515031 EM: Round [998] log likelihood: -1356.514827 EM: Round [999] log likelihood: -1356.514623 EM: Round [1000] log likelihood: -1356.514420 EM: Round [1001] log likelihood: -1356.514217 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 295561665 Execution Time = 6.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fa --gtf /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gtf > /tmp/nxf.sA3rneZbym/fi_workdir/microH.dat Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.sA3rneZbym/fi_workdir/microH.dat /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.sA3rneZbym/fi_workdir/microH.dat /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.sA3rneZbym --json_outfile /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.sA3rneZbym --json_outfile /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --file_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1 Running: touch /tmp/nxf.sA3rneZbym/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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.00 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.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.json --input_file_prefix 659_bNS-T1-TRNA-1_B23WHTKLT4_1 --html_output /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.sA3rneZbym/ctat_genome_lib_build_dir > /tmp/nxf.sA3rneZbym/659_bNS-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.sA3rneZbym/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory