Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/93e4f241c8415a8cf878162fbc054a/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/9d045c34510ae41eaf113c94c7c43b/.command.sh 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/17/370bfe1b9ac175e0e17f1e937a658f/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/9d045c34510ae41eaf113c94c7c43b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/93e4f241c8415a8cf878162fbc054a/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf > /tmp/nxf.77MBojOn4X/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf > /tmp/nxf.77MBojOn4X/cytoBand.txt Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.77MBojOn4X/fi_workdir --reads "/tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.77MBojOn4X/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.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 03 21:21:38 ..... started STAR run Jun 03 21:21:38 ..... loading genome Jun 03 21:23:18 ... generating Suffix Array index Jun 03 21:27:01 ... completed Suffix Array index Jun 03 21:27:01 ..... processing annotations GTF Jun 03 21:27:01 ..... inserting junctions into the genome indices Jun 03 21:28:02 ..... started mapping Jun 03 22:21:35 ..... finished mapping Jun 03 22:21:37 ..... started sorting BAM Jun 03 22:21:37 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 60.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.77MBojOn4X/fi_workdir --reads "/tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 22:21:45 : INFO : Done. Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] -done parsing /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'small anchor length' => 30, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 59, 'num genes matched < 2' => 7, 'per_id < 96' => 7151, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 48, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3, 'excessive soft clipping' => 10698, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 20, ' ** passed ** ' => 8354, 'seq-similar region overlap' => 3, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 26, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 20 }; -writing fusion junction support info. Execution Time = 0.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: ACOT11--GLIS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] -fusion SPANNING read extraction for scaff: EPC1--MYO3A [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] -fusion SPANNING read extraction for scaff: FGGY--ZMYM4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] -fusion SPANNING read extraction for scaff: GMDS--GSE1 [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] -fusion SPANNING read extraction for scaff: MAST2--AGBL4 [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] -fusion SPANNING read extraction for scaff: NFIA--DAB1 [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] -fusion SPANNING read extraction for scaff: NFIA--OMA1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] -fusion SPANNING read extraction for scaff: SSBP3--PATJ [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: STIL--LRRC42 [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] -fusion SPANNING read extraction for scaff: TACSTD2--AL603840.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] -fusion SPANNING read extraction for scaff: TACSTD2--AL353681.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] -fusion SPANNING read extraction for scaff: TCEANC2--ROR1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] -fusion SPANNING read extraction for scaff: ZNF362--STIL -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 16202, 'lacks exon overlap' => 12719 }; Execution Time = 1.79 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -7174.658568 EM: Round [1] log likelihood: -7173.347976 EM: Round [2] log likelihood: -7173.027477 EM: Round [3] log likelihood: -7172.742674 EM: Round [4] log likelihood: -7172.486782 EM: Round [5] log likelihood: -7172.254836 EM: Round [6] log likelihood: -7172.043046 EM: Round [7] log likelihood: -7171.848456 EM: Round [8] log likelihood: -7171.668711 EM: Round [9] log likelihood: -7171.501910 EM: Round [10] log likelihood: -7171.346492 EM: Round [11] log likelihood: -7171.201161 EM: Round [12] log likelihood: -7171.064831 EM: Round [13] log likelihood: -7170.936579 EM: Round [14] log likelihood: -7170.815618 EM: Round [15] log likelihood: -7170.701268 EM: Round [16] log likelihood: -7170.592940 EM: Round [17] log likelihood: -7170.490121 EM: Round [18] log likelihood: -7170.392357 EM: Round [19] log likelihood: -7170.299251 EM: Round [20] log likelihood: -7170.210446 EM: Round [21] log likelihood: -7170.125629 EM: Round [22] log likelihood: -7170.044515 EM: Round [23] log likelihood: -7169.966851 EM: Round [24] log likelihood: -7169.892407 EM: Round [25] log likelihood: -7169.820975 EM: Round [26] log likelihood: -7169.752368 EM: Round [27] log likelihood: -7169.686412 EM: Round [28] log likelihood: -7169.622952 EM: Round [29] log likelihood: -7169.561843 EM: Round [30] log likelihood: -7169.502953 EM: Round [31] log likelihood: -7169.446162 EM: Round [32] log likelihood: -7169.391356 EM: Round [33] log likelihood: -7169.338433 EM: Round [34] log likelihood: -7169.287297 EM: Round [35] log likelihood: -7169.237858 EM: Round [36] log likelihood: -7169.190034 EM: Round [37] log likelihood: -7169.143747 EM: Round [38] log likelihood: -7169.098927 EM: Round [39] log likelihood: -7169.055505 EM: Round [40] log likelihood: -7169.013419 EM: Round [41] log likelihood: -7168.972610 EM: Round [42] log likelihood: -7168.933023 EM: Round [43] log likelihood: -7168.894605 EM: Round [44] log likelihood: -7168.857309 EM: Round [45] log likelihood: -7168.821088 EM: Round [46] log likelihood: -7168.785899 EM: Round [47] log likelihood: -7168.751700 EM: Round [48] log likelihood: -7168.718454 EM: Round [49] log likelihood: -7168.686123 EM: Round [50] log likelihood: -7168.654674 EM: Round [51] log likelihood: -7168.624072 EM: Round [52] log likelihood: -7168.594288 EM: Round [53] log likelihood: -7168.565291 EM: Round [54] log likelihood: -7168.537053 EM: Round [55] log likelihood: -7168.509548 EM: Round [56] log likelihood: -7168.482750 EM: Round [57] log likelihood: -7168.456635 EM: Round [58] log likelihood: -7168.431180 EM: Round [59] log likelihood: -7168.406363 EM: Round [60] log likelihood: -7168.382163 EM: Round [61] log likelihood: -7168.358559 EM: Round [62] log likelihood: -7168.335533 EM: Round [63] log likelihood: -7168.313065 EM: Round [64] log likelihood: -7168.291140 EM: Round [65] log likelihood: -7168.269739 EM: Round [66] log likelihood: -7168.248846 EM: Round [67] log likelihood: -7168.228446 EM: Round [68] log likelihood: -7168.208525 EM: Round [69] log likelihood: -7168.189067 EM: Round [70] log likelihood: -7168.170060 EM: Round [71] log likelihood: -7168.151490 EM: Round [72] log likelihood: -7168.133344 EM: Round [73] log likelihood: -7168.115610 EM: Round [74] log likelihood: -7168.098276 EM: Round [75] log likelihood: -7168.081332 EM: Round [76] log likelihood: -7168.064767 EM: Round [77] log likelihood: -7168.048569 EM: Round [78] log likelihood: -7168.032729 EM: Round [79] log likelihood: -7168.017237 EM: Round [80] log likelihood: -7168.002083 EM: Round [81] log likelihood: -7167.987260 EM: Round [82] log likelihood: -7167.972757 EM: Round [83] log likelihood: -7167.958566 EM: Round [84] log likelihood: -7167.944680 EM: Round [85] log likelihood: -7167.931091 EM: Round [86] log likelihood: -7167.917790 EM: Round [87] log likelihood: -7167.904771 EM: Round [88] log likelihood: -7167.892025 EM: Round [89] log likelihood: -7167.879548 EM: Round [90] log likelihood: -7167.867331 EM: Round [91] log likelihood: -7167.855368 EM: Round [92] log likelihood: -7167.843653 EM: Round [93] log likelihood: -7167.832180 EM: Round [94] log likelihood: -7167.820943 EM: Round [95] log likelihood: -7167.809936 EM: Round [96] log likelihood: -7167.799154 EM: Round [97] log likelihood: -7167.788591 EM: Round [98] log likelihood: -7167.778242 EM: Round [99] log likelihood: -7167.768103 EM: Round [100] log likelihood: -7167.758168 EM: Round [101] log likelihood: -7167.748432 EM: Round [102] log likelihood: -7167.738891 EM: Round [103] log likelihood: -7167.729540 EM: Round [104] log likelihood: -7167.720375 EM: Round [105] log likelihood: -7167.711392 EM: Round [106] log likelihood: -7167.702586 EM: Round [107] log likelihood: -7167.693954 EM: Round [108] log likelihood: -7167.685492 EM: Round [109] log likelihood: -7167.677195 EM: Round [110] log likelihood: -7167.669060 EM: Round [111] log likelihood: -7167.661084 EM: Round [112] log likelihood: -7167.653264 EM: Round [113] log likelihood: -7167.645594 EM: Round [114] log likelihood: -7167.638073 EM: Round [115] log likelihood: -7167.630697 EM: Round [116] log likelihood: -7167.623464 EM: Round [117] log likelihood: -7167.616369 EM: Round [118] log likelihood: -7167.609409 EM: Round [119] log likelihood: -7167.602583 EM: Round [120] log likelihood: -7167.595887 EM: Round [121] log likelihood: -7167.589319 EM: Round [122] log likelihood: -7167.582875 EM: Round [123] log likelihood: -7167.576553 EM: Round [124] log likelihood: -7167.570351 EM: Round [125] log likelihood: -7167.564265 EM: Round [126] log likelihood: -7167.558295 EM: Round [127] log likelihood: -7167.552436 EM: Round [128] log likelihood: -7167.546687 EM: Round [129] log likelihood: -7167.541046 EM: Round [130] log likelihood: -7167.535511 EM: Round [131] log likelihood: -7167.530078 EM: Round [132] log likelihood: -7167.524747 EM: Round [133] log likelihood: -7167.519515 EM: Round [134] log likelihood: -7167.514379 EM: Round [135] log likelihood: -7167.509339 EM: Round [136] log likelihood: -7167.504392 EM: Round [137] log likelihood: -7167.499537 EM: Round [138] log likelihood: -7167.494771 EM: Round [139] log likelihood: -7167.490092 EM: Round [140] log likelihood: -7167.485500 EM: Round [141] log likelihood: -7167.480992 EM: Round [142] log likelihood: -7167.476566 EM: Round [143] log likelihood: -7167.472222 EM: Round [144] log likelihood: -7167.467956 EM: Round [145] log likelihood: -7167.463769 EM: Round [146] log likelihood: -7167.459657 EM: Round [147] log likelihood: -7167.455621 EM: Round [148] log likelihood: -7167.451658 EM: Round [149] log likelihood: -7167.447766 EM: Round [150] log likelihood: -7167.443946 EM: Round [151] log likelihood: -7167.440194 EM: Round [152] log likelihood: -7167.436510 EM: Round [153] log likelihood: -7167.432893 EM: Round [154] log likelihood: -7167.429341 EM: Round [155] log likelihood: -7167.425853 EM: Round [156] log likelihood: -7167.422427 EM: Round [157] log likelihood: -7167.419063 EM: Round [158] log likelihood: -7167.415760 EM: Round [159] log likelihood: -7167.412515 EM: Round [160] log likelihood: -7167.409329 EM: Round [161] log likelihood: -7167.406200 EM: Round [162] log likelihood: -7167.403127 EM: Round [163] log likelihood: -7167.400108 EM: Round [164] log likelihood: -7167.397144 EM: Round [165] log likelihood: -7167.394232 EM: Round [166] log likelihood: -7167.391372 EM: Round [167] log likelihood: -7167.388563 EM: Round [168] log likelihood: -7167.385803 EM: Round [169] log likelihood: -7167.383093 EM: Round [170] log likelihood: -7167.380431 EM: Round [171] log likelihood: -7167.377816 EM: Round [172] log likelihood: -7167.375247 EM: Round [173] log likelihood: -7167.372724 EM: Round [174] log likelihood: -7167.370245 EM: Round [175] log likelihood: -7167.367811 EM: Round [176] log likelihood: -7167.365419 EM: Round [177] log likelihood: -7167.363069 EM: Round [178] log likelihood: -7167.360760 EM: Round [179] log likelihood: -7167.358493 EM: Round [180] log likelihood: -7167.356265 EM: Round [181] log likelihood: -7167.354076 EM: Round [182] log likelihood: -7167.351926 EM: Round [183] log likelihood: -7167.349813 EM: Round [184] log likelihood: -7167.347738 EM: Round [185] log likelihood: -7167.345699 EM: Round [186] log likelihood: -7167.343696 EM: Round [187] log likelihood: -7167.341727 EM: Round [188] log likelihood: -7167.339793 EM: Round [189] log likelihood: -7167.337893 EM: Round [190] log likelihood: -7167.336027 EM: Round [191] log likelihood: -7167.334192 EM: Round [192] log likelihood: -7167.332390 EM: Round [193] log likelihood: -7167.330619 EM: Round [194] log likelihood: -7167.328879 EM: Round [195] log likelihood: -7167.327170 EM: Round [196] log likelihood: -7167.325490 EM: Round [197] log likelihood: -7167.323839 EM: Round [198] log likelihood: -7167.322217 EM: Round [199] log likelihood: -7167.320623 EM: Round [200] log likelihood: -7167.319057 EM: Round [201] log likelihood: -7167.317518 EM: Round [202] log likelihood: -7167.316006 EM: Round [203] log likelihood: -7167.314520 EM: Round [204] log likelihood: -7167.313060 EM: Round [205] log likelihood: -7167.311625 EM: Round [206] log likelihood: -7167.310215 EM: Round [207] log likelihood: -7167.308830 EM: Round [208] log likelihood: -7167.307468 EM: Round [209] log likelihood: -7167.306130 EM: Round [210] log likelihood: -7167.304815 EM: Round [211] log likelihood: -7167.303523 EM: Round [212] log likelihood: -7167.302253 EM: Round [213] log likelihood: -7167.301005 EM: Round [214] log likelihood: -7167.299778 EM: Round [215] log likelihood: -7167.298573 EM: Round [216] log likelihood: -7167.297389 EM: Round [217] log likelihood: -7167.296224 EM: Round [218] log likelihood: -7167.295080 EM: Round [219] log likelihood: -7167.293956 EM: Round [220] log likelihood: -7167.292851 EM: Round [221] log likelihood: -7167.291765 EM: Round [222] log likelihood: -7167.290698 EM: Round [223] log likelihood: -7167.289649 EM: Round [224] log likelihood: -7167.288618 EM: Round [225] log likelihood: -7167.287605 EM: Round [226] log likelihood: -7167.286609 EM: Round [227] log likelihood: -7167.285631 EM: Round [228] log likelihood: -7167.284669 EM: Round [229] log likelihood: -7167.283724 EM: Round [230] log likelihood: -7167.282794 EM: Round [231] log likelihood: -7167.281881 EM: Round [232] log likelihood: -7167.280984 EM: Round [233] log likelihood: -7167.280102 EM: Round [234] log likelihood: -7167.279235 EM: Round [235] log likelihood: -7167.278383 EM: Round [236] log likelihood: -7167.277545 EM: Round [237] log likelihood: -7167.276722 EM: Round [238] log likelihood: -7167.275913 EM: Round [239] log likelihood: -7167.275118 EM: Round [240] log likelihood: -7167.274336 EM: Round [241] log likelihood: -7167.273568 EM: Round [242] log likelihood: -7167.272813 EM: Round [243] log likelihood: -7167.272070 EM: Round [244] log likelihood: -7167.271341 EM: Round [245] log likelihood: -7167.270624 EM: Round [246] log likelihood: -7167.269919 EM: Round [247] log likelihood: -7167.269226 EM: Round [248] log likelihood: -7167.268545 EM: Round [249] log likelihood: -7167.267876 EM: Round [250] log likelihood: -7167.267218 EM: Round [251] log likelihood: -7167.266571 EM: Round [252] log likelihood: -7167.265936 EM: Round [253] log likelihood: -7167.265311 EM: Round [254] log likelihood: -7167.264697 EM: Round [255] log likelihood: -7167.264093 EM: Round [256] log likelihood: -7167.263500 EM: Round [257] log likelihood: -7167.262917 EM: Round [258] log likelihood: -7167.262343 EM: Round [259] log likelihood: -7167.261780 EM: Round [260] log likelihood: -7167.261226 EM: Round [261] log likelihood: -7167.260682 EM: Round [262] log likelihood: -7167.260146 EM: Round [263] log likelihood: -7167.259620 EM: Round [264] log likelihood: -7167.259103 EM: Round [265] log likelihood: -7167.258595 EM: Round [266] log likelihood: -7167.258095 EM: Round [267] log likelihood: -7167.257604 EM: Round [268] log likelihood: -7167.257121 EM: Round [269] log likelihood: -7167.256646 EM: Round [270] log likelihood: -7167.256180 EM: Round [271] log likelihood: -7167.255721 EM: Round [272] log likelihood: -7167.255270 EM: Round [273] log likelihood: -7167.254827 EM: Round [274] log likelihood: -7167.254392 EM: Round [275] log likelihood: -7167.253963 EM: Round [276] log likelihood: -7167.253543 EM: Round [277] log likelihood: -7167.253129 EM: Round [278] log likelihood: -7167.252722 EM: Round [279] log likelihood: -7167.252322 EM: Round [280] log likelihood: -7167.251929 EM: Round [281] log likelihood: -7167.251543 EM: Round [282] log likelihood: -7167.251163 EM: Round [283] log likelihood: -7167.250789 EM: Round [284] log likelihood: -7167.250422 EM: Round [285] log likelihood: -7167.250062 EM: Round [286] log likelihood: -7167.249707 EM: Round [287] log likelihood: -7167.249358 EM: Round [288] log likelihood: -7167.249016 EM: Round [289] log likelihood: -7167.248679 EM: Round [290] log likelihood: -7167.248347 EM: Round [291] log likelihood: -7167.248022 EM: Round [292] log likelihood: -7167.247702 EM: Round [293] log likelihood: -7167.247387 EM: Round [294] log likelihood: -7167.247078 EM: Round [295] log likelihood: -7167.246774 EM: Round [296] log likelihood: -7167.246475 EM: Round [297] log likelihood: -7167.246181 EM: Round [298] log likelihood: -7167.245892 EM: Round [299] log likelihood: -7167.245608 EM: Round [300] log likelihood: -7167.245329 EM: Round [301] log likelihood: -7167.245055 EM: Round [302] log likelihood: -7167.244785 EM: Round [303] log likelihood: -7167.244520 EM: Round [304] log likelihood: -7167.244259 EM: Round [305] log likelihood: -7167.244003 EM: Round [306] log likelihood: -7167.243751 EM: Round [307] log likelihood: -7167.243503 EM: Round [308] log likelihood: -7167.243259 EM: Round [309] log likelihood: -7167.243020 EM: Round [310] log likelihood: -7167.242785 EM: Round [311] log likelihood: -7167.242553 EM: Round [312] log likelihood: -7167.242326 EM: Round [313] log likelihood: -7167.242102 EM: Round [314] log likelihood: -7167.241883 EM: Round [315] log likelihood: -7167.241667 EM: Round [316] log likelihood: -7167.241454 EM: Round [317] log likelihood: -7167.241245 EM: Round [318] log likelihood: -7167.241040 EM: Round [319] log likelihood: -7167.240838 EM: Round [320] log likelihood: -7167.240640 EM: Round [321] log likelihood: -7167.240445 EM: Round [322] log likelihood: -7167.240253 EM: Round [323] log likelihood: -7167.240065 EM: Round [324] log likelihood: -7167.239879 EM: Round [325] log likelihood: -7167.239697 EM: Round [326] log likelihood: -7167.239518 EM: Round [327] log likelihood: -7167.239342 EM: Round [328] log likelihood: -7167.239169 EM: Round [329] log likelihood: -7167.238999 EM: Round [330] log likelihood: -7167.238831 EM: Round [331] log likelihood: -7167.238667 EM: Round [332] log likelihood: -7167.238505 EM: Round [333] log likelihood: -7167.238346 EM: Round [334] log likelihood: -7167.238190 EM: Round [335] log likelihood: -7167.238036 EM: Round [336] log likelihood: -7167.237885 EM: Round [337] log likelihood: -7167.237737 EM: Round [338] log likelihood: -7167.237591 EM: Round [339] log likelihood: -7167.237448 EM: Round [340] log likelihood: -7167.237307 EM: Round [341] log likelihood: -7167.237168 EM: Round [342] log likelihood: -7167.237032 EM: Round [343] log likelihood: -7167.236897 EM: Round [344] log likelihood: -7167.236766 EM: Round [345] log likelihood: -7167.236636 EM: Round [346] log likelihood: -7167.236509 EM: Round [347] log likelihood: -7167.236384 EM: Round [348] log likelihood: -7167.236261 EM: Round [349] log likelihood: -7167.236140 EM: Round [350] log likelihood: -7167.236021 EM: Round [351] log likelihood: -7167.235904 EM: Round [352] log likelihood: -7167.235789 EM: Round [353] log likelihood: -7167.235676 EM: Round [354] log likelihood: -7167.235565 EM: Round [355] log likelihood: -7167.235455 EM: Round [356] log likelihood: -7167.235348 EM: Round [357] log likelihood: -7167.235242 EM: Round [358] log likelihood: -7167.235139 EM: Round [359] log likelihood: -7167.235036 EM: Round [360] log likelihood: -7167.234936 EM: Round [361] log likelihood: -7167.234837 EM: Stopping iterations at round 361 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_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.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam || : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.FusionJuncSpan Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.Pfam.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa > /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.77MBojOn4X/fi_workdir/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir -done, see /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -6816.915798 EM: Round [1] log likelihood: -6816.426848 EM: Round [2] log likelihood: -6816.426782 EM: Stopping iterations at round 2 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296887005 Execution Time = 5.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf > /tmp/nxf.77MBojOn4X/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.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gtf > /tmp/nxf.77MBojOn4X/fi_workdir/microH.dat Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.77MBojOn4X/fi_workdir/microH.dat /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.77MBojOn4X/fi_workdir/microH.dat /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.77MBojOn4X --json_outfile /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.77MBojOn4X --json_outfile /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.77MBojOn4X/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.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1 --html_output /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1 --html_output /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000280136.2] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.77MBojOn4X/ctat_genome_lib_build_dir > /tmp/nxf.77MBojOn4X/aih-tih-sc-f2fa3a-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.77MBojOn4X/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory