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/56/4d5cd7c99b970a9a3ad5168704774d/tih_rna_sample_00766_B23MVV7LT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/180e5d94607dd74b3fc64de0f2538a/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/180e5d94607dd74b3fc64de0f2538a/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/df7312405d0fde5a2fecf816f75c5b/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/df7312405d0fde5a2fecf816f75c5b/tih_rna_sample_00766_B23MVV7LT4_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 tih_rna_sample_00766_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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 tih_rna_sample_00766_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/cytoBand.txt Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed -parsing GTF file: /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00766_B23MVV7LT4_1.star --out_dir /tmp/nxf.k6iMamKp4Y/fi_workdir --reads "/tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 09:21:32 ..... started STAR run Jun 08 09:21:32 ..... loading genome Jun 08 09:23:10 ... generating Suffix Array index Jun 08 09:27:04 ... completed Suffix Array index Jun 08 09:27:04 ..... processing annotations GTF Jun 08 09:27:04 ..... inserting junctions into the genome indices Jun 08 09:28:05 ..... started mapping Jun 08 10:05:00 ..... finished mapping Jun 08 10:05:02 ..... started sorting BAM Jun 08 10:05:02 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam Execution Time = 43.52 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00766_B23MVV7LT4_1.star --out_dir /tmp/nxf.k6iMamKp4Y/fi_workdir --reads "/tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups 10:05:08 : INFO : Done. Execution Time = 0.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf -parsing /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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] -done parsing /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4, 'seq-similar region overlap' => 547, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 56, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1, ' ** passed ** ' => 1147, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 81, 'per_id < 96' => 5998, 'small anchor length' => 2, 'low complexity anchor region' => 3, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 7, 'num genes matched < 2' => 30, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 18, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 8, 'excessive soft clipping' => 10146, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 16 }; -writing fusion junction support info. Execution Time = 0.54 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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] -fusion SPANNING read extraction for scaff: AC211476.4--CLIP2 [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] -fusion SPANNING read extraction for scaff: CDKAL1--E2F3 [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] 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-fusion SPANNING read extraction for scaff: FBRS--ITGAL [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] -fusion SPANNING read extraction for scaff: FBRS--SEPHS2 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [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] -fusion SPANNING read extraction for scaff: LARS1--AC011396.1 [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] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] -fusion SPANNING read extraction for scaff: LARS1--TCERG1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] -fusion SPANNING read extraction for scaff: RRP36--PEX6 [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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 39001, 'lacks exon overlap' => 11793 }; Execution Time = 1.38 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -1192.060136 EM: Round [1] log likelihood: -1192.049448 EM: Round [2] log likelihood: -1192.039108 EM: Round [3] log likelihood: -1192.029099 EM: Round [4] log likelihood: -1192.019409 EM: Round [5] log likelihood: -1192.010024 EM: Round [6] log likelihood: -1192.000932 EM: Round [7] log likelihood: -1191.992121 EM: Round [8] log likelihood: -1191.983581 EM: Round [9] log likelihood: -1191.975300 EM: Round [10] log likelihood: -1191.967269 EM: Round [11] log likelihood: -1191.959478 EM: Round [12] log likelihood: -1191.951919 EM: Round [13] log likelihood: -1191.944582 EM: Round [14] log likelihood: -1191.937460 EM: Round [15] log likelihood: -1191.930546 EM: Round [16] log likelihood: -1191.923830 EM: Round [17] log likelihood: -1191.917308 EM: Round [18] log likelihood: -1191.910971 EM: Round [19] log likelihood: -1191.904813 EM: Round [20] log likelihood: -1191.898829 EM: Round [21] log likelihood: -1191.893012 EM: Round [22] log likelihood: -1191.887357 EM: Round [23] log likelihood: -1191.881859 EM: Round [24] log likelihood: -1191.876511 EM: Round [25] log likelihood: -1191.871310 EM: Round [26] log likelihood: -1191.866251 EM: Round [27] log likelihood: -1191.861329 EM: Round [28] log likelihood: -1191.856539 EM: Round [29] log likelihood: -1191.851878 EM: Round [30] log likelihood: -1191.847341 EM: Round [31] log likelihood: -1191.842925 EM: Round [32] log likelihood: -1191.838626 EM: Round [33] log likelihood: -1191.834441 EM: Round [34] log likelihood: -1191.830365 EM: Round [35] log likelihood: -1191.826395 EM: Round [36] log likelihood: -1191.822529 EM: Round [37] log likelihood: -1191.818764 EM: Round [38] log likelihood: -1191.815096 EM: Round [39] log likelihood: -1191.811522 EM: Round [40] log likelihood: -1191.808040 EM: Round [41] log likelihood: -1191.804647 EM: Round [42] log likelihood: -1191.801340 EM: Round [43] log likelihood: -1191.798118 EM: Round [44] log likelihood: -1191.794977 EM: Round [45] log likelihood: -1191.791915 EM: Round [46] log likelihood: -1191.788931 EM: Round [47] log likelihood: -1191.786021 EM: Round [48] log likelihood: -1191.783184 EM: Round [49] log likelihood: -1191.780418 EM: Round [50] log likelihood: -1191.777721 EM: Round [51] log likelihood: -1191.775091 EM: Round [52] log likelihood: -1191.772526 EM: Round [53] log likelihood: -1191.770024 EM: Round [54] log likelihood: -1191.767584 EM: Round [55] log likelihood: -1191.765204 EM: Round [56] log likelihood: -1191.762882 EM: Round [57] log likelihood: -1191.760617 EM: Round [58] log likelihood: -1191.758408 EM: Round [59] log likelihood: -1191.756252 EM: Round [60] log likelihood: -1191.754148 EM: Round [61] log likelihood: -1191.752096 EM: Round [62] log likelihood: -1191.750093 EM: Round [63] log likelihood: -1191.748139 EM: Round [64] log likelihood: -1191.746232 EM: Round [65] log likelihood: -1191.744370 EM: Round [66] log likelihood: -1191.742553 EM: Round [67] log likelihood: -1191.740780 EM: Round [68] log likelihood: -1191.739050 EM: Round [69] log likelihood: -1191.737360 EM: Round [70] log likelihood: -1191.735711 EM: Round [71] log likelihood: -1191.734101 EM: Round [72] log likelihood: -1191.732530 EM: Round [73] log likelihood: -1191.730996 EM: Round [74] log likelihood: -1191.729498 EM: Round [75] log likelihood: -1191.728036 EM: Round [76] log likelihood: -1191.726608 EM: Round [77] log likelihood: -1191.725214 EM: Round [78] log likelihood: -1191.723852 EM: Round [79] log likelihood: -1191.722523 EM: Round [80] log likelihood: -1191.721225 EM: Round [81] log likelihood: -1191.719958 EM: Round [82] log likelihood: -1191.718720 EM: Round [83] log likelihood: -1191.717511 EM: Round [84] log likelihood: -1191.716331 EM: Round [85] log likelihood: -1191.715178 EM: Round [86] log likelihood: -1191.714052 EM: Round [87] log likelihood: -1191.712952 EM: Round [88] log likelihood: -1191.711878 EM: Round [89] log likelihood: -1191.710828 EM: Round [90] log likelihood: -1191.709804 EM: Round [91] log likelihood: -1191.708803 EM: Round [92] log likelihood: -1191.707825 EM: Round [93] log likelihood: -1191.706870 EM: Round [94] log likelihood: -1191.705936 EM: Round [95] log likelihood: -1191.705025 EM: Round [96] log likelihood: -1191.704135 EM: Round [97] log likelihood: -1191.703265 EM: Round [98] log likelihood: -1191.702415 EM: Round [99] log likelihood: -1191.701585 EM: Round [100] log likelihood: -1191.700774 EM: Round [101] log likelihood: -1191.699981 EM: Round [102] log likelihood: -1191.699207 EM: Round [103] log likelihood: -1191.698450 EM: Round [104] log likelihood: -1191.697711 EM: Round [105] log likelihood: -1191.696989 EM: Round [106] log likelihood: -1191.696284 EM: Round [107] log likelihood: -1191.695594 EM: Round [108] log likelihood: -1191.694921 EM: Round [109] log likelihood: -1191.694262 EM: Round [110] log likelihood: -1191.693619 EM: Round [111] log likelihood: -1191.692991 EM: Round [112] log likelihood: -1191.692376 EM: Round [113] log likelihood: -1191.691776 EM: Round [114] log likelihood: -1191.691190 EM: Round [115] log likelihood: -1191.690617 EM: Round [116] log likelihood: -1191.690057 EM: Round [117] log likelihood: -1191.689509 EM: Round [118] log likelihood: -1191.688975 EM: Round [119] log likelihood: -1191.688452 EM: Round [120] log likelihood: -1191.687941 EM: Round [121] log likelihood: -1191.687442 EM: Round [122] log likelihood: -1191.686954 EM: Round [123] log likelihood: -1191.686477 EM: Round [124] log likelihood: -1191.686011 EM: Round [125] log likelihood: -1191.685556 EM: Round [126] log likelihood: -1191.685111 EM: Round [127] log likelihood: -1191.684676 EM: Round [128] log likelihood: -1191.684251 EM: Round [129] log likelihood: -1191.683835 EM: Round [130] log likelihood: -1191.683429 EM: Round [131] log likelihood: -1191.683032 EM: Round [132] log likelihood: -1191.682644 EM: Round [133] log likelihood: -1191.682265 EM: Round [134] log likelihood: -1191.681894 EM: Round [135] log likelihood: -1191.681532 EM: Round [136] log likelihood: -1191.681178 EM: Round [137] log likelihood: -1191.680832 EM: Round [138] log likelihood: -1191.680493 EM: Round [139] log likelihood: -1191.680163 EM: Round [140] log likelihood: -1191.679840 EM: Round [141] log likelihood: -1191.679524 EM: Round [142] log likelihood: -1191.679215 EM: Round [143] log likelihood: -1191.678913 EM: Round [144] log likelihood: -1191.678618 EM: Round [145] log likelihood: -1191.678330 EM: Round [146] log likelihood: -1191.678048 EM: Round [147] log likelihood: -1191.677772 EM: Round [148] log likelihood: -1191.677503 EM: Round [149] log likelihood: -1191.677239 EM: Round [150] log likelihood: -1191.676982 EM: Round [151] log likelihood: -1191.676730 EM: Round [152] log likelihood: -1191.676484 EM: Round [153] log likelihood: -1191.676244 EM: Round [154] log likelihood: -1191.676009 EM: Round [155] log likelihood: -1191.675779 EM: Round [156] log likelihood: -1191.675554 EM: Round [157] log likelihood: -1191.675335 EM: Round [158] log likelihood: -1191.675120 EM: Round [159] log likelihood: -1191.674910 EM: Round [160] log likelihood: -1191.674705 EM: Round [161] log likelihood: -1191.674505 EM: Round [162] log likelihood: -1191.674309 EM: Round [163] log likelihood: -1191.674117 EM: Round [164] log likelihood: -1191.673930 EM: Round [165] log likelihood: -1191.673746 EM: Round [166] log likelihood: -1191.673567 EM: Round [167] log likelihood: -1191.673392 EM: Round [168] log likelihood: -1191.673221 EM: Round [169] log likelihood: -1191.673054 EM: Round [170] log likelihood: -1191.672890 EM: Round [171] log likelihood: -1191.672730 EM: Round [172] log likelihood: -1191.672574 EM: Round [173] log likelihood: -1191.672421 EM: Round [174] log likelihood: -1191.672272 EM: Round [175] log likelihood: -1191.672126 EM: Round [176] log likelihood: -1191.671983 EM: Round [177] log likelihood: -1191.671843 EM: Round [178] log likelihood: -1191.671707 EM: Round [179] log likelihood: -1191.671574 EM: Round [180] log likelihood: -1191.671443 EM: Round [181] log likelihood: -1191.671316 EM: Round [182] log likelihood: -1191.671191 EM: Round [183] log likelihood: -1191.671069 EM: Round [184] log likelihood: -1191.670950 EM: Round [185] log likelihood: -1191.670833 EM: Round [186] log likelihood: -1191.670719 EM: Round [187] log likelihood: -1191.670608 EM: Round [188] log likelihood: -1191.670499 EM: Round [189] log likelihood: -1191.670393 EM: Round [190] log likelihood: -1191.670289 EM: Round [191] log likelihood: -1191.670187 EM: Round [192] log likelihood: -1191.670088 EM: Stopping iterations at round 192 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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam" Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/tih_rna_sample_00766_B23MVV7LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa > /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/tih_rna_sample_00766_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir -done, see /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -1131.300251 EM: Round [1] log likelihood: -1131.300251 EM: Stopping iterations at round 1 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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz: 202924806 Execution Time = 3.70 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa --gtf /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fa --gtf /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.gtf > /tmp/nxf.k6iMamKp4Y/fi_workdir/microH.dat Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.k6iMamKp4Y/fi_workdir/microH.dat /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/fi_workdir/microH.dat /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.k6iMamKp4Y --json_outfile /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00766_B23MVV7LT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.k6iMamKp4Y --json_outfile /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00766_B23MVV7LT4_1 Running: touch /tmp/nxf.k6iMamKp4Y/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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00766_B23MVV7LT4_1 --html_output /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_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.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00766_B23MVV7LT4_1 --html_output /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000277125.1] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.k6iMamKp4Y/ctat_genome_lib_build_dir > /tmp/nxf.k6iMamKp4Y/tih_rna_sample_00766_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.k6iMamKp4Y/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory