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/68/4a0da696c676371f95252e47ddd4ed/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/4a0da696c676371f95252e47ddd4ed/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/f8a3bb7f17cf873e112d486a6b7ac4/659_bTo-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/f8a3bb7f17cf873e112d486a6b7ac4/659_bTo-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/9602cbd1f5a8afe6784f353c54c5d4/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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 659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.rfBVp77kqy/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.rfBVp77kqy/cytoBand.txt Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed -parsing GTF file: /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.rfBVp77kqy/fi_workdir --reads "/tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:00:10 ..... started STAR run Jun 08 10:00:10 ..... loading genome Jun 08 10:01:57 ... generating Suffix Array index Jun 08 10:06:00 ... completed Suffix Array index Jun 08 10:06:00 ..... processing annotations GTF Jun 08 10:06:00 ..... inserting junctions into the genome indices Jun 08 10:07:01 ..... started mapping Jun 08 11:20:15 ..... finished mapping Jun 08 11:20:16 ..... started sorting BAM Jun 08 11:20:17 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam Execution Time = 80.15 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.rfBVp77kqy/fi_workdir --reads "/tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:20:29 : INFO : Done. Execution Time = 0.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf -parsing /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_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] [1300000] [1310000] [1320000] [1330000] [1340000] [1350000] [1360000] [1370000] [1380000] [1390000] [1400000] [1410000] [1420000] [1430000] [1440000] [1450000] [1460000] [1470000] [1480000] [1490000] [1500000] [1510000] [1520000] [1530000] [1540000] [1550000] [1560000] [1570000] [1580000] [1590000] [1600000] [1610000] [1620000] [1630000] [1640000] [1650000] [1660000] [1670000] [1680000] [1690000] [1700000] [1710000] [1720000] [1730000] [1740000] [1750000] [1760000] [1770000] [1780000] [1790000] [1800000] [1810000] [1820000] [1830000] [1840000] [1850000] [1860000] [1870000] [1880000] [1890000] [1900000] [1910000] [1920000] [1930000] -done parsing /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'low complexity anchor region' => 15, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 222, 'excessive soft clipping' => 11580, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 13, 'exons hit < 2' => 4, 'num genes matched < 2' => 42, 'per_id < 96' => 6869, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 66, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 116, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 95, ' ** passed ** ' => 17566, 'small anchor length' => 223, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2 }; -writing fusion junction support info. Execution Time = 1.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] -fusion SPANNING read extraction for scaff: AC010904.1--ZC3H7B [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] -fusion SPANNING read extraction for scaff: AC013460.1--ZC3H7B [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] 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[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] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] -fusion SPANNING read extraction for scaff: AKAP12--PHBP1 [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] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] -fusion SPANNING read extraction for scaff: AKAP12--ULBP3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: ANKRD46--STK3 [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: ARPC3--LINC02827 [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] -fusion SPANNING read extraction for scaff: CDV3--MT-RNR2 [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] -fusion SPANNING read extraction for scaff: ETV6--RASA3 [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] -fusion SPANNING read extraction for scaff: FHOD3--KIAA1328 [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] -fusion SPANNING read extraction for scaff: NF1--SEPTIN4-AS1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [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] -fusion SPANNING read extraction for scaff: RIOK3--LINC01894 [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: RPSAP52--HMGA2 [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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: TAF4B--B4GALT6 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2 [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] -fusion SPANNING read extraction for scaff: TOPORS--TJP2 [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: UBE2O--AANAT [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: UST--TMTC2 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 9366, 'seq similar region alignment' => 6623 }; Execution Time = 2.47 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -5826.409646 EM: Round [1] log likelihood: -5825.130666 EM: Round [2] log likelihood: -5825.127677 EM: Round [3] log likelihood: -5825.127671 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam" Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.49 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir -done, see /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -5527.723264 EM: Round [1] log likelihood: -5526.628723 EM: Round [2] log likelihood: -5526.625890 EM: Round [3] log likelihood: -5526.625884 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 296183793 Execution Time = 5.83 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.rfBVp77kqy/fi_workdir/microH.dat Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.rfBVp77kqy/fi_workdir/microH.dat /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/fi_workdir/microH.dat /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.rfBVp77kqy --json_outfile /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.rfBVp77kqy --json_outfile /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1 Running: touch /tmp/nxf.rfBVp77kqy/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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_bTo-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_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 [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000264345.2] WARNING, no entry stored in dbm for [ENSG00000264345.2] WARNING, no entry stored in dbm for [ENSG00000264345.2] WARNING, no entry stored in dbm for [ENSG00000210082.2] WARNING, no entry stored in dbm for [ENSG00000236908.2] WARNING, no entry stored in dbm for [ENSG00000241749.4] WARNING, no entry stored in dbm for [ENSG00000264672.6] WARNING, no entry stored in dbm for [ENSG00000264672.6] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.rfBVp77kqy/ctat_genome_lib_build_dir > /tmp/nxf.rfBVp77kqy/659_bTo-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.rfBVp77kqy/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory