Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/2f93855d9aa2a18c4371fa0ddd78e7/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/68/c195ee4328eb5b350b2b58ec48cef6/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/67dbb04b02ece8475f8e9e69fea094/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/67dbb04b02ece8475f8e9e69fea094/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/2f93855d9aa2a18c4371fa0ddd78e7/659_wQ-T1-TRNA-1_B23MHV2LT4_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 659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusionreport.tsv --gtf /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/cytoBand.txt Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed -parsing GTF file: /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.G4FK4Af86Y/fi_workdir --reads "/tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:07:21 ..... started STAR run Jun 08 10:07:22 ..... loading genome Jun 08 10:09:09 ... generating Suffix Array index Jun 08 10:12:52 ... completed Suffix Array index Jun 08 10:12:52 ..... processing annotations GTF Jun 08 10:12:53 ..... inserting junctions into the genome indices Jun 08 10:13:54 ..... started mapping Jun 08 11:28:05 ..... finished mapping Jun 08 11:28:07 ..... started sorting BAM Jun 08 11:28:08 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam Execution Time = 80.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --CPU 8 --out_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1.star --out_dir /tmp/nxf.G4FK4Af86Y/fi_workdir --reads "/tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:28:17 : INFO : Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf -parsing /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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] -done parsing /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 11, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 174, 'exons hit < 2' => 5, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8, 'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 4, 'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 6, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6, 'small anchor length' => 2, 'excessive soft clipping' => 9651, 'per_id < 96' => 5169, 'low complexity anchor region' => 1, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 16, 'seq-similar region overlap' => 387, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8, ' ** passed ** ' => 7264, 'num genes matched < 2' => 12 }; -writing fusion junction support info. Execution Time = 0.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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] -fusion SPANNING read extraction for scaff: AC007529.2--SOX5 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: AC107419.1--PHEX [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] -fusion SPANNING read extraction for scaff: ANKRD17--CCDC158 [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: ARPC1B--CLTCL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: E2F1--ZNF341 [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] -fusion SPANNING read extraction for scaff: EIF2A--TSC22D2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: ETNK1--AC087235.1 [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] -fusion SPANNING read extraction for scaff: ETNK1--SOX5 [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] -fusion SPANNING read extraction for scaff: IPO9--AC013470.2 [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] -fusion SPANNING read extraction for scaff: ITPR2--AC007529.2 [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] -fusion SPANNING read extraction for scaff: ITPR2--SKP1P2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: PCDHA10--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] -fusion SPANNING read extraction for scaff: PCDHA10--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] -fusion SPANNING read extraction for scaff: PCDHA10--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] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] -fusion SPANNING read extraction for scaff: PCDHGA4--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] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: PCDHGA4--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] -fusion SPANNING read extraction for scaff: PCDHGA4--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] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PHEX--AC004470.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PXMP4--ZNF341 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: RASSF8--CMAS [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] -fusion SPANNING read extraction for scaff: RNF217--PARD3B [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] -fusion SPANNING read extraction for scaff: SENP6--EYS [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: SKP1P2--SOX5 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: SLC2A13--IL1RAPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A [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] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] -fusion SPANNING read extraction for scaff: TRHDE--CYP27B1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 66817, 'lacks exon overlap' => 16884 }; Execution Time = 1.90 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -4385.554985 EM: Round [1] log likelihood: -4382.836654 EM: Round [2] log likelihood: -4382.122546 EM: Round [3] log likelihood: -4381.504305 EM: Round [4] log likelihood: -4380.962129 EM: Round [5] log likelihood: -4380.485415 EM: Round [6] log likelihood: -4380.065278 EM: Round [7] log likelihood: -4379.694209 EM: Round [8] log likelihood: -4379.365830 EM: Round [9] log likelihood: -4379.074697 EM: Round [10] log likelihood: -4378.816142 EM: Round [11] log likelihood: -4378.586153 EM: Round [12] log likelihood: -4378.381263 EM: Round [13] log likelihood: -4378.198473 EM: Round [14] log likelihood: -4378.035179 EM: Round [15] log likelihood: -4377.889113 EM: Round [16] log likelihood: -4377.758299 EM: Round [17] log likelihood: -4377.641007 EM: Round [18] log likelihood: -4377.535722 EM: Round [19] log likelihood: -4377.441114 EM: Round [20] log likelihood: -4377.356014 EM: Round [21] log likelihood: -4377.279391 EM: Round [22] log likelihood: -4377.210336 EM: Round [23] log likelihood: -4377.148046 EM: Round [24] log likelihood: -4377.091809 EM: Round [25] log likelihood: -4377.040997 EM: Round [26] log likelihood: -4376.995049 EM: Round [27] log likelihood: -4376.953468 EM: Round [28] log likelihood: -4376.915812 EM: Round [29] log likelihood: -4376.881687 EM: Round [30] log likelihood: -4376.850742 EM: Round [31] log likelihood: -4376.822662 EM: Round [32] log likelihood: -4376.797166 EM: Round [33] log likelihood: -4376.774004 EM: Round [34] log likelihood: -4376.752951 EM: Round [35] log likelihood: -4376.733803 EM: Round [36] log likelihood: -4376.716381 EM: Round [37] log likelihood: -4376.700521 EM: Round [38] log likelihood: -4376.686076 EM: Round [39] log likelihood: -4376.672914 EM: Round [40] log likelihood: -4376.660917 EM: Round [41] log likelihood: -4376.649978 EM: Round [42] log likelihood: -4376.639998 EM: Round [43] log likelihood: -4376.630892 EM: Round [44] log likelihood: -4376.622579 EM: Round [45] log likelihood: -4376.614988 EM: Round [46] log likelihood: -4376.608055 EM: Round [47] log likelihood: -4376.601720 EM: Round [48] log likelihood: -4376.595931 EM: Round [49] log likelihood: -4376.590638 EM: Round [50] log likelihood: -4376.585799 EM: Round [51] log likelihood: -4376.581373 EM: Round [52] log likelihood: -4376.577325 EM: Round [53] log likelihood: -4376.573620 EM: Round [54] log likelihood: -4376.570230 EM: Round [55] log likelihood: -4376.567127 EM: Round [56] log likelihood: -4376.564287 EM: Round [57] log likelihood: -4376.561686 EM: Round [58] log likelihood: -4376.559304 EM: Round [59] log likelihood: -4376.557123 EM: Round [60] log likelihood: -4376.555124 EM: Round [61] log likelihood: -4376.553294 EM: Round [62] log likelihood: -4376.551616 EM: Round [63] log likelihood: -4376.550079 EM: Round [64] log likelihood: -4376.548671 EM: Round [65] log likelihood: -4376.547380 EM: Round [66] log likelihood: -4376.546196 EM: Round [67] log likelihood: -4376.545111 EM: Round [68] log likelihood: -4376.544117 EM: Round [69] log likelihood: -4376.543205 EM: Round [70] log likelihood: -4376.542369 EM: Round [71] log likelihood: -4376.541602 EM: Round [72] log likelihood: -4376.540899 EM: Round [73] log likelihood: -4376.540254 EM: Round [74] log likelihood: -4376.539662 EM: Round [75] log likelihood: -4376.539119 EM: Round [76] log likelihood: -4376.538622 EM: Round [77] log likelihood: -4376.538165 EM: Round [78] log likelihood: -4376.537746 EM: Round [79] log likelihood: -4376.537362 EM: Round [80] log likelihood: -4376.537009 EM: Round [81] log likelihood: -4376.536686 EM: Round [82] log likelihood: -4376.536389 EM: Round [83] log likelihood: -4376.536117 EM: Round [84] log likelihood: -4376.535867 EM: Round [85] log likelihood: -4376.535637 EM: Round [86] log likelihood: -4376.535427 EM: Round [87] log likelihood: -4376.535234 EM: Round [88] log likelihood: -4376.535057 EM: Round [89] log likelihood: -4376.534894 EM: Round [90] log likelihood: -4376.534745 EM: Round [91] log likelihood: -4376.534608 EM: Round [92] log likelihood: -4376.534482 EM: Round [93] log likelihood: -4376.534367 EM: Round [94] log likelihood: -4376.534261 EM: Round [95] log likelihood: -4376.534163 EM: Stopping iterations at round 95 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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam" Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.35 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.gff3 > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa > /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir -done, see /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -3842.033512 EM: Round [1] log likelihood: -3841.500271 EM: Round [2] log likelihood: -3841.498032 EM: Round [3] log likelihood: -3841.498010 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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295130272 Execution Time = 5.89 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fa --gtf /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.gtf > /tmp/nxf.G4FK4Af86Y/fi_workdir/microH.dat Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.G4FK4Af86Y/fi_workdir/microH.dat /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/fi_workdir/microH.dat /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.G4FK4Af86Y --json_outfile /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_wQ-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.G4FK4Af86Y --json_outfile /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --file_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1 Running: touch /tmp/nxf.G4FK4Af86Y/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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.json --input_file_prefix 659_wQ-T1-TRNA-1_B23MHV2LT4_1 --html_output /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-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.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000280136.2] 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 [ENSG00000288546.1] WARNING, no entry stored in dbm for [ENSG00000288546.1] 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 [ENSG00000228933.8] WARNING, no entry stored in dbm for [ENSG00000228933.8] WARNING, no entry stored in dbm for [ENSG00000228933.8] WARNING, no entry stored in dbm for [ENSG00000228933.8] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.G4FK4Af86Y/ctat_genome_lib_build_dir > /tmp/nxf.G4FK4Af86Y/659_wQ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.G4FK4Af86Y/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory