Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/f19a6fad5dc3d2a21269e4560e9e47/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusionreport.tsv 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/c2/81fe36c6a5dd6bc2cb96de477fa890/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/81fe36c6a5dd6bc2cb96de477fa890/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/26162d8dd95a18ecbc3c02288a446c/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/26162d8dd95a18ecbc3c02288a446c/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.VleedfCDzv/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.VleedfCDzv/cytoBand.txt Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.VleedfCDzv/fi_workdir --reads "/tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.VleedfCDzv/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.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:21:16 ..... started STAR run Jun 08 10:21:16 ..... loading genome Jun 08 10:22:58 ... generating Suffix Array index Jun 08 10:27:16 ... completed Suffix Array index Jun 08 10:27:16 ..... processing annotations GTF Jun 08 10:27:16 ..... inserting junctions into the genome indices Jun 08 10:28:19 ..... started mapping Jun 08 11:27:11 ..... finished mapping Jun 08 11:27:13 ..... started sorting BAM Jun 08 11:27:13 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 65.97 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.VleedfCDzv/fi_workdir --reads "/tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:27:18 : INFO : Done. Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] -done parsing /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 32, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24, ' ** passed ** ' => 3968, 'small anchor length' => 14, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2, 'low complexity anchor region' => 5, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 45, 'num genes matched < 2' => 76, 'excessive soft clipping' => 5967, 'per_id < 96' => 2875 }; -writing fusion junction support info. Execution Time = 0.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: AC006197.2--NKAIN2 [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] 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[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] -fusion SPANNING read extraction for scaff: AC136431.1--PKD1P5 [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: ENOPH1--AC002451.1 [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] -fusion SPANNING read extraction for scaff: ENOPH1--DYNC1I1 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: LINC00381--NKAIN2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PTPN20--BMS1P7 [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] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -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] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [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] -fusion SPANNING read extraction for scaff: WAC--AC023141.7 [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] -fusion SPANNING read extraction for scaff: WAC--AC128676.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: ZNF66--ZNF626 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 30566 }; Execution Time = 1.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -3160.781060 EM: Round [1] log likelihood: -3147.275592 EM: Round [2] log likelihood: -3141.923629 EM: Round [3] log likelihood: -3139.613174 EM: Round [4] log likelihood: -3138.384885 EM: Round [5] log likelihood: -3137.537748 EM: Round [6] log likelihood: -3136.849239 EM: Round [7] log likelihood: -3136.252073 EM: Round [8] log likelihood: -3135.723109 EM: Round [9] log likelihood: -3135.251283 EM: Round [10] log likelihood: -3134.829226 EM: Round [11] log likelihood: -3134.451113 EM: Round [12] log likelihood: -3134.112029 EM: Round [13] log likelihood: -3133.807735 EM: Round [14] log likelihood: -3133.534536 EM: Round [15] log likelihood: -3133.289186 EM: Round [16] log likelihood: -3133.068825 EM: Round [17] log likelihood: -3132.870919 EM: Round [18] log likelihood: -3132.693215 EM: Round [19] log likelihood: -3132.533703 EM: Round [20] log likelihood: -3132.390583 EM: Round [21] log likelihood: -3132.262244 EM: Round [22] log likelihood: -3132.147233 EM: Round [23] log likelihood: -3132.044243 EM: Round [24] log likelihood: -3131.952093 EM: Round [25] log likelihood: -3131.869718 EM: Round [26] log likelihood: -3131.796151 EM: Round [27] log likelihood: -3131.730518 EM: Round [28] log likelihood: -3131.672027 EM: Round [29] log likelihood: -3131.619959 EM: Round [30] log likelihood: -3131.573663 EM: Round [31] log likelihood: -3131.532548 EM: Round [32] log likelihood: -3131.496080 EM: Round [33] log likelihood: -3131.463772 EM: Round [34] log likelihood: -3131.435186 EM: Round [35] log likelihood: -3131.409925 EM: Round [36] log likelihood: -3131.387631 EM: Round [37] log likelihood: -3131.367980 EM: Round [38] log likelihood: -3131.350679 EM: Round [39] log likelihood: -3131.335467 EM: Round [40] log likelihood: -3131.322107 EM: Round [41] log likelihood: -3131.310388 EM: Round [42] log likelihood: -3131.300121 EM: Round [43] log likelihood: -3131.291135 EM: Round [44] log likelihood: -3131.283280 EM: Round [45] log likelihood: -3131.276420 EM: Round [46] log likelihood: -3131.270436 EM: Round [47] log likelihood: -3131.265221 EM: Round [48] log likelihood: -3131.260680 EM: Round [49] log likelihood: -3131.256730 EM: Round [50] log likelihood: -3131.253297 EM: Round [51] log likelihood: -3131.250317 EM: Round [52] log likelihood: -3131.247730 EM: Round [53] log likelihood: -3131.245488 EM: Round [54] log likelihood: -3131.243545 EM: Round [55] log likelihood: -3131.241863 EM: Round [56] log likelihood: -3131.240408 EM: Round [57] log likelihood: -3131.239150 EM: Round [58] log likelihood: -3131.238063 EM: Round [59] log likelihood: -3131.237123 EM: Round [60] log likelihood: -3131.236313 EM: Round [61] log likelihood: -3131.235613 EM: Round [62] log likelihood: -3131.235010 EM: Round [63] log likelihood: -3131.234490 EM: Round [64] log likelihood: -3131.234042 EM: Round [65] log likelihood: -3131.233656 EM: Round [66] log likelihood: -3131.233323 EM: Round [67] log likelihood: -3131.233037 EM: Round [68] log likelihood: -3131.232791 EM: Round [69] log likelihood: -3131.232579 EM: Round [70] log likelihood: -3131.232397 EM: Round [71] log likelihood: -3131.232240 EM: Round [72] log likelihood: -3131.232106 EM: Round [73] log likelihood: -3131.231990 EM: Round [74] log likelihood: -3131.231891 EM: Stopping iterations at round 74 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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam || : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.20 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.FusionJuncSpan Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.Pfam.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa > /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.VleedfCDzv/fi_workdir/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir -done, see /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -3015.222079 EM: Round [1] log likelihood: -3001.716611 EM: Round [2] log likelihood: -2996.364649 EM: Round [3] log likelihood: -2994.054193 EM: Round [4] log likelihood: -2992.825904 EM: Round [5] log likelihood: -2991.978768 EM: Round [6] log likelihood: -2991.290258 EM: Round [7] log likelihood: -2990.693092 EM: Round [8] log likelihood: -2990.164128 EM: Round [9] log likelihood: -2989.692302 EM: Round [10] log likelihood: -2989.270245 EM: Round [11] log likelihood: -2988.892132 EM: Round [12] log likelihood: -2988.553048 EM: Round [13] log likelihood: -2988.248755 EM: Round [14] log likelihood: -2987.975555 EM: Round [15] log likelihood: -2987.730205 EM: Round [16] log likelihood: -2987.509844 EM: Round [17] log likelihood: -2987.311938 EM: Round [18] log likelihood: -2987.134234 EM: Round [19] log likelihood: -2986.974722 EM: Round [20] log likelihood: -2986.831603 EM: Round [21] log likelihood: -2986.703263 EM: Round [22] log likelihood: -2986.588252 EM: Round [23] log likelihood: -2986.485262 EM: Round [24] log likelihood: -2986.393112 EM: Round [25] log likelihood: -2986.310737 EM: Round [26] log likelihood: -2986.237170 EM: Round [27] log likelihood: -2986.171537 EM: Round [28] log likelihood: -2986.113046 EM: Round [29] log likelihood: -2986.060978 EM: Round [30] log likelihood: -2986.014682 EM: Round [31] log likelihood: -2985.973567 EM: Round [32] log likelihood: -2985.937099 EM: Round [33] log likelihood: -2985.904791 EM: Round [34] log likelihood: -2985.876205 EM: Round [35] log likelihood: -2985.850945 EM: Round [36] log likelihood: -2985.828650 EM: Round [37] log likelihood: -2985.808999 EM: Round [38] log likelihood: -2985.791698 EM: Round [39] log likelihood: -2985.776486 EM: Round [40] log likelihood: -2985.763126 EM: Round [41] log likelihood: -2985.751408 EM: Round [42] log likelihood: -2985.741140 EM: Round [43] log likelihood: -2985.732154 EM: Round [44] log likelihood: -2985.724299 EM: Round [45] log likelihood: -2985.717439 EM: Round [46] log likelihood: -2985.711455 EM: Round [47] log likelihood: -2985.706240 EM: Round [48] log likelihood: -2985.701699 EM: Round [49] log likelihood: -2985.697749 EM: Round [50] log likelihood: -2985.694317 EM: Round [51] log likelihood: -2985.691336 EM: Round [52] log likelihood: -2985.688749 EM: Round [53] log likelihood: -2985.686507 EM: Round [54] log likelihood: -2985.684564 EM: Round [55] log likelihood: -2985.682882 EM: Round [56] log likelihood: -2985.681427 EM: Round [57] log likelihood: -2985.680169 EM: Round [58] log likelihood: -2985.679082 EM: Round [59] log likelihood: -2985.678142 EM: Round [60] log likelihood: -2985.677332 EM: Round [61] log likelihood: -2985.676632 EM: Round [62] log likelihood: -2985.676029 EM: Round [63] log likelihood: -2985.675509 EM: Round [64] log likelihood: -2985.675061 EM: Round [65] log likelihood: -2985.674675 EM: Round [66] log likelihood: -2985.674342 EM: Round [67] log likelihood: -2985.674056 EM: Round [68] log likelihood: -2985.673810 EM: Round [69] log likelihood: -2985.673598 EM: Round [70] log likelihood: -2985.673416 EM: Round [71] log likelihood: -2985.673259 EM: Round [72] log likelihood: -2985.673125 EM: Round [73] log likelihood: -2985.673009 EM: Round [74] log likelihood: -2985.672910 EM: Stopping iterations at round 74 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.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 295708708 Execution Time = 5.63 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.VleedfCDzv/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.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.VleedfCDzv/fi_workdir/microH.dat Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.VleedfCDzv/fi_workdir/microH.dat /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.VleedfCDzv/fi_workdir/microH.dat /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.VleedfCDzv --json_outfile /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-966ec5-R1_A23YTGFLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.VleedfCDzv --json_outfile /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-966ec5-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.VleedfCDzv/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.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-966ec5-R1_A23YTGFLT4_1 --html_output /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-966ec5-R1_A23YTGFLT4_1 --html_output /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000226240.2] WARNING, no entry stored in dbm for [ENSG00000286591.1] WARNING, no entry stored in dbm for [ENSG00000123201.14] WARNING, no entry stored in dbm for [ENSG00000123201.14] WARNING, no entry stored in dbm for [ENSG00000260126.2] WARNING, no entry stored in dbm for [ENSG00000254681.6] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.VleedfCDzv/ctat_genome_lib_build_dir > /tmp/nxf.VleedfCDzv/aih-tih-sc-966ec5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.VleedfCDzv/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory