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/8d/f2acef8ebad4bef109e179f1c93982/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/5c31aa0ed6d22b6d0ddcf6cd271511/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/08f9108ec704f76025bcbedc9fb117/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/08f9108ec704f76025bcbedc9fb117/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/5c31aa0ed6d22b6d0ddcf6cd271511/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_1.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-9703f5-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5ewXSTqSxx/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5ewXSTqSxx/cytoBand.txt Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.5ewXSTqSxx/fi_workdir --reads "/tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 08:55:26 ..... started STAR run Jun 08 08:55:26 ..... loading genome Jun 08 08:57:04 ... generating Suffix Array index Jun 08 09:00:47 ... completed Suffix Array index Jun 08 09:00:48 ..... processing annotations GTF Jun 08 09:00:48 ..... inserting junctions into the genome indices Jun 08 09:01:49 ..... started mapping Jun 08 09:32:52 ..... finished mapping Jun 08 09:32:53 ..... started sorting BAM Jun 08 09:32:53 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 37.45 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.5ewXSTqSxx/fi_workdir --reads "/tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 09:32:56 : INFO : Done. Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-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] -done parsing /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 18, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3, ' ** passed ** ' => 1072, 'num genes matched < 2' => 10, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 55, 'excessive soft clipping' => 4865, 'per_id < 96' => 3597, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 10, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 20 }; -writing fusion junction support info. Execution Time = 0.28 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: AC016831.6--SRBD1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: CPT1C--ZNF614 [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] -fusion SPANNING read extraction for scaff: IKBKB--AC021613.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] -fusion SPANNING read extraction for scaff: PLEKHA7--NAV2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: VDAC3--CHRNB3 [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] -fusion SPANNING read extraction for scaff: YTHDF3--MPPED2 [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] -fusion SPANNING read extraction for scaff: ZNF71--IKBKB [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: ZNF71--AC021613.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] -fusion SPANNING read extraction for scaff: ZNF714--MED25 [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: ZNF83--CPT1C -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 3377 }; Execution Time = 0.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -1323.249056 EM: Round [1] log likelihood: -1323.249056 EM: Stopping iterations at round 1 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.14 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa > /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir -done, see /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -1219.785156 EM: Round [1] log likelihood: -1219.785156 EM: Stopping iterations at round 1 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 168472012 Execution Time = 2.95 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.gtf > /tmp/nxf.5ewXSTqSxx/fi_workdir/microH.dat Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.5ewXSTqSxx/fi_workdir/microH.dat /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/fi_workdir/microH.dat /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.5ewXSTqSxx --json_outfile /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-9703f5-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.5ewXSTqSxx --json_outfile /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-9703f5-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.5ewXSTqSxx/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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-9703f5-R1_A23YTGFLT4_1 --html_output /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-9703f5-R1_A23YTGFLT4_1 --html_output /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-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.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000285106.2] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.5ewXSTqSxx/ctat_genome_lib_build_dir > /tmp/nxf.5ewXSTqSxx/aih-tih-sc-9703f5-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.5ewXSTqSxx/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory