Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/5f335dda2c01d8bcd5f0a6698449ac/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/5f335dda2c01d8bcd5f0a6698449ac/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/02caa8bce6b3540e8868c61087f08d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/02caa8bce6b3540e8868c61087f08d/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/1d392152b87f9b946fb603a6a9ea00/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29297095 29297246 . - . gene_id "5_8S_rRNA^ENSG00000283568.1"; transcript_id "ENST00000637374.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.9-201"; exon_number 1; exon_id "ENSE00003799614.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283568.1"; orig_coord_info "chr20,29297095,29297246,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29741510 29741661 . - . gene_id "5_8S_rRNA^ENSG00000283291.1"; transcript_id "ENST00000638132.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.8-201"; exon_number 1; exon_id "ENSE00003794628.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283291.1"; orig_coord_info "chr20,29741510,29741661,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 30484925 30485076 . - . gene_id "5_8S_rRNA^ENSG00000275877.1"; transcript_id "ENST00000614365.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.3-201"; exon_number 1; exon_id "ENSE00003742842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000275877.1"; orig_coord_info "chr20,30484925,30485076,-"; Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 8256781 8256933 . + . gene_id "5_8S_rRNA^ENSG00000277739.1"; transcript_id "ENST00000610460.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.5-201"; exon_number 1; exon_id "ENSE00003746458.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000277739.1"; orig_coord_info "chr21,8256781,8256933,+"; Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 11249809 11249959 . - . gene_id "5_8S_rRNA^ENSG00000276871.1"; transcript_id "ENST00000612732.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.4-201"; exon_number 1; exon_id "ENSE00003735240.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000276871.1"; orig_coord_info "chr22,11249809,11249959,-"; Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusionreport.tsv --gtf /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf > /tmp/nxf.C0cAtwyrvW/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf > /tmp/nxf.C0cAtwyrvW/cytoBand.txt Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed -parsing GTF file: /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.sorted.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.C0cAtwyrvW/fi_workdir --reads "/tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 03 21:10:10 ..... started STAR run Jun 03 21:10:10 ..... loading genome Jun 03 21:12:00 ... generating Suffix Array index Jun 03 21:15:54 ... completed Suffix Array index Jun 03 21:15:54 ..... processing annotations GTF Jun 03 21:15:55 ..... inserting junctions into the genome indices Jun 03 21:16:56 ..... started mapping Jun 03 22:28:46 ..... finished mapping Jun 03 22:28:47 ..... started sorting BAM Jun 03 22:28:49 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam Execution Time = 78.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star --out_dir /tmp/nxf.C0cAtwyrvW/fi_workdir --reads "/tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups 22:29:15 : INFO : Done. Execution Time = 0.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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] 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[4270000] [4280000] [4290000] -done parsing /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'seq-similar region overlap' => 304, 'num genes matched < 2' => 89, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 35, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 277, 'per_id < 96' => 15186, 'excessive soft clipping' => 31810, ' ** passed ** ' => 5684, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 64, 'small anchor length' => 13, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 34, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12, 'low complexity anchor region' => 6 }; -writing fusion junction support info. Execution Time = 2.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] -fusion SPANNING read extraction for scaff: AATF--AC243830.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] -fusion SPANNING read extraction for scaff: AATF--AC243830.3 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] -fusion SPANNING read extraction for scaff: AKAP7--PTPRK [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] -fusion SPANNING read extraction for scaff: AMOTL2--ME1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: ATXN8OS--KLHL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: C1QTNF3--AMACR [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: CACNB1--ADAP2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: CILK1--AL033504.1 [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] 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for scaff: EXT1--AC084114.1 [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] -fusion SPANNING read extraction for scaff: EXT1--MED30 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] -fusion SPANNING read extraction for scaff: FLACC1--TRAK2 [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] -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] -fusion SPANNING read extraction for scaff: LINC02693--AATF [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] 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[336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] -fusion SPANNING read extraction for scaff: NF1--IKZF3 [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] -fusion SPANNING read extraction for scaff: NFKB2--DENND10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] -fusion SPANNING read extraction for scaff: NPEPPSP1--AC003101.1 [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] -fusion SPANNING read extraction for scaff: NPEPPSP1--MIR4725 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] -fusion SPANNING read extraction for scaff: NSD3--5_8S_rRNA [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] -fusion SPANNING read extraction for scaff: NSD3--CR383658.1 [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] -fusion SPANNING read extraction for scaff: PAPSS1--HADH [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] [373000] [374000] [375000] [376000] [377000] [378000] [379000] [380000] [381000] [382000] [383000] [384000] [385000] [386000] [387000] [388000] [389000] [390000] [391000] [392000] [393000] [394000] [395000] [396000] [397000] [398000] [399000] [400000] [401000] [402000] [403000] [404000] [405000] [406000] [407000] [408000] [409000] [410000] [411000] [412000] [413000] [414000] [415000] [416000] [417000] [418000] [419000] [420000] [421000] [422000] [423000] [424000] -fusion SPANNING read extraction for scaff: PGAP3--MED1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] -fusion SPANNING read extraction for scaff: PHF12--LINC02693 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] -fusion SPANNING read extraction for scaff: PHF12--RPL21P120 [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: PTPRK--TRDN [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: RANBP9--AKAP7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: RAPGEF5--UNC5D [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] -fusion SPANNING read extraction for scaff: RAPGEF5--EGFR [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] -fusion SPANNING read extraction for scaff: RERE--SHANK2 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: RIMS1--TRDN [1000] -fusion SPANNING read extraction for scaff: RNU4-66P--TRDN [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: RNU6-54P--KLHL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] -fusion SPANNING read extraction for scaff: RPL23A--GOSR1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] -fusion SPANNING read extraction for scaff: SMG7--CACNA1E [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] -fusion SPANNING read extraction for scaff: STK4--ARHGEF3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: STON1--GTF2A1L [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: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [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--FAM157A [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] -fusion SPANNING read extraction for scaff: TMTC2--ACSS3 [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] -fusion SPANNING read extraction for scaff: TRAK1--ULK4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] [312000] [313000] [314000] [315000] [316000] [317000] [318000] [319000] [320000] [321000] [322000] [323000] [324000] [325000] [326000] [327000] [328000] [329000] [330000] [331000] [332000] [333000] [334000] [335000] [336000] [337000] [338000] [339000] [340000] [341000] [342000] [343000] [344000] [345000] [346000] [347000] [348000] [349000] [350000] [351000] [352000] [353000] [354000] [355000] [356000] [357000] [358000] [359000] [360000] [361000] [362000] [363000] [364000] [365000] [366000] [367000] [368000] [369000] [370000] [371000] [372000] -fusion SPANNING read extraction for scaff: TRPS1--LINC00824 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 23403, 'lacks exon overlap' => 39837 }; Execution Time = 6.26 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -9056.657967 EM: Round [1] log likelihood: -9054.735816 EM: Round [2] log likelihood: -9054.320558 EM: Round [3] log likelihood: -9053.953688 EM: Round [4] log likelihood: -9053.626148 EM: Round [5] log likelihood: -9053.332702 EM: Round [6] log likelihood: -9053.068981 EM: Round [7] log likelihood: -9052.831304 EM: Round [8] log likelihood: -9052.616550 EM: Round [9] log likelihood: -9052.422051 EM: Round [10] log likelihood: -9052.245515 EM: Round [11] log likelihood: -9052.084964 EM: Round [12] log likelihood: -9051.938676 EM: Round [13] log likelihood: -9051.805151 EM: Round [14] log likelihood: -9051.683076 EM: Round [15] log likelihood: -9051.571295 EM: Round [16] log likelihood: -9051.468787 EM: Round [17] log likelihood: -9051.374649 EM: Round [18] log likelihood: -9051.288079 EM: Round [19] log likelihood: -9051.208361 EM: Round [20] log likelihood: -9051.134859 EM: Round [21] log likelihood: -9051.067000 EM: Round [22] log likelihood: -9051.004272 EM: Round [23] log likelihood: -9050.946213 EM: Round [24] log likelihood: -9050.892410 EM: Round [25] log likelihood: -9050.842488 EM: Round [26] log likelihood: -9050.796107 EM: Round [27] log likelihood: -9050.752964 EM: Round [28] log likelihood: -9050.712779 EM: Round [29] log likelihood: -9050.675301 EM: Round [30] log likelihood: -9050.640302 EM: Round [31] log likelihood: -9050.607574 EM: Round [32] log likelihood: -9050.576928 EM: Round [33] log likelihood: -9050.548192 EM: Round [34] log likelihood: -9050.521209 EM: Round [35] log likelihood: -9050.495836 EM: Round [36] log likelihood: -9050.471942 EM: Round [37] log likelihood: -9050.449409 EM: Round [38] log likelihood: -9050.428127 EM: Round [39] log likelihood: -9050.407996 EM: Round [40] log likelihood: -9050.388927 EM: Round [41] log likelihood: -9050.370834 EM: Round [42] log likelihood: -9050.353643 EM: Round [43] log likelihood: -9050.337284 EM: Round [44] log likelihood: -9050.321692 EM: Round [45] log likelihood: -9050.306809 EM: Round [46] log likelihood: -9050.292582 EM: Round [47] log likelihood: -9050.278960 EM: Round [48] log likelihood: -9050.265900 EM: Round [49] log likelihood: -9050.253360 EM: Round [50] log likelihood: -9050.241302 EM: Round [51] log likelihood: -9050.229692 EM: Round [52] log likelihood: -9050.218496 EM: Round [53] log likelihood: -9050.207687 EM: Round [54] log likelihood: -9050.197236 EM: Round [55] log likelihood: -9050.187121 EM: Round [56] log likelihood: -9050.177317 EM: Round [57] log likelihood: -9050.167803 EM: Round [58] log likelihood: -9050.158562 EM: Round [59] log likelihood: -9050.149575 EM: Round [60] log likelihood: -9050.140826 EM: Round [61] log likelihood: -9050.132300 EM: Round [62] log likelihood: -9050.123983 EM: Round [63] log likelihood: -9050.115863 EM: Round [64] log likelihood: -9050.107929 EM: Round [65] log likelihood: -9050.100169 EM: Round [66] log likelihood: -9050.092573 EM: Round [67] log likelihood: -9050.085133 EM: Round [68] log likelihood: -9050.077841 EM: Round [69] log likelihood: -9050.070687 EM: Round [70] log likelihood: -9050.063667 EM: Round [71] log likelihood: -9050.056771 EM: Round [72] log likelihood: -9050.049996 EM: Round [73] log likelihood: -9050.043335 EM: Round [74] log likelihood: -9050.036782 EM: Round [75] log likelihood: -9050.030334 EM: Round [76] log likelihood: -9050.023985 EM: Round [77] log likelihood: -9050.017732 EM: Round [78] log likelihood: -9050.011571 EM: Round [79] log likelihood: -9050.005497 EM: Round [80] log likelihood: -9049.999508 EM: Round [81] log likelihood: -9049.993601 EM: Round [82] log likelihood: -9049.987773 EM: Round [83] log likelihood: -9049.982020 EM: Round [84] log likelihood: -9049.976342 EM: Round [85] log likelihood: -9049.970735 EM: Round [86] log likelihood: -9049.965197 EM: Round [87] log likelihood: -9049.959726 EM: Round [88] log likelihood: -9049.954320 EM: Round [89] log likelihood: -9049.948978 EM: Round [90] log likelihood: -9049.943697 EM: Round [91] log likelihood: -9049.938477 EM: Round [92] log likelihood: -9049.933315 EM: Round [93] log likelihood: -9049.928211 EM: Round [94] log likelihood: -9049.923162 EM: Round [95] log likelihood: -9049.918168 EM: Round [96] log likelihood: -9049.913228 EM: Round [97] log likelihood: -9049.908340 EM: Round [98] log likelihood: -9049.903504 EM: Round [99] log likelihood: -9049.898717 EM: Round [100] log likelihood: -9049.893981 EM: Round [101] log likelihood: -9049.889292 EM: Round [102] log likelihood: -9049.884651 EM: Round [103] log likelihood: -9049.880057 EM: Round [104] log likelihood: -9049.875509 EM: Round [105] log likelihood: -9049.871006 EM: Round [106] log likelihood: -9049.866547 EM: Round [107] log likelihood: -9049.862132 EM: Round [108] log likelihood: -9049.857760 EM: Round [109] log likelihood: -9049.853431 EM: Round [110] log likelihood: -9049.849143 EM: Round [111] log likelihood: -9049.844896 EM: Round [112] log likelihood: -9049.840690 EM: Round [113] log likelihood: -9049.836524 EM: Round [114] log likelihood: -9049.832397 EM: Round [115] log likelihood: -9049.828309 EM: Round [116] log likelihood: -9049.824259 EM: Round [117] log likelihood: -9049.820247 EM: Round [118] log likelihood: -9049.816273 EM: Round [119] log likelihood: -9049.812335 EM: Round [120] log likelihood: -9049.808434 EM: Round [121] log likelihood: -9049.804569 EM: Round [122] log likelihood: -9049.800739 EM: Round [123] log likelihood: -9049.796944 EM: Round [124] log likelihood: -9049.793184 EM: Round [125] log likelihood: -9049.789458 EM: Round [126] log likelihood: -9049.785766 EM: Round [127] log likelihood: -9049.782107 EM: Round [128] log likelihood: -9049.778482 EM: Round [129] log likelihood: -9049.774889 EM: Round [130] log likelihood: -9049.771328 EM: Round [131] log likelihood: -9049.767799 EM: Round [132] log likelihood: -9049.764302 EM: Round [133] log likelihood: -9049.760836 EM: Round [134] log likelihood: -9049.757400 EM: Round [135] log likelihood: -9049.753996 EM: Round [136] log likelihood: -9049.750621 EM: Round [137] log likelihood: -9049.747276 EM: Round [138] log likelihood: -9049.743961 EM: Round [139] log likelihood: -9049.740675 EM: Round [140] log likelihood: -9049.737418 EM: Round [141] log likelihood: -9049.734189 EM: Round [142] log likelihood: -9049.730989 EM: Round [143] log likelihood: -9049.727816 EM: Round [144] log likelihood: -9049.724672 EM: Round [145] log likelihood: -9049.721554 EM: Round [146] log likelihood: -9049.718464 EM: Round [147] log likelihood: -9049.715401 EM: Round [148] log likelihood: -9049.712364 EM: Round [149] log likelihood: -9049.709353 EM: Round [150] log likelihood: -9049.706369 EM: Round [151] log likelihood: -9049.703410 EM: Round [152] log likelihood: -9049.700476 EM: Round [153] log likelihood: -9049.697568 EM: Round [154] log likelihood: -9049.694685 EM: Round [155] log likelihood: -9049.691826 EM: Round [156] log likelihood: -9049.688992 EM: Round [157] log likelihood: -9049.686183 EM: Round [158] log likelihood: -9049.683397 EM: Round [159] log likelihood: -9049.680634 EM: Round [160] log likelihood: -9049.677896 EM: Round [161] log likelihood: -9049.675180 EM: Round [162] log likelihood: -9049.672488 EM: Round [163] log likelihood: -9049.669818 EM: Round [164] log likelihood: -9049.667171 EM: Round [165] log likelihood: -9049.664547 EM: Round [166] log likelihood: -9049.661944 EM: Round [167] log likelihood: -9049.659364 EM: Round [168] log likelihood: -9049.656805 EM: Round [169] log likelihood: -9049.654267 EM: Round [170] log likelihood: -9049.651751 EM: Round [171] log likelihood: -9049.649256 EM: Round [172] log likelihood: -9049.646782 EM: Round [173] log likelihood: -9049.644329 EM: Round [174] log likelihood: -9049.641896 EM: Round [175] log likelihood: -9049.639483 EM: Round [176] log likelihood: -9049.637090 EM: Round [177] log likelihood: -9049.634718 EM: Round [178] log likelihood: -9049.632365 EM: Round [179] log likelihood: -9049.630031 EM: Round [180] log likelihood: -9049.627717 EM: Round [181] log likelihood: -9049.625422 EM: Round [182] log likelihood: -9049.623146 EM: Round [183] log likelihood: -9049.620889 EM: Round [184] log likelihood: -9049.618651 EM: Round [185] log likelihood: -9049.616430 EM: Round [186] log likelihood: -9049.614229 EM: Round [187] log likelihood: -9049.612045 EM: Round [188] log likelihood: -9049.609879 EM: Round [189] log likelihood: -9049.607731 EM: Round [190] log likelihood: -9049.605601 EM: Round [191] log likelihood: -9049.603488 EM: Round [192] log likelihood: -9049.601392 EM: Round [193] log likelihood: -9049.599314 EM: Round [194] log likelihood: -9049.597252 EM: Round [195] log likelihood: -9049.595207 EM: Round [196] log likelihood: -9049.593179 EM: Round [197] log likelihood: -9049.591167 EM: Round [198] log likelihood: -9049.589172 EM: Round [199] log likelihood: -9049.587193 EM: Round [200] log likelihood: -9049.585230 EM: Round [201] log likelihood: -9049.583283 EM: Round [202] log likelihood: -9049.581351 EM: Round [203] log likelihood: -9049.579436 EM: Round [204] log likelihood: -9049.577535 EM: Round [205] log likelihood: -9049.575651 EM: Round [206] log likelihood: -9049.573781 EM: Round [207] log likelihood: -9049.571926 EM: Round [208] log likelihood: -9049.570087 EM: Round [209] log likelihood: -9049.568262 EM: Round [210] log likelihood: -9049.566451 EM: Round [211] log likelihood: -9049.564656 EM: Round [212] log likelihood: -9049.562874 EM: Round [213] log likelihood: -9049.561107 EM: Round [214] log likelihood: -9049.559354 EM: Round [215] log likelihood: -9049.557616 EM: Round [216] log likelihood: -9049.555891 EM: Round [217] log likelihood: -9049.554179 EM: Round [218] log likelihood: -9049.552482 EM: Round [219] log likelihood: -9049.550798 EM: Round [220] log likelihood: -9049.549127 EM: Round [221] log likelihood: -9049.547470 EM: Round [222] log likelihood: -9049.545826 EM: Round [223] log likelihood: -9049.544195 EM: Round [224] log likelihood: -9049.542577 EM: Round [225] log likelihood: -9049.540972 EM: Round [226] log likelihood: -9049.539379 EM: Round [227] log likelihood: -9049.537799 EM: Round [228] log likelihood: -9049.536232 EM: Round [229] log likelihood: -9049.534677 EM: Round [230] log likelihood: -9049.533134 EM: Round [231] log likelihood: -9049.531604 EM: Round [232] log likelihood: -9049.530085 EM: Round [233] log likelihood: -9049.528579 EM: Round [234] log likelihood: -9049.527084 EM: Round [235] log likelihood: -9049.525601 EM: Round [236] log likelihood: -9049.524130 EM: Round [237] log likelihood: -9049.522670 EM: Round [238] log likelihood: -9049.521222 EM: Round [239] log likelihood: -9049.519785 EM: Round [240] log likelihood: -9049.518360 EM: Round [241] log likelihood: -9049.516946 EM: Round [242] log likelihood: -9049.515542 EM: Round [243] log likelihood: -9049.514150 EM: Round [244] log likelihood: -9049.512769 EM: Round [245] log likelihood: -9049.511398 EM: Round [246] log likelihood: -9049.510038 EM: Round [247] log likelihood: -9049.508689 EM: Round [248] log likelihood: -9049.507350 EM: Round [249] log likelihood: -9049.506022 EM: Round [250] log likelihood: -9049.504704 EM: Round [251] log likelihood: -9049.503396 EM: Round [252] log likelihood: -9049.502099 EM: Round [253] log likelihood: -9049.500811 EM: Round [254] log likelihood: -9049.499534 EM: Round [255] log likelihood: -9049.498266 EM: Round [256] log likelihood: -9049.497009 EM: Round [257] log likelihood: -9049.495761 EM: Round [258] log likelihood: -9049.494522 EM: Round [259] log likelihood: -9049.493294 EM: Round [260] log likelihood: -9049.492075 EM: Round [261] log likelihood: -9049.490865 EM: Round [262] log likelihood: -9049.489665 EM: Round [263] log likelihood: -9049.488474 EM: Round [264] log likelihood: -9049.487292 EM: Round [265] log likelihood: -9049.486119 EM: Round [266] log likelihood: -9049.484955 EM: Round [267] log likelihood: -9049.483800 EM: Round [268] log likelihood: -9049.482655 EM: Round [269] log likelihood: -9049.481517 EM: Round [270] log likelihood: -9049.480389 EM: Round [271] log likelihood: -9049.479270 EM: Round [272] log likelihood: -9049.478159 EM: Round [273] log likelihood: -9049.477056 EM: Round [274] log likelihood: -9049.475962 EM: Round [275] log likelihood: -9049.474877 EM: Round [276] log likelihood: -9049.473799 EM: Round [277] log likelihood: -9049.472730 EM: Round [278] log likelihood: -9049.471669 EM: Round [279] log likelihood: -9049.470617 EM: Round [280] log likelihood: -9049.469572 EM: Round [281] log likelihood: -9049.468535 EM: Round [282] log likelihood: -9049.467507 EM: Round [283] log likelihood: -9049.466486 EM: Round [284] log likelihood: -9049.465473 EM: Round [285] log likelihood: -9049.464467 EM: Round [286] log likelihood: -9049.463470 EM: Round [287] log likelihood: -9049.462480 EM: Round [288] log likelihood: -9049.461497 EM: Round [289] log likelihood: -9049.460522 EM: Round [290] log likelihood: -9049.459555 EM: Round [291] log likelihood: -9049.458594 EM: Round [292] log likelihood: -9049.457641 EM: Round [293] log likelihood: -9049.456696 EM: Round [294] log likelihood: -9049.455757 EM: Round [295] log likelihood: -9049.454826 EM: Round [296] log likelihood: -9049.453902 EM: Round [297] log likelihood: -9049.452984 EM: Round [298] log likelihood: -9049.452074 EM: Round [299] log likelihood: -9049.451171 EM: Round [300] log likelihood: -9049.450274 EM: Round [301] log likelihood: -9049.449384 EM: Round [302] log likelihood: -9049.448501 EM: Round [303] log likelihood: -9049.447625 EM: Round [304] log likelihood: -9049.446755 EM: Round [305] log likelihood: -9049.445892 EM: Round [306] log likelihood: -9049.445035 EM: Round [307] log likelihood: -9049.444185 EM: Round [308] log likelihood: -9049.443342 EM: Round [309] log likelihood: -9049.442504 EM: Round [310] log likelihood: -9049.441673 EM: Round [311] log likelihood: -9049.440848 EM: Round [312] log likelihood: -9049.440030 EM: Round [313] log likelihood: -9049.439217 EM: Round [314] log likelihood: -9049.438411 EM: Round [315] log likelihood: -9049.437611 EM: Round [316] log likelihood: -9049.436817 EM: Round [317] log likelihood: -9049.436029 EM: Round [318] log likelihood: -9049.435246 EM: Round [319] log likelihood: -9049.434470 EM: Round [320] log likelihood: -9049.433700 EM: Round [321] log likelihood: -9049.432935 EM: Round [322] log likelihood: -9049.432176 EM: Round [323] log likelihood: -9049.431422 EM: Round [324] log likelihood: -9049.430675 EM: Round [325] log likelihood: -9049.429933 EM: Round [326] log likelihood: -9049.429196 EM: Round [327] log likelihood: -9049.428465 EM: Round [328] log likelihood: -9049.427740 EM: Round [329] log likelihood: -9049.427020 EM: Round [330] log likelihood: -9049.426305 EM: Round [331] log likelihood: -9049.425596 EM: Round [332] log likelihood: -9049.424892 EM: Round [333] log likelihood: -9049.424193 EM: Round [334] log likelihood: -9049.423500 EM: Round [335] log likelihood: -9049.422811 EM: Round [336] log likelihood: -9049.422128 EM: Round [337] log likelihood: -9049.421450 EM: Round [338] log likelihood: -9049.420777 EM: Round [339] log likelihood: -9049.420109 EM: Round [340] log likelihood: -9049.419446 EM: Round [341] log likelihood: -9049.418788 EM: Round [342] log likelihood: -9049.418135 EM: Round [343] log likelihood: -9049.417487 EM: Round [344] log likelihood: -9049.416843 EM: Round [345] log likelihood: -9049.416204 EM: Round [346] log likelihood: -9049.415571 EM: Round [347] log likelihood: -9049.414941 EM: Round [348] log likelihood: -9049.414317 EM: Round [349] log likelihood: -9049.413697 EM: Round [350] log likelihood: -9049.413082 EM: Round [351] log likelihood: -9049.412471 EM: Round [352] log likelihood: -9049.411865 EM: Round [353] log likelihood: -9049.411263 EM: Round [354] log likelihood: -9049.410666 EM: Round [355] log likelihood: -9049.410073 EM: Round [356] log likelihood: -9049.409485 EM: Round [357] log likelihood: -9049.408901 EM: Round [358] log likelihood: -9049.408322 EM: Round [359] log likelihood: -9049.407746 EM: Round [360] log likelihood: -9049.407175 EM: Round [361] log likelihood: -9049.406608 EM: Round [362] log likelihood: -9049.406046 EM: Round [363] log likelihood: -9049.405487 EM: Round [364] log likelihood: -9049.404933 EM: Round [365] log likelihood: -9049.404383 EM: Round [366] log likelihood: -9049.403837 EM: Round [367] log likelihood: -9049.403295 EM: Round [368] log likelihood: -9049.402756 EM: Round [369] log likelihood: -9049.402222 EM: Round [370] log likelihood: -9049.401692 EM: Round [371] log likelihood: -9049.401166 EM: Round [372] log likelihood: -9049.400644 EM: Round [373] log likelihood: -9049.400125 EM: Round [374] log likelihood: -9049.399611 EM: Round [375] log likelihood: -9049.399100 EM: Round [376] log likelihood: -9049.398593 EM: Round [377] log likelihood: -9049.398089 EM: Round [378] log likelihood: -9049.397590 EM: Round [379] log likelihood: -9049.397094 EM: Round [380] log likelihood: -9049.396601 EM: Round [381] log likelihood: -9049.396113 EM: Round [382] log likelihood: -9049.395628 EM: Round [383] log likelihood: -9049.395146 EM: Round [384] log likelihood: -9049.394668 EM: Round [385] log likelihood: -9049.394194 EM: Round [386] log likelihood: -9049.393723 EM: Round [387] log likelihood: -9049.393256 EM: Round [388] log likelihood: -9049.392792 EM: Round [389] log likelihood: -9049.392331 EM: Round [390] log likelihood: -9049.391874 EM: Round [391] log likelihood: -9049.391420 EM: Round [392] log likelihood: -9049.390969 EM: Round [393] log likelihood: -9049.390522 EM: Round [394] log likelihood: -9049.390078 EM: Round [395] log likelihood: -9049.389638 EM: Round [396] log likelihood: -9049.389200 EM: Round [397] log likelihood: -9049.388766 EM: Round [398] log likelihood: -9049.388335 EM: Round [399] log likelihood: -9049.387907 EM: Round [400] log likelihood: -9049.387483 EM: Round [401] log likelihood: -9049.387061 EM: Round [402] log likelihood: -9049.386643 EM: Round [403] log likelihood: -9049.386227 EM: Round [404] log likelihood: -9049.385815 EM: Round [405] log likelihood: -9049.385406 EM: Round [406] log likelihood: -9049.384999 EM: Round [407] log likelihood: -9049.384596 EM: Round [408] log likelihood: -9049.384195 EM: Round [409] log likelihood: -9049.383798 EM: Round [410] log likelihood: -9049.383403 EM: Round [411] log likelihood: -9049.383012 EM: Round [412] log likelihood: -9049.382623 EM: Round [413] log likelihood: -9049.382237 EM: Round [414] log likelihood: -9049.381854 EM: Round [415] log likelihood: -9049.381474 EM: Round [416] log likelihood: -9049.381096 EM: Round [417] log likelihood: -9049.380721 EM: Round [418] log likelihood: -9049.380349 EM: Round [419] log likelihood: -9049.379980 EM: Round [420] log likelihood: -9049.379613 EM: Round [421] log likelihood: -9049.379249 EM: Round [422] log likelihood: -9049.378888 EM: Round [423] log likelihood: -9049.378529 EM: Round [424] log likelihood: -9049.378173 EM: Round [425] log likelihood: -9049.377820 EM: Round [426] log likelihood: -9049.377469 EM: Round [427] log likelihood: -9049.377121 EM: Round [428] log likelihood: -9049.376775 EM: Round [429] log likelihood: -9049.376432 EM: Round [430] log likelihood: -9049.376091 EM: Round [431] log likelihood: -9049.375753 EM: Round [432] log likelihood: -9049.375417 EM: Round [433] log likelihood: -9049.375084 EM: Round [434] log likelihood: -9049.374753 EM: Round [435] log likelihood: -9049.374425 EM: Round [436] log likelihood: -9049.374099 EM: Round [437] log likelihood: -9049.373775 EM: Round [438] log likelihood: -9049.373454 EM: Round [439] log likelihood: -9049.373135 EM: Round [440] log likelihood: -9049.372818 EM: Round [441] log likelihood: -9049.372504 EM: Round [442] log likelihood: -9049.372192 EM: Round [443] log likelihood: -9049.371882 EM: Round [444] log likelihood: -9049.371574 EM: Round [445] log likelihood: -9049.371269 EM: Round [446] log likelihood: -9049.370966 EM: Round [447] log likelihood: -9049.370665 EM: Round [448] log likelihood: -9049.370366 EM: Round [449] log likelihood: -9049.370070 EM: Round [450] log likelihood: -9049.369775 EM: Round [451] log likelihood: -9049.369483 EM: Round [452] log likelihood: -9049.369193 EM: Round [453] log likelihood: -9049.368905 EM: Round [454] log likelihood: -9049.368619 EM: Round [455] log likelihood: -9049.368336 EM: Round [456] log likelihood: -9049.368054 EM: Round [457] log likelihood: -9049.367774 EM: Round [458] log likelihood: -9049.367496 EM: Round [459] log likelihood: -9049.367221 EM: Round [460] log likelihood: -9049.366947 EM: Round [461] log likelihood: -9049.366676 EM: Round [462] log likelihood: -9049.366406 EM: Round [463] log likelihood: -9049.366138 EM: Round [464] log likelihood: -9049.365872 EM: Round [465] log likelihood: -9049.365608 EM: Round [466] log likelihood: -9049.365347 EM: Round [467] log likelihood: -9049.365087 EM: Round [468] log likelihood: -9049.364828 EM: Round [469] log likelihood: -9049.364572 EM: Round [470] log likelihood: -9049.364318 EM: Round [471] log likelihood: -9049.364065 EM: Round [472] log likelihood: -9049.363814 EM: Round [473] log likelihood: -9049.363565 EM: Round [474] log likelihood: -9049.363318 EM: Round [475] log likelihood: -9049.363073 EM: Round [476] log likelihood: -9049.362829 EM: Round [477] log likelihood: -9049.362588 EM: Round [478] log likelihood: -9049.362348 EM: Round [479] log likelihood: -9049.362109 EM: Round [480] log likelihood: -9049.361873 EM: Round [481] log likelihood: -9049.361638 EM: Round [482] log likelihood: -9049.361405 EM: Round [483] log likelihood: -9049.361173 EM: Round [484] log likelihood: -9049.360944 EM: Round [485] log likelihood: -9049.360715 EM: Round [486] log likelihood: -9049.360489 EM: Round [487] log likelihood: -9049.360264 EM: Round [488] log likelihood: -9049.360041 EM: Round [489] log likelihood: -9049.359819 EM: Round [490] log likelihood: -9049.359599 EM: Round [491] log likelihood: -9049.359381 EM: Round [492] log likelihood: -9049.359164 EM: Round [493] log likelihood: -9049.358949 EM: Round [494] log likelihood: -9049.358735 EM: Round [495] log likelihood: -9049.358523 EM: Round [496] log likelihood: -9049.358312 EM: Round [497] log likelihood: -9049.358103 EM: Round [498] log likelihood: -9049.357896 EM: Round [499] log likelihood: -9049.357690 EM: Round [500] log likelihood: -9049.357485 EM: Round [501] log likelihood: -9049.357282 EM: Round [502] log likelihood: -9049.357080 EM: Round [503] log likelihood: -9049.356880 EM: Round [504] log likelihood: -9049.356681 EM: Round [505] log likelihood: -9049.356484 EM: Round [506] log likelihood: -9049.356288 EM: Round [507] log likelihood: -9049.356094 EM: Round [508] log likelihood: -9049.355901 EM: Round [509] log likelihood: -9049.355709 EM: Round [510] log likelihood: -9049.355519 EM: Round [511] log likelihood: -9049.355330 EM: Round [512] log likelihood: -9049.355142 EM: Round [513] log likelihood: -9049.354956 EM: Round [514] log likelihood: -9049.354771 EM: Round [515] log likelihood: -9049.354588 EM: Round [516] log likelihood: -9049.354406 EM: Round [517] log likelihood: -9049.354225 EM: Round [518] log likelihood: -9049.354045 EM: Round [519] log likelihood: -9049.353867 EM: Round [520] log likelihood: -9049.353690 EM: Round [521] log likelihood: -9049.353514 EM: Round [522] log likelihood: -9049.353340 EM: Round [523] log likelihood: -9049.353166 EM: Round [524] log likelihood: -9049.352995 EM: Round [525] log likelihood: -9049.352824 EM: Round [526] log likelihood: -9049.352654 EM: Round [527] log likelihood: -9049.352486 EM: Round [528] log likelihood: -9049.352319 EM: Round [529] log likelihood: -9049.352153 EM: Round [530] log likelihood: -9049.351989 EM: Round [531] log likelihood: -9049.351825 EM: Round [532] log likelihood: -9049.351663 EM: Round [533] log likelihood: -9049.351502 EM: Round [534] log likelihood: -9049.351342 EM: Round [535] log likelihood: -9049.351183 EM: Round [536] log likelihood: -9049.351025 EM: Round [537] log likelihood: -9049.350869 EM: Round [538] log likelihood: -9049.350713 EM: Round [539] log likelihood: -9049.350559 EM: Round [540] log likelihood: -9049.350406 EM: Round [541] log likelihood: -9049.350254 EM: Round [542] log likelihood: -9049.350103 EM: Round [543] log likelihood: -9049.349953 EM: Round [544] log likelihood: -9049.349804 EM: Round [545] log likelihood: -9049.349657 EM: Round [546] log likelihood: -9049.349510 EM: Round [547] log likelihood: -9049.349364 EM: Round [548] log likelihood: -9049.349220 EM: Round [549] log likelihood: -9049.349076 EM: Round [550] log likelihood: -9049.348934 EM: Round [551] log likelihood: -9049.348792 EM: Round [552] log likelihood: -9049.348652 EM: Round [553] log likelihood: -9049.348512 EM: Round [554] log likelihood: -9049.348374 EM: Round [555] log likelihood: -9049.348237 EM: Round [556] log likelihood: -9049.348100 EM: Round [557] log likelihood: -9049.347965 EM: Round [558] log likelihood: -9049.347830 EM: Round [559] log likelihood: -9049.347697 EM: Round [560] log likelihood: -9049.347564 EM: Round [561] log likelihood: -9049.347432 EM: Round [562] log likelihood: -9049.347302 EM: Round [563] log likelihood: -9049.347172 EM: Round [564] log likelihood: -9049.347043 EM: Round [565] log likelihood: -9049.346915 EM: Round [566] log likelihood: -9049.346788 EM: Round [567] log likelihood: -9049.346662 EM: Round [568] log likelihood: -9049.346537 EM: Round [569] log likelihood: -9049.346413 EM: Round [570] log likelihood: -9049.346290 EM: Round [571] log likelihood: -9049.346167 EM: Round [572] log likelihood: -9049.346046 EM: Round [573] log likelihood: -9049.345925 EM: Round [574] log likelihood: -9049.345805 EM: Round [575] log likelihood: -9049.345686 EM: Round [576] log likelihood: -9049.345568 EM: Round [577] log likelihood: -9049.345451 EM: Round [578] log likelihood: -9049.345334 EM: Round [579] log likelihood: -9049.345219 EM: Round [580] log likelihood: -9049.345104 EM: Round [581] log likelihood: -9049.344990 EM: Round [582] log likelihood: -9049.344877 EM: Round [583] log likelihood: -9049.344765 EM: Round [584] log likelihood: -9049.344653 EM: Round [585] log likelihood: -9049.344542 EM: Round [586] log likelihood: -9049.344432 EM: Round [587] log likelihood: -9049.344323 EM: Round [588] log likelihood: -9049.344215 EM: Round [589] log likelihood: -9049.344107 EM: Round [590] log likelihood: -9049.344001 EM: Round [591] log likelihood: -9049.343895 EM: Round [592] log likelihood: -9049.343789 EM: Round [593] log likelihood: -9049.343685 EM: Round [594] log likelihood: -9049.343581 EM: Round [595] log likelihood: -9049.343478 EM: Round [596] log likelihood: -9049.343376 EM: Round [597] log likelihood: -9049.343274 EM: Round [598] log likelihood: -9049.343173 EM: Round [599] log likelihood: -9049.343073 EM: Round [600] log likelihood: -9049.342974 EM: Stopping iterations at round 600 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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam" Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 1.09 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.Pfam.gff3 > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa > /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir -done, see /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -8641.808258 EM: Round [1] log likelihood: -8641.160562 EM: Round [2] log likelihood: -8641.160249 EM: Round [3] log likelihood: -8641.160249 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296397279 Execution Time = 5.66 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf > /tmp/nxf.C0cAtwyrvW/fi_workdir/microH.dat Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fa --gtf /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gtf > /tmp/nxf.C0cAtwyrvW/fi_workdir/microH.dat Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.C0cAtwyrvW/fi_workdir/microH.dat /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/fi_workdir/microH.dat /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.C0cAtwyrvW --json_outfile /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-6d9e6f-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.C0cAtwyrvW --json_outfile /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1 Running: touch /tmp/nxf.C0cAtwyrvW/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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1 --html_output /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.02 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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1 --html_output /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-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.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000223726.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000254275.6] WARNING, no entry stored in dbm for [ENSG00000274487.2] WARNING, no entry stored in dbm for [ENSG00000228768.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.C0cAtwyrvW/ctat_genome_lib_build_dir > /tmp/nxf.C0cAtwyrvW/aih-tih-sc-6d9e6f-R1_A23YTGFLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.C0cAtwyrvW/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory