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/db/5f8f1fa6f6349d23d679d0e69e25b6/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/5f8f1fa6f6349d23d679d0e69e25b6/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/8484a4abd3fff18b10ebb14514a352/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/8c5c614ebc4fb9b2d2925ad3c5d891/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/8484a4abd3fff18b10ebb14514a352/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusionreport.tsv --gtf /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/cytoBand.txt Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed -parsing GTF file: /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.FBo812kcg8/fi_workdir --reads "/tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.FBo812kcg8/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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:15:29 ..... started STAR run Jun 08 10:15:29 ..... loading genome Jun 08 10:17:14 ... generating Suffix Array index Jun 08 10:21:05 ... completed Suffix Array index Jun 08 10:21:05 ..... processing annotations GTF Jun 08 10:21:06 ..... inserting junctions into the genome indices Jun 08 10:22:07 ..... started mapping Jun 08 11:49:11 ..... finished mapping Jun 08 11:49:12 ..... started sorting BAM Jun 08 11:49:13 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam Execution Time = 93.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --CPU 8 --out_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star --out_dir /tmp/nxf.FBo812kcg8/fi_workdir --reads "/tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:49:17 : INFO : Done. Execution Time = 0.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf -parsing /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] -done parsing /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'per_id < 96' => 1747, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8, ' ** passed ** ' => 8697, 'num genes matched < 2' => 24, 'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18, 'low complexity anchor region' => 7, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 17, 'small anchor length' => 36, 'exons hit < 2' => 4, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4, 'seq-similar region overlap' => 350, 'excessive soft clipping' => 3440, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6 }; -writing fusion junction support info. Execution Time = 0.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: AC079781.4--ASNS [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: LHFPL5--CLPSL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: 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] -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] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -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] -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] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] -fusion SPANNING read extraction for scaff: PDCL--RC3H2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: TLK2--LINC01347 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 34002, 'lacks exon overlap' => 1963 }; Execution Time = 0.73 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -5646.071269 EM: Round [1] log likelihood: -5642.783408 EM: Round [2] log likelihood: -5641.809488 EM: Round [3] log likelihood: -5641.028046 EM: Round [4] log likelihood: -5640.379261 EM: Round [5] log likelihood: -5639.828661 EM: Round [6] log likelihood: -5639.353353 EM: Round [7] log likelihood: -5638.937372 EM: Round [8] log likelihood: -5638.569177 EM: Round [9] log likelihood: -5638.240193 EM: Round [10] log likelihood: -5637.943903 EM: Round [11] log likelihood: -5637.675257 EM: Round [12] log likelihood: -5637.430278 EM: Round [13] log likelihood: -5637.205783 EM: Round [14] log likelihood: -5636.999191 EM: Round [15] log likelihood: -5636.808379 EM: Round [16] log likelihood: -5636.631582 EM: Round [17] log likelihood: -5636.467315 EM: Round [18] log likelihood: -5636.314315 EM: Round [19] log likelihood: -5636.171500 EM: Round [20] log likelihood: -5636.037930 EM: Round [21] log likelihood: -5635.912789 EM: Round [22] log likelihood: -5635.795358 EM: Round [23] log likelihood: -5635.685001 EM: Round [24] log likelihood: -5635.581153 EM: Round [25] log likelihood: -5635.483310 EM: Round [26] log likelihood: -5635.391018 EM: Round [27] log likelihood: -5635.303869 EM: Round [28] log likelihood: -5635.221492 EM: Round [29] log likelihood: -5635.143552 EM: Round [30] log likelihood: -5635.069743 EM: Round [31] log likelihood: -5634.999786 EM: Round [32] log likelihood: -5634.933424 EM: Round [33] log likelihood: -5634.870423 EM: Round [34] log likelihood: -5634.810568 EM: Round [35] log likelihood: -5634.753658 EM: Round [36] log likelihood: -5634.699510 EM: Round [37] log likelihood: -5634.647955 EM: Round [38] log likelihood: -5634.598834 EM: Round [39] log likelihood: -5634.552002 EM: Round [40] log likelihood: -5634.507322 EM: Round [41] log likelihood: -5634.464668 EM: Round [42] log likelihood: -5634.423924 EM: Round [43] log likelihood: -5634.384978 EM: Round [44] log likelihood: -5634.347730 EM: Round [45] log likelihood: -5634.312082 EM: Round [46] log likelihood: -5634.277946 EM: Round [47] log likelihood: -5634.245239 EM: Round [48] log likelihood: -5634.213881 EM: Round [49] log likelihood: -5634.183799 EM: Round [50] log likelihood: -5634.154925 EM: Round [51] log likelihood: -5634.127194 EM: Round [52] log likelihood: -5634.100545 EM: Round [53] log likelihood: -5634.074922 EM: Round [54] log likelihood: -5634.050269 EM: Round [55] log likelihood: -5634.026538 EM: Round [56] log likelihood: -5634.003681 EM: Round [57] log likelihood: -5633.981653 EM: Round [58] log likelihood: -5633.960412 EM: Round [59] log likelihood: -5633.939918 EM: Round [60] log likelihood: -5633.920135 EM: Round [61] log likelihood: -5633.901026 EM: Round [62] log likelihood: -5633.882559 EM: Round [63] log likelihood: -5633.864703 EM: Round [64] log likelihood: -5633.847427 EM: Round [65] log likelihood: -5633.830704 EM: Round [66] log likelihood: -5633.814508 EM: Round [67] log likelihood: -5633.798813 EM: Round [68] log likelihood: -5633.783597 EM: Round [69] log likelihood: -5633.768837 EM: Round [70] log likelihood: -5633.754511 EM: Round [71] log likelihood: -5633.740600 EM: Round [72] log likelihood: -5633.727086 EM: Round [73] log likelihood: -5633.713950 EM: Round [74] log likelihood: -5633.701175 EM: Round [75] log likelihood: -5633.688747 EM: Round [76] log likelihood: -5633.676648 EM: Round [77] log likelihood: -5633.664866 EM: Round [78] log likelihood: -5633.653387 EM: Round [79] log likelihood: -5633.642197 EM: Round [80] log likelihood: -5633.631286 EM: Round [81] log likelihood: -5633.620640 EM: Round [82] log likelihood: -5633.610250 EM: Round [83] log likelihood: -5633.600104 EM: Round [84] log likelihood: -5633.590194 EM: Round [85] log likelihood: -5633.580509 EM: Round [86] log likelihood: -5633.571041 EM: Round [87] log likelihood: -5633.561781 EM: Round [88] log likelihood: -5633.552722 EM: Round [89] log likelihood: -5633.543855 EM: Round [90] log likelihood: -5633.535174 EM: Round [91] log likelihood: -5633.526672 EM: Round [92] log likelihood: -5633.518342 EM: Round [93] log likelihood: -5633.510177 EM: Round [94] log likelihood: -5633.502173 EM: Round [95] log likelihood: -5633.494323 EM: Round [96] log likelihood: -5633.486623 EM: Round [97] log likelihood: -5633.479066 EM: Round [98] log likelihood: -5633.471648 EM: Round [99] log likelihood: -5633.464365 EM: Round [100] log likelihood: -5633.457211 EM: Round [101] log likelihood: -5633.450184 EM: Round [102] log likelihood: -5633.443278 EM: Round [103] log likelihood: -5633.436491 EM: Round [104] log likelihood: -5633.429817 EM: Round [105] log likelihood: -5633.423255 EM: Round [106] log likelihood: -5633.416799 EM: Round [107] log likelihood: -5633.410448 EM: Round [108] log likelihood: -5633.404199 EM: Round [109] log likelihood: -5633.398047 EM: Round [110] log likelihood: -5633.391991 EM: Round [111] log likelihood: -5633.386028 EM: Round [112] log likelihood: -5633.380156 EM: Round [113] log likelihood: -5633.374371 EM: Round [114] log likelihood: -5633.368671 EM: Round [115] log likelihood: -5633.363055 EM: Round [116] log likelihood: -5633.357519 EM: Round [117] log likelihood: -5633.352063 EM: Round [118] log likelihood: -5633.346683 EM: Round [119] log likelihood: -5633.341379 EM: Round [120] log likelihood: -5633.336148 EM: Round [121] log likelihood: -5633.330988 EM: Round [122] log likelihood: -5633.325898 EM: Round [123] log likelihood: -5633.320876 EM: Round [124] log likelihood: -5633.315921 EM: Round [125] log likelihood: -5633.311030 EM: Round [126] log likelihood: -5633.306203 EM: Round [127] log likelihood: -5633.301439 EM: Round [128] log likelihood: -5633.296735 EM: Round [129] log likelihood: -5633.292090 EM: Round [130] log likelihood: -5633.287504 EM: Round [131] log likelihood: -5633.282975 EM: Round [132] log likelihood: -5633.278501 EM: Round [133] log likelihood: -5633.274083 EM: Round [134] log likelihood: -5633.269717 EM: Round [135] log likelihood: -5633.265405 EM: Round [136] log likelihood: -5633.261144 EM: Round [137] log likelihood: -5633.256933 EM: Round [138] log likelihood: -5633.252772 EM: Round [139] log likelihood: -5633.248659 EM: Round [140] log likelihood: -5633.244594 EM: Round [141] log likelihood: -5633.240576 EM: Round [142] log likelihood: -5633.236604 EM: Round [143] log likelihood: -5633.232677 EM: Round [144] log likelihood: -5633.228794 EM: Round [145] log likelihood: -5633.224954 EM: Round [146] log likelihood: -5633.221158 EM: Round [147] log likelihood: -5633.217403 EM: Round [148] log likelihood: -5633.213690 EM: Round [149] log likelihood: -5633.210018 EM: Round [150] log likelihood: -5633.206385 EM: Round [151] log likelihood: -5633.202792 EM: Round [152] log likelihood: -5633.199237 EM: Round [153] log likelihood: -5633.195721 EM: Round [154] log likelihood: -5633.192242 EM: Round [155] log likelihood: -5633.188799 EM: Round [156] log likelihood: -5633.185393 EM: Round [157] log likelihood: -5633.182023 EM: Round [158] log likelihood: -5633.178687 EM: Round [159] log likelihood: -5633.175387 EM: Round [160] log likelihood: -5633.172120 EM: Round [161] log likelihood: -5633.168887 EM: Round [162] log likelihood: -5633.165687 EM: Round [163] log likelihood: -5633.162519 EM: Round [164] log likelihood: -5633.159384 EM: Round [165] log likelihood: -5633.156280 EM: Round [166] log likelihood: -5633.153207 EM: Round [167] log likelihood: -5633.150165 EM: Round [168] log likelihood: -5633.147154 EM: Round [169] log likelihood: -5633.144172 EM: Round [170] log likelihood: -5633.141219 EM: Round [171] log likelihood: -5633.138296 EM: Round [172] log likelihood: -5633.135401 EM: Round [173] log likelihood: -5633.132535 EM: Round [174] log likelihood: -5633.129696 EM: Round [175] log likelihood: -5633.126884 EM: Round [176] log likelihood: -5633.124100 EM: Round [177] log likelihood: -5633.121343 EM: Round [178] log likelihood: -5633.118612 EM: Round [179] log likelihood: -5633.115907 EM: Round [180] log likelihood: -5633.113227 EM: Round [181] log likelihood: -5633.110573 EM: Round [182] log likelihood: -5633.107944 EM: Round [183] log likelihood: -5633.105340 EM: Round [184] log likelihood: -5633.102760 EM: Round [185] log likelihood: -5633.100204 EM: Round [186] log likelihood: -5633.097672 EM: Round [187] log likelihood: -5633.095163 EM: Round [188] log likelihood: -5633.092677 EM: Round [189] log likelihood: -5633.090214 EM: Round [190] log likelihood: -5633.087774 EM: Round [191] log likelihood: -5633.085356 EM: Round [192] log likelihood: -5633.082961 EM: Round [193] log likelihood: -5633.080586 EM: Round [194] log likelihood: -5633.078234 EM: Round [195] log likelihood: -5633.075902 EM: Round [196] log likelihood: -5633.073592 EM: Round [197] log likelihood: -5633.071302 EM: Round [198] log likelihood: -5633.069033 EM: Round [199] log likelihood: -5633.066784 EM: Round [200] log likelihood: -5633.064555 EM: Round [201] log likelihood: -5633.062345 EM: Round [202] log likelihood: -5633.060155 EM: Round [203] log likelihood: -5633.057985 EM: Round [204] log likelihood: -5633.055833 EM: Round [205] log likelihood: -5633.053700 EM: Round [206] log likelihood: -5633.051586 EM: Round [207] log likelihood: -5633.049490 EM: Round [208] log likelihood: -5633.047413 EM: Round [209] log likelihood: -5633.045353 EM: Round [210] log likelihood: -5633.043311 EM: Round [211] log likelihood: -5633.041287 EM: Round [212] log likelihood: -5633.039280 EM: Round [213] log likelihood: -5633.037290 EM: Round [214] log likelihood: -5633.035317 EM: Round [215] log likelihood: -5633.033361 EM: Round [216] log likelihood: -5633.031422 EM: Round [217] log likelihood: -5633.029498 EM: Round [218] log likelihood: -5633.027591 EM: Round [219] log likelihood: -5633.025700 EM: Round [220] log likelihood: -5633.023825 EM: Round [221] log likelihood: -5633.021966 EM: Round [222] log likelihood: -5633.020122 EM: Round [223] log likelihood: -5633.018293 EM: Round [224] log likelihood: -5633.016480 EM: Round [225] log likelihood: -5633.014682 EM: Round [226] log likelihood: -5633.012898 EM: Round [227] log likelihood: -5633.011129 EM: Round [228] log likelihood: -5633.009375 EM: Round [229] log likelihood: -5633.007634 EM: Round [230] log likelihood: -5633.005909 EM: Round [231] log likelihood: -5633.004197 EM: Round [232] log likelihood: -5633.002499 EM: Round [233] log likelihood: -5633.000815 EM: Round [234] log likelihood: -5632.999144 EM: Round [235] log likelihood: -5632.997487 EM: Round [236] log likelihood: -5632.995843 EM: Round [237] log likelihood: -5632.994212 EM: Round [238] log likelihood: -5632.992595 EM: Round [239] log likelihood: -5632.990990 EM: Round [240] log likelihood: -5632.989398 EM: Round [241] log likelihood: -5632.987819 EM: Round [242] log likelihood: -5632.986252 EM: Round [243] log likelihood: -5632.984697 EM: Round [244] log likelihood: -5632.983155 EM: Round [245] log likelihood: -5632.981625 EM: Round [246] log likelihood: -5632.980107 EM: Round [247] log likelihood: -5632.978600 EM: Round [248] log likelihood: -5632.977106 EM: Round [249] log likelihood: -5632.975623 EM: Round [250] log likelihood: -5632.974151 EM: Round [251] log likelihood: -5632.972691 EM: Round [252] log likelihood: -5632.971242 EM: Round [253] log likelihood: -5632.969805 EM: Round [254] log likelihood: -5632.968378 EM: Round [255] log likelihood: -5632.966962 EM: Round [256] log likelihood: -5632.965558 EM: Round [257] log likelihood: -5632.964163 EM: Round [258] log likelihood: -5632.962780 EM: Round [259] log likelihood: -5632.961407 EM: Round [260] log likelihood: -5632.960044 EM: Round [261] log likelihood: -5632.958692 EM: Round [262] log likelihood: -5632.957350 EM: Round [263] log likelihood: -5632.956017 EM: Round [264] log likelihood: -5632.954695 EM: Round [265] log likelihood: -5632.953383 EM: Round [266] log likelihood: -5632.952081 EM: Round [267] log likelihood: -5632.950788 EM: Round [268] log likelihood: -5632.949505 EM: Round [269] log likelihood: -5632.948231 EM: Round [270] log likelihood: -5632.946967 EM: Round [271] log likelihood: -5632.945712 EM: Round [272] log likelihood: -5632.944466 EM: Round [273] log likelihood: -5632.943230 EM: Round [274] log likelihood: -5632.942002 EM: Round [275] log likelihood: -5632.940784 EM: Round [276] log likelihood: -5632.939574 EM: Round [277] log likelihood: -5632.938373 EM: Round [278] log likelihood: -5632.937181 EM: Round [279] log likelihood: -5632.935997 EM: Round [280] log likelihood: -5632.934822 EM: Round [281] log likelihood: -5632.933656 EM: Round [282] log likelihood: -5632.932498 EM: Round [283] log likelihood: -5632.931348 EM: Round [284] log likelihood: -5632.930206 EM: Round [285] log likelihood: -5632.929073 EM: Round [286] log likelihood: -5632.927948 EM: Round [287] log likelihood: -5632.926830 EM: Round [288] log likelihood: -5632.925721 EM: Round [289] log likelihood: -5632.924619 EM: Round [290] log likelihood: -5632.923525 EM: Round [291] log likelihood: -5632.922439 EM: Round [292] log likelihood: -5632.921361 EM: Round [293] log likelihood: -5632.920290 EM: Round [294] log likelihood: -5632.919226 EM: Round [295] log likelihood: -5632.918170 EM: Round [296] log likelihood: -5632.917122 EM: Round [297] log likelihood: -5632.916080 EM: Round [298] log likelihood: -5632.915046 EM: Round [299] log likelihood: -5632.914019 EM: Round [300] log likelihood: -5632.912999 EM: Round [301] log likelihood: -5632.911986 EM: Round [302] log likelihood: -5632.910980 EM: Round [303] log likelihood: -5632.909981 EM: Round [304] log likelihood: -5632.908989 EM: Round [305] log likelihood: -5632.908004 EM: Round [306] log likelihood: -5632.907025 EM: Round [307] log likelihood: -5632.906053 EM: Round [308] log likelihood: -5632.905087 EM: Round [309] log likelihood: -5632.904129 EM: Round [310] log likelihood: -5632.903176 EM: Round [311] log likelihood: -5632.902230 EM: Round [312] log likelihood: -5632.901290 EM: Round [313] log likelihood: -5632.900357 EM: Round [314] log likelihood: -5632.899430 EM: Round [315] log likelihood: -5632.898509 EM: Round [316] log likelihood: -5632.897594 EM: Round [317] log likelihood: -5632.896686 EM: Round [318] log likelihood: -5632.895783 EM: Round [319] log likelihood: -5632.894886 EM: Round [320] log likelihood: -5632.893996 EM: Round [321] log likelihood: -5632.893111 EM: Round [322] log likelihood: -5632.892232 EM: Round [323] log likelihood: -5632.891358 EM: Round [324] log likelihood: -5632.890491 EM: Round [325] log likelihood: -5632.889629 EM: Round [326] log likelihood: -5632.888773 EM: Round [327] log likelihood: -5632.887922 EM: Round [328] log likelihood: -5632.887077 EM: Round [329] log likelihood: -5632.886237 EM: Round [330] log likelihood: -5632.885403 EM: Round [331] log likelihood: -5632.884574 EM: Round [332] log likelihood: -5632.883751 EM: Round [333] log likelihood: -5632.882933 EM: Round [334] log likelihood: -5632.882120 EM: Round [335] log likelihood: -5632.881312 EM: Round [336] log likelihood: -5632.880510 EM: Round [337] log likelihood: -5632.879712 EM: Round [338] log 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likelihood: -5632.862692 EM: Round [361] log likelihood: -5632.862006 EM: Round [362] log likelihood: -5632.861324 EM: Round [363] log likelihood: -5632.860646 EM: Round [364] log likelihood: -5632.859972 EM: Round [365] log likelihood: -5632.859302 EM: Round [366] log likelihood: -5632.858636 EM: Round [367] log likelihood: -5632.857974 EM: Round [368] log likelihood: -5632.857316 EM: Round [369] log likelihood: -5632.856662 EM: Round [370] log likelihood: -5632.856012 EM: Round [371] log likelihood: -5632.855366 EM: Round [372] log likelihood: -5632.854724 EM: Round [373] log likelihood: -5632.854086 EM: Round [374] log likelihood: -5632.853451 EM: Round [375] log likelihood: -5632.852820 EM: Round [376] log likelihood: -5632.852193 EM: Round [377] log likelihood: -5632.851569 EM: Round [378] log likelihood: -5632.850950 EM: Round [379] log likelihood: -5632.850334 EM: Round [380] log likelihood: -5632.849721 EM: Round [381] log likelihood: -5632.849112 EM: Round [382] log 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likelihood: -5632.798789 EM: Round [493] log likelihood: -5632.798456 EM: Round [494] log likelihood: -5632.798124 EM: Round [495] log likelihood: -5632.797794 EM: Round [496] log likelihood: -5632.797466 EM: Round [497] log likelihood: -5632.797139 EM: Round [498] log likelihood: -5632.796814 EM: Round [499] log likelihood: -5632.796490 EM: Round [500] log likelihood: -5632.796168 EM: Round [501] log likelihood: -5632.795848 EM: Round [502] log likelihood: -5632.795529 EM: Round [503] log likelihood: -5632.795212 EM: Round [504] log likelihood: -5632.794896 EM: Round [505] log likelihood: -5632.794582 EM: Round [506] log likelihood: -5632.794270 EM: Round [507] log likelihood: -5632.793958 EM: Round [508] log likelihood: -5632.793649 EM: Round [509] log likelihood: -5632.793341 EM: Round [510] log likelihood: -5632.793034 EM: Round [511] log likelihood: -5632.792729 EM: Round [512] log likelihood: -5632.792426 EM: Round [513] log likelihood: -5632.792123 EM: Round [514] log likelihood: -5632.791823 EM: Round [515] log likelihood: -5632.791524 EM: Round [516] log likelihood: -5632.791226 EM: Round [517] log likelihood: -5632.790929 EM: Round [518] log likelihood: -5632.790635 EM: Round [519] log likelihood: -5632.790341 EM: Round [520] log likelihood: -5632.790049 EM: Round [521] log likelihood: -5632.789758 EM: Round [522] log likelihood: -5632.789469 EM: Round [523] log likelihood: -5632.789181 EM: Round [524] log likelihood: -5632.788895 EM: Round [525] log likelihood: -5632.788610 EM: Round [526] log likelihood: -5632.788326 EM: Round [527] log likelihood: -5632.788044 EM: Round [528] log likelihood: -5632.787762 EM: Round [529] log likelihood: -5632.787483 EM: Round [530] log likelihood: -5632.787204 EM: Round [531] log likelihood: -5632.786927 EM: Round [532] log likelihood: -5632.786652 EM: Round [533] log likelihood: -5632.786377 EM: Round [534] log likelihood: -5632.786104 EM: Round [535] log likelihood: -5632.785832 EM: Round [536] log likelihood: -5632.785562 EM: Round [537] log likelihood: -5632.785292 EM: Round [538] log likelihood: -5632.785024 EM: Round [539] log likelihood: -5632.784758 EM: Round [540] log likelihood: -5632.784492 EM: Round [541] log likelihood: -5632.784228 EM: Round [542] log likelihood: -5632.783965 EM: Round [543] log likelihood: -5632.783703 EM: Round [544] log likelihood: -5632.783443 EM: Round [545] log likelihood: -5632.783184 EM: Round [546] log likelihood: -5632.782926 EM: Round [547] log likelihood: -5632.782669 EM: Round [548] log likelihood: -5632.782413 EM: Round [549] log likelihood: -5632.782159 EM: Round [550] log likelihood: -5632.781905 EM: Round [551] log likelihood: -5632.781653 EM: Round [552] log likelihood: -5632.781402 EM: Round [553] log likelihood: -5632.781153 EM: Round [554] log likelihood: -5632.780904 EM: Round [555] log likelihood: -5632.780657 EM: Round [556] log likelihood: -5632.780410 EM: Round [557] log likelihood: -5632.780165 EM: Round [558] log likelihood: -5632.779921 EM: Round [559] log likelihood: -5632.779678 EM: Round [560] log likelihood: -5632.779437 EM: Round [561] log likelihood: -5632.779196 EM: Round [562] log likelihood: -5632.778957 EM: Round [563] log likelihood: -5632.778718 EM: Round [564] log likelihood: -5632.778481 EM: Round [565] log likelihood: -5632.778245 EM: Round [566] log likelihood: -5632.778010 EM: Round [567] log likelihood: -5632.777776 EM: Round [568] log likelihood: -5632.777543 EM: Round [569] log likelihood: -5632.777311 EM: Round [570] log likelihood: -5632.777080 EM: Round [571] log likelihood: -5632.776850 EM: Round [572] log likelihood: -5632.776622 EM: Round [573] log likelihood: -5632.776394 EM: Round [574] log likelihood: -5632.776167 EM: Round [575] log likelihood: -5632.775942 EM: Round [576] log likelihood: -5632.775717 EM: Round [577] log likelihood: -5632.775494 EM: Round [578] log likelihood: -5632.775271 EM: Round [579] log likelihood: -5632.775050 EM: Round [580] log likelihood: -5632.774830 EM: Round [581] log likelihood: -5632.774610 EM: Round [582] log likelihood: -5632.774392 EM: Round [583] log likelihood: -5632.774174 EM: Round [584] log likelihood: -5632.773958 EM: Round [585] log likelihood: -5632.773742 EM: Round [586] log likelihood: -5632.773528 EM: Round [587] log likelihood: -5632.773314 EM: Round [588] log likelihood: -5632.773102 EM: Round [589] log likelihood: -5632.772890 EM: Round [590] log likelihood: -5632.772679 EM: Round [591] log likelihood: -5632.772470 EM: Round [592] log likelihood: -5632.772261 EM: Round [593] log likelihood: -5632.772053 EM: Round [594] log likelihood: -5632.771846 EM: Round [595] log likelihood: -5632.771640 EM: Round [596] log likelihood: -5632.771435 EM: Round [597] log likelihood: -5632.771231 EM: Round [598] log likelihood: -5632.771028 EM: Round [599] log likelihood: -5632.770826 EM: Round [600] log likelihood: -5632.770625 EM: Round [601] log likelihood: -5632.770424 EM: Round [602] log likelihood: -5632.770225 EM: Round [603] log likelihood: -5632.770026 EM: Round [604] log likelihood: -5632.769828 EM: Round [605] log likelihood: -5632.769631 EM: Round [606] log likelihood: -5632.769435 EM: Round [607] log likelihood: -5632.769240 EM: Round [608] log likelihood: -5632.769046 EM: Round [609] log likelihood: -5632.768853 EM: Round [610] log likelihood: -5632.768660 EM: Round [611] log likelihood: -5632.768469 EM: Round [612] log likelihood: -5632.768278 EM: Round [613] log likelihood: -5632.768088 EM: Round [614] log likelihood: -5632.767899 EM: Round [615] log likelihood: -5632.767711 EM: Round [616] log likelihood: -5632.767523 EM: Round [617] log likelihood: -5632.767337 EM: Round [618] log likelihood: -5632.767151 EM: Round [619] log likelihood: -5632.766966 EM: Round [620] log likelihood: -5632.766782 EM: Round [621] log likelihood: -5632.766599 EM: Round [622] log likelihood: -5632.766416 EM: Round [623] log likelihood: -5632.766234 EM: Round [624] log likelihood: -5632.766054 EM: Round [625] log likelihood: -5632.765874 EM: Round [626] log likelihood: -5632.765694 EM: Round [627] log likelihood: -5632.765516 EM: Round [628] log likelihood: -5632.765338 EM: Round [629] log likelihood: -5632.765161 EM: Round [630] log likelihood: -5632.764985 EM: Round [631] log likelihood: -5632.764810 EM: Round [632] log likelihood: -5632.764635 EM: Round [633] log likelihood: -5632.764461 EM: Round [634] log likelihood: -5632.764288 EM: Round [635] log likelihood: -5632.764116 EM: Round [636] log likelihood: -5632.763945 EM: Round [637] log likelihood: -5632.763774 EM: Round [638] log likelihood: -5632.763604 EM: Round [639] log likelihood: -5632.763434 EM: Round [640] log likelihood: -5632.763266 EM: Round [641] log likelihood: -5632.763098 EM: Round [642] log likelihood: -5632.762931 EM: Round [643] log likelihood: -5632.762765 EM: Round [644] log likelihood: -5632.762599 EM: Round [645] log likelihood: -5632.762434 EM: Round [646] log likelihood: -5632.762270 EM: Round [647] log likelihood: -5632.762107 EM: Round [648] log likelihood: -5632.761944 EM: Round [649] log likelihood: -5632.761782 EM: Round [650] log likelihood: -5632.761621 EM: Round [651] log likelihood: -5632.761460 EM: Round [652] log likelihood: -5632.761300 EM: Round [653] log likelihood: -5632.761141 EM: Round [654] log likelihood: -5632.760982 EM: Round [655] log likelihood: -5632.760825 EM: Round [656] log likelihood: -5632.760668 EM: Round [657] log likelihood: -5632.760511 EM: Round [658] log likelihood: -5632.760355 EM: Round [659] log likelihood: -5632.760200 EM: Round [660] log likelihood: -5632.760046 EM: Round [661] log likelihood: -5632.759892 EM: Round [662] log likelihood: -5632.759739 EM: Round [663] log likelihood: -5632.759587 EM: Round [664] log likelihood: -5632.759435 EM: Round [665] log likelihood: -5632.759284 EM: Round [666] log likelihood: -5632.759133 EM: Round [667] log likelihood: -5632.758983 EM: Round [668] log likelihood: -5632.758834 EM: Round [669] log likelihood: -5632.758686 EM: Round [670] log likelihood: -5632.758538 EM: Round [671] log likelihood: -5632.758391 EM: Round [672] log likelihood: -5632.758244 EM: Round [673] log likelihood: -5632.758098 EM: Round [674] log likelihood: -5632.757953 EM: Round [675] log likelihood: -5632.757808 EM: Round [676] log likelihood: -5632.757664 EM: Round [677] log likelihood: -5632.757521 EM: Round [678] log likelihood: -5632.757378 EM: Round [679] log likelihood: -5632.757236 EM: Round [680] log likelihood: -5632.757094 EM: Round [681] log likelihood: -5632.756953 EM: Round [682] log likelihood: -5632.756812 EM: Round [683] log likelihood: -5632.756673 EM: Round [684] log likelihood: -5632.756533 EM: Round [685] log likelihood: -5632.756395 EM: Round [686] log likelihood: -5632.756257 EM: Round [687] log likelihood: -5632.756119 EM: Round [688] log likelihood: -5632.755983 EM: Round [689] log likelihood: -5632.755846 EM: Round [690] log likelihood: -5632.755711 EM: Round [691] log likelihood: -5632.755576 EM: Round [692] log likelihood: -5632.755441 EM: Round [693] log likelihood: -5632.755307 EM: Round [694] log likelihood: -5632.755174 EM: Round [695] log likelihood: -5632.755041 EM: Round [696] log likelihood: -5632.754909 EM: Round [697] log likelihood: -5632.754777 EM: Round [698] log likelihood: -5632.754646 EM: Round [699] log likelihood: -5632.754516 EM: Round [700] log likelihood: -5632.754386 EM: Round [701] log likelihood: -5632.754256 EM: Round [702] log likelihood: -5632.754127 EM: Round [703] log likelihood: -5632.753999 EM: Round [704] log likelihood: -5632.753871 EM: Round [705] log likelihood: -5632.753744 EM: Round [706] log likelihood: -5632.753617 EM: Round [707] log likelihood: -5632.753491 EM: Round [708] log likelihood: -5632.753366 EM: Round [709] log likelihood: -5632.753241 EM: Round [710] log likelihood: -5632.753116 EM: Round [711] log likelihood: -5632.752992 EM: Round [712] log likelihood: -5632.752869 EM: Round [713] log likelihood: -5632.752746 EM: Round [714] log likelihood: -5632.752623 EM: Round [715] log likelihood: -5632.752501 EM: Round [716] log likelihood: -5632.752380 EM: Round [717] log likelihood: -5632.752259 EM: Round [718] log likelihood: -5632.752139 EM: Round [719] log likelihood: -5632.752019 EM: Round [720] log likelihood: -5632.751899 EM: Round [721] log likelihood: -5632.751781 EM: Round [722] log likelihood: -5632.751662 EM: Round [723] log likelihood: -5632.751544 EM: Round [724] log likelihood: -5632.751427 EM: Round [725] log likelihood: -5632.751310 EM: Round [726] log likelihood: -5632.751194 EM: Round [727] log likelihood: -5632.751078 EM: Round [728] log likelihood: -5632.750963 EM: Round [729] log likelihood: -5632.750848 EM: Round [730] log likelihood: -5632.750733 EM: Round [731] log likelihood: -5632.750619 EM: Round [732] log likelihood: -5632.750506 EM: Round [733] log likelihood: -5632.750393 EM: Round [734] log likelihood: -5632.750281 EM: Round [735] log likelihood: -5632.750169 EM: Round [736] log likelihood: -5632.750057 EM: Round [737] log likelihood: -5632.749946 EM: Round [738] log likelihood: -5632.749835 EM: Round [739] log likelihood: -5632.749725 EM: Round [740] log likelihood: -5632.749615 EM: Round [741] log likelihood: -5632.749506 EM: Round [742] log likelihood: -5632.749398 EM: Round [743] log likelihood: -5632.749289 EM: Round [744] log likelihood: -5632.749181 EM: Round [745] log likelihood: -5632.749074 EM: Round [746] log likelihood: -5632.748967 EM: Round [747] log likelihood: -5632.748861 EM: Round [748] log likelihood: -5632.748755 EM: Round [749] log likelihood: -5632.748649 EM: Round [750] log likelihood: -5632.748544 EM: Round [751] log likelihood: -5632.748439 EM: Round [752] log likelihood: -5632.748335 EM: Round [753] log likelihood: -5632.748231 EM: Round [754] log likelihood: -5632.748128 EM: Round [755] log likelihood: -5632.748025 EM: Round [756] log likelihood: -5632.747922 EM: Round [757] log likelihood: -5632.747820 EM: Round [758] log likelihood: -5632.747718 EM: Round [759] log likelihood: -5632.747617 EM: Round [760] log likelihood: -5632.747516 EM: Round [761] log likelihood: -5632.747416 EM: Round [762] log likelihood: -5632.747316 EM: Stopping iterations at round 762 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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam" Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam into /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.read_coords > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.FusionJuncSpan Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.consolidated.bam.frag_coords > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.gff3 > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa > /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir -done, see /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -4329.281678 EM: Round [1] log likelihood: -4329.012271 EM: Round [2] log likelihood: -4329.008266 EM: Round [3] log likelihood: -4329.004374 EM: Round [4] log likelihood: -4329.000513 EM: Round [5] log likelihood: -4328.996682 EM: Round [6] log likelihood: -4328.992880 EM: Round [7] log likelihood: -4328.989108 EM: Round [8] log likelihood: -4328.985366 EM: Round [9] log likelihood: -4328.981652 EM: Round [10] log likelihood: -4328.977966 EM: Round [11] log likelihood: -4328.974309 EM: Round [12] log likelihood: -4328.970680 EM: Round [13] log likelihood: -4328.967078 EM: Round [14] log likelihood: -4328.963503 EM: Round [15] log likelihood: -4328.959956 EM: Round [16] log likelihood: -4328.956435 EM: Round [17] log likelihood: -4328.952940 EM: Round [18] log likelihood: -4328.949471 EM: Round [19] log likelihood: -4328.946028 EM: Round [20] log likelihood: -4328.942611 EM: Round [21] log likelihood: -4328.939219 EM: Round [22] log likelihood: -4328.935852 EM: Round [23] log likelihood: -4328.932509 EM: Round [24] log likelihood: -4328.929191 EM: Round [25] log likelihood: -4328.925897 EM: Round [26] log likelihood: -4328.922627 EM: Round [27] log likelihood: -4328.919381 EM: Round [28] log likelihood: -4328.916158 EM: Round [29] log likelihood: -4328.912958 EM: Round [30] log likelihood: -4328.909781 EM: Round [31] log likelihood: -4328.906627 EM: Round [32] log likelihood: -4328.903495 EM: Round [33] log likelihood: -4328.900385 EM: Round [34] log likelihood: -4328.897298 EM: Round [35] log likelihood: -4328.894232 EM: Round [36] log likelihood: -4328.891188 EM: Round [37] log likelihood: -4328.888165 EM: Round [38] log likelihood: -4328.885163 EM: Round [39] log likelihood: -4328.882182 EM: Round [40] log likelihood: -4328.879222 EM: Round [41] log likelihood: -4328.876283 EM: Round [42] log likelihood: -4328.873363 EM: Round [43] log likelihood: -4328.870464 EM: Round [44] log likelihood: -4328.867585 EM: Round [45] log likelihood: -4328.864725 EM: Round [46] log likelihood: -4328.861885 EM: Round [47] log likelihood: -4328.859065 EM: Round [48] log likelihood: -4328.856263 EM: Round [49] log likelihood: -4328.853481 EM: Round [50] log likelihood: -4328.850717 EM: Round [51] log likelihood: -4328.847972 EM: Round [52] log likelihood: -4328.845245 EM: Round [53] log likelihood: -4328.842536 EM: Round [54] log likelihood: -4328.839846 EM: Round [55] log likelihood: -4328.837174 EM: Round [56] log likelihood: -4328.834519 EM: Round [57] log likelihood: -4328.831882 EM: Round [58] log likelihood: -4328.829262 EM: Round [59] log likelihood: -4328.826660 EM: Round [60] log likelihood: -4328.824074 EM: Round [61] log likelihood: -4328.821506 EM: Round [62] log likelihood: -4328.818954 EM: Round [63] log likelihood: -4328.816419 EM: Round [64] log likelihood: -4328.813901 EM: Round [65] log likelihood: -4328.811399 EM: Round [66] log likelihood: -4328.808913 EM: Round [67] log likelihood: -4328.806443 EM: Round [68] log likelihood: -4328.803989 EM: Round [69] log likelihood: -4328.801551 EM: Round [70] log likelihood: -4328.799129 EM: Round [71] log likelihood: -4328.796722 EM: Round [72] log likelihood: -4328.794330 EM: Round [73] log likelihood: -4328.791953 EM: Round [74] log likelihood: -4328.789592 EM: Round [75] log likelihood: -4328.787246 EM: Round [76] log likelihood: -4328.784914 EM: Round [77] log likelihood: -4328.782597 EM: Round [78] log likelihood: -4328.780295 EM: Round [79] log likelihood: -4328.778007 EM: Round [80] log likelihood: -4328.775734 EM: Round [81] log likelihood: -4328.773474 EM: Round [82] log likelihood: -4328.771229 EM: Round [83] log likelihood: -4328.768998 EM: Round [84] log likelihood: -4328.766781 EM: Round [85] log likelihood: -4328.764577 EM: Round [86] log likelihood: -4328.762387 EM: Round [87] log likelihood: -4328.760210 EM: Round [88] log likelihood: -4328.758047 EM: Round [89] log likelihood: -4328.755897 EM: Round [90] log likelihood: -4328.753761 EM: Round [91] log likelihood: -4328.751637 EM: Round [92] log likelihood: -4328.749526 EM: Round [93] log likelihood: -4328.747428 EM: Round [94] log likelihood: -4328.745343 EM: Round [95] log likelihood: -4328.743271 EM: Round [96] log likelihood: -4328.741211 EM: Round [97] log likelihood: -4328.739164 EM: Round [98] log likelihood: -4328.737128 EM: Round [99] log likelihood: -4328.735105 EM: Round [100] log likelihood: -4328.733095 EM: Round [101] log likelihood: -4328.731096 EM: Round [102] log likelihood: -4328.729109 EM: Round [103] log likelihood: -4328.727134 EM: Round [104] log likelihood: -4328.725171 EM: Round [105] log likelihood: -4328.723220 EM: Round [106] log likelihood: -4328.721280 EM: Round [107] log likelihood: -4328.719351 EM: Round [108] log likelihood: -4328.717434 EM: Round [109] log likelihood: -4328.715528 EM: Round [110] log likelihood: -4328.713634 EM: Round [111] log likelihood: -4328.711750 EM: Round [112] log likelihood: -4328.709878 EM: Round [113] log likelihood: -4328.708017 EM: Round [114] log likelihood: -4328.706166 EM: Round [115] log likelihood: -4328.704326 EM: Round [116] log likelihood: -4328.702497 EM: Round [117] log likelihood: -4328.700679 EM: Round [118] log likelihood: -4328.698871 EM: Round [119] log likelihood: -4328.697074 EM: Round [120] log likelihood: -4328.695287 EM: Round [121] log likelihood: -4328.693510 EM: Round [122] log likelihood: -4328.691743 EM: Round [123] log likelihood: -4328.689987 EM: Round [124] log likelihood: -4328.688241 EM: Round [125] log likelihood: -4328.686504 EM: Round [126] log likelihood: -4328.684778 EM: Round [127] log likelihood: -4328.683062 EM: Round [128] log likelihood: -4328.681355 EM: Round [129] log likelihood: -4328.679658 EM: Round [130] log likelihood: -4328.677970 EM: Round [131] log likelihood: -4328.676293 EM: Round [132] log likelihood: -4328.674624 EM: Round [133] log likelihood: -4328.672965 EM: Round [134] log likelihood: -4328.671316 EM: Round [135] log likelihood: -4328.669676 EM: Round [136] log likelihood: -4328.668045 EM: Round [137] log likelihood: -4328.666423 EM: Round [138] log likelihood: -4328.664810 EM: Round [139] log likelihood: -4328.663206 EM: Round [140] log likelihood: -4328.661611 EM: Round [141] log likelihood: -4328.660025 EM: Round [142] log likelihood: -4328.658448 EM: Round [143] log likelihood: -4328.656880 EM: Round [144] log likelihood: -4328.655320 EM: Round [145] log likelihood: -4328.653769 EM: Round [146] log likelihood: -4328.652227 EM: Round [147] log likelihood: -4328.650693 EM: Round [148] log likelihood: -4328.649168 EM: Round [149] log likelihood: -4328.647651 EM: Round [150] log likelihood: -4328.646142 EM: Round [151] log likelihood: -4328.644642 EM: Round [152] log likelihood: -4328.643150 EM: Round [153] log likelihood: -4328.641666 EM: Round [154] log likelihood: -4328.640190 EM: Round [155] log likelihood: -4328.638722 EM: Round [156] log likelihood: -4328.637262 EM: Round [157] log likelihood: -4328.635810 EM: Round [158] log likelihood: -4328.634366 EM: Round [159] log likelihood: -4328.632930 EM: Round [160] log likelihood: -4328.631502 EM: Round [161] log likelihood: -4328.630081 EM: Round [162] log likelihood: -4328.628668 EM: Round [163] log likelihood: -4328.627263 EM: Round [164] log likelihood: -4328.625865 EM: Round [165] log likelihood: -4328.624475 EM: Round [166] log likelihood: -4328.623092 EM: Round [167] log likelihood: -4328.621717 EM: Round [168] log likelihood: -4328.620349 EM: Round [169] log likelihood: -4328.618988 EM: Round [170] log likelihood: -4328.617635 EM: Round [171] log likelihood: -4328.616289 EM: Round [172] log likelihood: -4328.614950 EM: Round [173] log likelihood: -4328.613618 EM: Round [174] log likelihood: -4328.612293 EM: Round [175] log likelihood: -4328.610975 EM: Round [176] log likelihood: -4328.609664 EM: Round [177] log likelihood: -4328.608361 EM: Round [178] log likelihood: -4328.607064 EM: Round [179] log likelihood: -4328.605774 EM: Round [180] log likelihood: -4328.604490 EM: Round [181] log likelihood: -4328.603214 EM: Round [182] log likelihood: -4328.601944 EM: Round [183] log likelihood: -4328.600681 EM: Round [184] log likelihood: -4328.599424 EM: Round [185] log likelihood: -4328.598175 EM: Round [186] log likelihood: -4328.596931 EM: Round [187] log likelihood: -4328.595694 EM: Round [188] log likelihood: -4328.594464 EM: Round [189] log likelihood: -4328.593240 EM: Round [190] log likelihood: -4328.592022 EM: Round [191] log likelihood: -4328.590811 EM: Round [192] log likelihood: -4328.589606 EM: Round [193] log likelihood: -4328.588407 EM: Round [194] log likelihood: -4328.587215 EM: Round [195] log likelihood: -4328.586029 EM: Round [196] log likelihood: -4328.584848 EM: Round [197] log likelihood: -4328.583674 EM: Round [198] log likelihood: -4328.582506 EM: Round [199] log likelihood: -4328.581344 EM: Round [200] log likelihood: -4328.580188 EM: Round [201] log likelihood: -4328.579038 EM: Round [202] log likelihood: -4328.577894 EM: Round [203] log likelihood: -4328.576755 EM: Round [204] log likelihood: -4328.575623 EM: Round [205] log likelihood: -4328.574496 EM: Round [206] log likelihood: -4328.573375 EM: Round [207] log likelihood: -4328.572260 EM: Round [208] log likelihood: -4328.571151 EM: Round [209] log likelihood: -4328.570047 EM: Round [210] log likelihood: -4328.568949 EM: Round [211] log likelihood: -4328.567856 EM: Round [212] log likelihood: -4328.566769 EM: Round [213] log likelihood: -4328.565687 EM: Round [214] log likelihood: -4328.564611 EM: Round [215] log likelihood: -4328.563540 EM: Round [216] log likelihood: -4328.562475 EM: Round [217] log likelihood: -4328.561415 EM: Round [218] log likelihood: -4328.560361 EM: Round [219] log likelihood: -4328.559311 EM: Round [220] log likelihood: -4328.558267 EM: Round [221] log likelihood: -4328.557229 EM: Round [222] log likelihood: -4328.556195 EM: Round [223] log likelihood: -4328.555167 EM: Round [224] log likelihood: -4328.554144 EM: Round [225] log likelihood: -4328.553126 EM: Round [226] log likelihood: -4328.552113 EM: Round [227] log likelihood: -4328.551105 EM: Round [228] log likelihood: -4328.550102 EM: Round [229] log likelihood: -4328.549105 EM: Round [230] log likelihood: -4328.548112 EM: Round [231] log likelihood: -4328.547124 EM: Round [232] log likelihood: -4328.546141 EM: Round [233] log likelihood: -4328.545163 EM: Round [234] log likelihood: -4328.544190 EM: Round [235] log likelihood: -4328.543221 EM: Round [236] log likelihood: -4328.542258 EM: Round [237] log likelihood: -4328.541299 EM: Round [238] log likelihood: -4328.540345 EM: Round [239] log likelihood: -4328.539395 EM: Round [240] log likelihood: -4328.538451 EM: Round [241] log likelihood: -4328.537511 EM: Round [242] log likelihood: -4328.536575 EM: Round [243] log likelihood: -4328.535645 EM: Round [244] log likelihood: -4328.534718 EM: Round [245] log likelihood: -4328.533797 EM: Round [246] log likelihood: -4328.532880 EM: Round [247] log likelihood: -4328.531967 EM: Round [248] log likelihood: -4328.531059 EM: Round [249] log likelihood: -4328.530155 EM: Round [250] log likelihood: -4328.529256 EM: Round [251] log likelihood: -4328.528361 EM: Round [252] log likelihood: -4328.527470 EM: Round [253] log likelihood: -4328.526584 EM: Round [254] log likelihood: -4328.525702 EM: Round [255] log likelihood: -4328.524825 EM: Round [256] log likelihood: -4328.523951 EM: Round [257] log likelihood: -4328.523082 EM: Round [258] log likelihood: -4328.522217 EM: Round [259] log likelihood: -4328.521357 EM: Round [260] log likelihood: -4328.520500 EM: Round [261] log likelihood: -4328.519648 EM: Round [262] log likelihood: -4328.518800 EM: Round [263] log likelihood: -4328.517956 EM: Round [264] log likelihood: -4328.517116 EM: Round [265] log likelihood: -4328.516280 EM: Round [266] log likelihood: -4328.515448 EM: Round [267] log likelihood: -4328.514620 EM: Round [268] log likelihood: -4328.513796 EM: Round [269] log likelihood: -4328.512976 EM: Round [270] log likelihood: -4328.512160 EM: Round [271] log likelihood: -4328.511348 EM: Round [272] log likelihood: -4328.510540 EM: Round [273] log likelihood: -4328.509735 EM: Round [274] log likelihood: -4328.508935 EM: Round [275] log likelihood: -4328.508138 EM: Round [276] log likelihood: -4328.507345 EM: Round [277] log likelihood: -4328.506556 EM: Round [278] log likelihood: -4328.505771 EM: Round [279] log likelihood: -4328.504990 EM: Round [280] log likelihood: -4328.504212 EM: Round [281] log likelihood: -4328.503438 EM: Round [282] log likelihood: -4328.502667 EM: Round [283] log likelihood: -4328.501901 EM: Round [284] log likelihood: -4328.501138 EM: Round [285] log likelihood: -4328.500378 EM: Round [286] log likelihood: -4328.499622 EM: Round [287] log likelihood: -4328.498870 EM: Round [288] log likelihood: -4328.498121 EM: Round [289] log likelihood: -4328.497376 EM: Round [290] log likelihood: -4328.496634 EM: Round [291] log likelihood: -4328.495896 EM: Round [292] log likelihood: -4328.495162 EM: Round [293] log likelihood: -4328.494431 EM: Round [294] log likelihood: -4328.493703 EM: Round [295] log likelihood: -4328.492979 EM: Round [296] log likelihood: -4328.492258 EM: Round [297] log likelihood: -4328.491540 EM: Round [298] log likelihood: -4328.490826 EM: Round [299] log likelihood: -4328.490115 EM: Round [300] log likelihood: -4328.489408 EM: Round [301] log likelihood: -4328.488704 EM: Round [302] log likelihood: -4328.488003 EM: Round [303] log likelihood: -4328.487306 EM: Round [304] log likelihood: -4328.486612 EM: Round [305] log likelihood: -4328.485921 EM: Round [306] log likelihood: -4328.485233 EM: Round [307] log likelihood: -4328.484548 EM: Round [308] log likelihood: -4328.483867 EM: Round [309] log likelihood: -4328.483189 EM: Round [310] log likelihood: -4328.482514 EM: Round [311] log likelihood: -4328.481842 EM: Round [312] log likelihood: -4328.481173 EM: Round [313] log likelihood: -4328.480508 EM: Round [314] log likelihood: -4328.479845 EM: Round [315] log likelihood: -4328.479186 EM: Round [316] log likelihood: -4328.478530 EM: Round [317] log likelihood: -4328.477876 EM: Round [318] log likelihood: -4328.477226 EM: Round [319] log likelihood: -4328.476579 EM: Round [320] log likelihood: -4328.475935 EM: Round [321] log likelihood: -4328.475294 EM: Round [322] log likelihood: -4328.474655 EM: Round [323] log likelihood: -4328.474020 EM: Round [324] log likelihood: -4328.473388 EM: Round [325] log likelihood: -4328.472758 EM: Round [326] log likelihood: -4328.472132 EM: Round [327] log likelihood: -4328.471508 EM: Round [328] log likelihood: -4328.470887 EM: Round [329] log likelihood: -4328.470269 EM: Round [330] log likelihood: -4328.469654 EM: Round [331] log likelihood: -4328.469042 EM: Round [332] log likelihood: -4328.468433 EM: Round [333] log likelihood: -4328.467826 EM: Round [334] log likelihood: -4328.467222 EM: Round [335] log likelihood: -4328.466621 EM: Round [336] log likelihood: -4328.466023 EM: Round [337] log likelihood: -4328.465427 EM: Round [338] log likelihood: -4328.464834 EM: Round [339] log likelihood: -4328.464244 EM: Round [340] log likelihood: -4328.463657 EM: Round [341] log likelihood: -4328.463072 EM: Round [342] log likelihood: -4328.462490 EM: Round [343] log likelihood: -4328.461911 EM: Round [344] log likelihood: -4328.461334 EM: Round [345] log likelihood: -4328.460760 EM: Round [346] log likelihood: -4328.460188 EM: Round [347] log likelihood: -4328.459620 EM: Round [348] log likelihood: -4328.459053 EM: Round [349] log likelihood: -4328.458490 EM: Round [350] log likelihood: -4328.457929 EM: Round [351] log likelihood: -4328.457370 EM: Round [352] log likelihood: -4328.456814 EM: Round [353] log likelihood: -4328.456260 EM: Round [354] log likelihood: -4328.455709 EM: Round [355] log likelihood: -4328.455161 EM: Round [356] log likelihood: -4328.454615 EM: Round [357] log likelihood: -4328.454071 EM: Round [358] log likelihood: -4328.453530 EM: Round [359] log likelihood: -4328.452992 EM: Round [360] log likelihood: -4328.452456 EM: Round [361] log likelihood: -4328.451922 EM: Round [362] log likelihood: -4328.451391 EM: Round [363] log likelihood: -4328.450862 EM: Round [364] log likelihood: -4328.450335 EM: Round [365] log likelihood: -4328.449811 EM: Round [366] log likelihood: -4328.449289 EM: Round [367] log likelihood: -4328.448770 EM: Round [368] log likelihood: -4328.448253 EM: Round [369] log likelihood: -4328.447738 EM: Round [370] log likelihood: -4328.447225 EM: Round [371] log likelihood: -4328.446715 EM: Round [372] log likelihood: -4328.446208 EM: Round [373] log likelihood: -4328.445702 EM: Round [374] log likelihood: -4328.445199 EM: Round [375] log likelihood: -4328.444698 EM: Round [376] log likelihood: -4328.444199 EM: Round [377] log likelihood: -4328.443702 EM: Round [378] log likelihood: -4328.443208 EM: Round [379] log likelihood: -4328.442716 EM: Round [380] log likelihood: -4328.442226 EM: Round [381] log likelihood: -4328.441738 EM: Round [382] log likelihood: -4328.441253 EM: Round [383] log likelihood: -4328.440770 EM: Round [384] log likelihood: -4328.440288 EM: Round [385] log likelihood: -4328.439809 EM: Round [386] log likelihood: -4328.439333 EM: Round [387] log likelihood: -4328.438858 EM: Round [388] log likelihood: -4328.438385 EM: Round [389] log likelihood: -4328.437915 EM: Round [390] log likelihood: -4328.437446 EM: Round [391] log likelihood: -4328.436980 EM: Round [392] log likelihood: -4328.436516 EM: Round [393] log likelihood: -4328.436054 EM: Round [394] log likelihood: -4328.435593 EM: Round [395] log likelihood: -4328.435135 EM: Round [396] log likelihood: -4328.434679 EM: Round [397] log likelihood: -4328.434225 EM: Round [398] log likelihood: -4328.433773 EM: Round [399] log likelihood: -4328.433323 EM: Round [400] log likelihood: -4328.432875 EM: Round [401] log likelihood: -4328.432429 EM: Round [402] log likelihood: -4328.431985 EM: Round [403] log likelihood: -4328.431543 EM: Round [404] log likelihood: -4328.431103 EM: Round [405] log likelihood: -4328.430665 EM: Round [406] log likelihood: -4328.430229 EM: Round [407] log 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likelihood: -4328.420711 EM: Round [430] log likelihood: -4328.420319 EM: Round [431] log likelihood: -4328.419928 EM: Round [432] log likelihood: -4328.419539 EM: Round [433] log likelihood: -4328.419152 EM: Round [434] log likelihood: -4328.418767 EM: Round [435] log likelihood: -4328.418383 EM: Round [436] log likelihood: -4328.418001 EM: Round [437] log likelihood: -4328.417620 EM: Round [438] log likelihood: -4328.417241 EM: Round [439] log likelihood: -4328.416864 EM: Round [440] log likelihood: -4328.416489 EM: Round [441] log likelihood: -4328.416115 EM: Round [442] log likelihood: -4328.415743 EM: Round [443] log likelihood: -4328.415372 EM: Round [444] log likelihood: -4328.415003 EM: Round [445] log likelihood: -4328.414636 EM: Round [446] log likelihood: -4328.414270 EM: Round [447] log likelihood: -4328.413906 EM: Round [448] log likelihood: -4328.413543 EM: Round [449] log likelihood: -4328.413182 EM: Round [450] log likelihood: -4328.412823 EM: Round [451] log likelihood: -4328.412465 EM: Round [452] log likelihood: -4328.412108 EM: Round [453] log likelihood: -4328.411754 EM: Round [454] log likelihood: -4328.411400 EM: Round [455] log likelihood: -4328.411049 EM: Round [456] log likelihood: -4328.410699 EM: Round [457] log likelihood: -4328.410350 EM: Round [458] log likelihood: -4328.410003 EM: Round [459] log likelihood: -4328.409657 EM: Round [460] log likelihood: -4328.409313 EM: Round [461] log likelihood: -4328.408970 EM: Round [462] log likelihood: -4328.408629 EM: Round [463] log likelihood: -4328.408290 EM: Round [464] log likelihood: -4328.407951 EM: Round [465] log likelihood: -4328.407615 EM: Round [466] log likelihood: -4328.407279 EM: Round [467] log likelihood: -4328.406945 EM: Round [468] log likelihood: -4328.406613 EM: Round [469] log likelihood: -4328.406282 EM: Round [470] log likelihood: -4328.405953 EM: Round [471] log likelihood: -4328.405624 EM: Round [472] log likelihood: -4328.405298 EM: Round [473] log likelihood: -4328.404973 EM: Round [474] log likelihood: -4328.404649 EM: Round [475] log likelihood: -4328.404326 EM: Round [476] log likelihood: -4328.404005 EM: Round [477] log likelihood: -4328.403685 EM: Round [478] log likelihood: -4328.403367 EM: Round [479] log likelihood: -4328.403050 EM: Round [480] log likelihood: -4328.402735 EM: Round [481] log likelihood: -4328.402420 EM: Round [482] log likelihood: -4328.402108 EM: Round [483] log likelihood: -4328.401796 EM: Round [484] log likelihood: -4328.401486 EM: Round [485] log likelihood: -4328.401177 EM: Round [486] log likelihood: -4328.400869 EM: Round [487] log likelihood: -4328.400563 EM: Round [488] log likelihood: -4328.400258 EM: Round [489] log likelihood: -4328.399955 EM: Round [490] log likelihood: -4328.399653 EM: Round [491] log likelihood: -4328.399352 EM: Round [492] log likelihood: -4328.399052 EM: Round [493] log likelihood: -4328.398754 EM: Round [494] log likelihood: -4328.398456 EM: Round [495] log likelihood: -4328.398161 EM: Round [496] log likelihood: -4328.397866 EM: Round [497] log likelihood: -4328.397573 EM: Round [498] log likelihood: -4328.397281 EM: Round [499] log likelihood: -4328.396990 EM: Round [500] log likelihood: -4328.396700 EM: Round [501] log likelihood: -4328.396412 EM: Round [502] log likelihood: -4328.396125 EM: Round [503] log likelihood: -4328.395839 EM: Round [504] log likelihood: -4328.395555 EM: Round [505] log likelihood: -4328.395271 EM: Round [506] log likelihood: -4328.394989 EM: Round [507] log likelihood: -4328.394708 EM: Round [508] log likelihood: -4328.394428 EM: Round [509] log likelihood: -4328.394150 EM: Round [510] log likelihood: -4328.393872 EM: Round [511] log likelihood: -4328.393596 EM: Round [512] log likelihood: -4328.393321 EM: Round [513] log likelihood: -4328.393047 EM: Round [514] log likelihood: -4328.392774 EM: Round [515] log likelihood: -4328.392503 EM: Round [516] log likelihood: -4328.392232 EM: Round [517] log likelihood: -4328.391963 EM: Round [518] log likelihood: -4328.391695 EM: Round [519] log likelihood: -4328.391428 EM: Round [520] log likelihood: -4328.391162 EM: Round [521] log likelihood: -4328.390898 EM: Round [522] log likelihood: -4328.390634 EM: Round [523] log likelihood: -4328.390372 EM: Round [524] log likelihood: -4328.390111 EM: Round [525] log likelihood: -4328.389850 EM: Round [526] log likelihood: -4328.389591 EM: Round [527] log likelihood: -4328.389333 EM: Round [528] log likelihood: -4328.389076 EM: Round [529] log likelihood: -4328.388821 EM: Round [530] log likelihood: -4328.388566 EM: Round [531] log likelihood: -4328.388312 EM: Round [532] log likelihood: -4328.388060 EM: Round [533] log likelihood: -4328.387808 EM: Round [534] log likelihood: -4328.387558 EM: Round [535] log likelihood: -4328.387308 EM: Round [536] log likelihood: -4328.387060 EM: Round [537] log likelihood: -4328.386813 EM: Round [538] log likelihood: -4328.386567 EM: Round [539] log likelihood: -4328.386322 EM: Round [540] log likelihood: -4328.386078 EM: Round [541] log likelihood: -4328.385834 EM: Round [542] log likelihood: -4328.385592 EM: Round [543] log likelihood: -4328.385351 EM: Round [544] log likelihood: -4328.385111 EM: Round [545] log likelihood: -4328.384872 EM: Round [546] log likelihood: -4328.384634 EM: Round [547] log likelihood: -4328.384397 EM: Round [548] log likelihood: -4328.384162 EM: Round [549] log likelihood: -4328.383927 EM: Round [550] log likelihood: -4328.383693 EM: Round [551] log likelihood: -4328.383460 EM: Round [552] log likelihood: -4328.383228 EM: Round [553] log likelihood: -4328.382997 EM: Round [554] log likelihood: -4328.382767 EM: Round [555] log likelihood: -4328.382537 EM: Round [556] log likelihood: -4328.382309 EM: Round [557] log likelihood: -4328.382082 EM: Round [558] log likelihood: -4328.381856 EM: Round [559] log likelihood: -4328.381631 EM: Round [560] log likelihood: -4328.381407 EM: Round [561] log likelihood: -4328.381183 EM: Round [562] log likelihood: -4328.380961 EM: Round [563] log likelihood: -4328.380739 EM: Round [564] log likelihood: -4328.380519 EM: Round [565] log likelihood: -4328.380299 EM: Round [566] log likelihood: -4328.380081 EM: Round [567] log likelihood: -4328.379863 EM: Round [568] log likelihood: -4328.379646 EM: Round [569] log likelihood: -4328.379430 EM: Round [570] log likelihood: -4328.379215 EM: Round [571] log likelihood: -4328.379001 EM: Round [572] log likelihood: -4328.378788 EM: Round [573] log likelihood: -4328.378575 EM: Round [574] log likelihood: -4328.378364 EM: Round [575] log likelihood: -4328.378154 EM: Round [576] log likelihood: -4328.377944 EM: Round [577] log likelihood: -4328.377735 EM: Round [578] log likelihood: -4328.377527 EM: Round [579] log likelihood: -4328.377320 EM: Round [580] log likelihood: -4328.377114 EM: Round [581] log likelihood: -4328.376909 EM: Round [582] log likelihood: -4328.376704 EM: Round [583] log likelihood: -4328.376501 EM: Round [584] log likelihood: -4328.376298 EM: Round [585] log likelihood: -4328.376096 EM: Round [586] log likelihood: -4328.375895 EM: Round [587] log likelihood: -4328.375695 EM: Round [588] log likelihood: -4328.375496 EM: Round [589] log likelihood: -4328.375297 EM: Round [590] log likelihood: -4328.375100 EM: Round [591] log likelihood: -4328.374903 EM: Round [592] log likelihood: -4328.374707 EM: Round [593] log likelihood: -4328.374512 EM: Round [594] log likelihood: -4328.374317 EM: Round [595] log likelihood: -4328.374124 EM: Round [596] log likelihood: -4328.373931 EM: Round [597] log likelihood: -4328.373739 EM: Round [598] log likelihood: -4328.373548 EM: Round [599] log likelihood: -4328.373358 EM: Round [600] log likelihood: -4328.373168 EM: Round [601] log likelihood: -4328.372979 EM: Round [602] log likelihood: -4328.372791 EM: Round [603] log likelihood: -4328.372604 EM: Round [604] log likelihood: -4328.372418 EM: Round [605] log likelihood: -4328.372232 EM: Round [606] log likelihood: -4328.372047 EM: Round [607] log likelihood: -4328.371863 EM: Round [608] log likelihood: -4328.371680 EM: Round [609] log likelihood: -4328.371498 EM: Round [610] log likelihood: -4328.371316 EM: Round [611] log likelihood: -4328.371135 EM: Round [612] log likelihood: -4328.370955 EM: Round [613] log likelihood: -4328.370775 EM: Round [614] log likelihood: -4328.370596 EM: Round [615] log likelihood: -4328.370418 EM: Round [616] log likelihood: -4328.370241 EM: Round [617] log likelihood: -4328.370065 EM: Round [618] log likelihood: -4328.369889 EM: Round [619] log likelihood: -4328.369714 EM: Round [620] log likelihood: -4328.369539 EM: Round [621] log likelihood: -4328.369366 EM: Round [622] log likelihood: -4328.369193 EM: Round [623] log likelihood: -4328.369021 EM: Round [624] log likelihood: -4328.368849 EM: Round [625] log likelihood: -4328.368679 EM: Round [626] log likelihood: -4328.368509 EM: Round [627] log likelihood: -4328.368339 EM: Round [628] log likelihood: -4328.368171 EM: Round [629] log likelihood: -4328.368003 EM: Round [630] log likelihood: -4328.367836 EM: Round [631] log likelihood: -4328.367669 EM: Round [632] log likelihood: -4328.367503 EM: Round [633] log likelihood: -4328.367338 EM: Round [634] log likelihood: -4328.367174 EM: Round [635] log likelihood: -4328.367010 EM: Round [636] log likelihood: -4328.366847 EM: Round [637] log likelihood: -4328.366685 EM: Round [638] log likelihood: -4328.366523 EM: Round [639] log likelihood: -4328.366362 EM: Round [640] log likelihood: -4328.366202 EM: Round [641] log likelihood: -4328.366042 EM: Round [642] log likelihood: -4328.365883 EM: Round [643] log likelihood: -4328.365724 EM: Round [644] log likelihood: -4328.365567 EM: Round [645] log likelihood: -4328.365410 EM: Round [646] log likelihood: -4328.365253 EM: Round [647] log likelihood: -4328.365097 EM: Round [648] log likelihood: -4328.364942 EM: Round [649] log likelihood: -4328.364788 EM: Round [650] log likelihood: -4328.364634 EM: Round [651] log likelihood: -4328.364481 EM: Round [652] log likelihood: -4328.364328 EM: Round [653] log likelihood: -4328.364176 EM: Round [654] log likelihood: -4328.364025 EM: Round [655] log likelihood: -4328.363874 EM: Round [656] log likelihood: -4328.363724 EM: Round [657] log likelihood: -4328.363575 EM: Round [658] log likelihood: -4328.363426 EM: Round [659] log likelihood: -4328.363278 EM: Round [660] log likelihood: -4328.363130 EM: Round [661] log likelihood: -4328.362983 EM: Round [662] log likelihood: -4328.362837 EM: Round [663] log likelihood: -4328.362691 EM: Round [664] log likelihood: -4328.362546 EM: Round [665] log likelihood: -4328.362401 EM: Round [666] log likelihood: -4328.362257 EM: Round [667] log likelihood: -4328.362114 EM: Round [668] log likelihood: -4328.361971 EM: Round [669] log likelihood: -4328.361829 EM: Round [670] log likelihood: -4328.361688 EM: Round [671] log likelihood: -4328.361547 EM: Round [672] log likelihood: -4328.361406 EM: Round [673] log likelihood: -4328.361266 EM: Round [674] log likelihood: -4328.361127 EM: Round [675] log likelihood: -4328.360988 EM: Round [676] log likelihood: -4328.360850 EM: Round [677] log likelihood: -4328.360713 EM: Round [678] log likelihood: -4328.360576 EM: Round [679] log likelihood: -4328.360439 EM: Round [680] log likelihood: -4328.360303 EM: Round [681] log likelihood: -4328.360168 EM: Round [682] log likelihood: -4328.360033 EM: Round [683] log likelihood: -4328.359899 EM: Round [684] log likelihood: -4328.359766 EM: Round [685] log likelihood: -4328.359633 EM: Round [686] log likelihood: -4328.359500 EM: Round [687] log likelihood: -4328.359368 EM: Round [688] log likelihood: -4328.359237 EM: Round [689] log likelihood: -4328.359106 EM: Round [690] log likelihood: -4328.358975 EM: Round [691] log likelihood: -4328.358846 EM: Round [692] log likelihood: -4328.358716 EM: Round [693] log likelihood: -4328.358588 EM: Round [694] log likelihood: -4328.358459 EM: Round [695] log likelihood: -4328.358332 EM: Round [696] log likelihood: -4328.358205 EM: Round [697] log likelihood: -4328.358078 EM: Round [698] log likelihood: -4328.357952 EM: Round [699] log likelihood: -4328.357826 EM: Round [700] log likelihood: -4328.357701 EM: Round [701] log likelihood: -4328.357577 EM: Round [702] log likelihood: -4328.357453 EM: Round [703] log likelihood: -4328.357329 EM: Round [704] log likelihood: -4328.357206 EM: Round [705] log likelihood: -4328.357083 EM: Round [706] log likelihood: -4328.356961 EM: Round [707] log likelihood: -4328.356840 EM: Round [708] log likelihood: -4328.356719 EM: Round [709] log likelihood: -4328.356598 EM: Round [710] log likelihood: -4328.356478 EM: Round [711] log likelihood: -4328.356359 EM: Round [712] log likelihood: -4328.356240 EM: Round [713] log likelihood: -4328.356121 EM: Round [714] log likelihood: -4328.356003 EM: Round [715] log likelihood: -4328.355886 EM: Round [716] log likelihood: -4328.355769 EM: Round [717] log likelihood: -4328.355652 EM: Round [718] log likelihood: -4328.355536 EM: Round [719] log likelihood: -4328.355420 EM: Round [720] log likelihood: -4328.355305 EM: Round [721] log likelihood: -4328.355190 EM: Round [722] log likelihood: -4328.355076 EM: Round [723] log likelihood: -4328.354962 EM: Round [724] log likelihood: -4328.354849 EM: Round [725] log likelihood: -4328.354736 EM: Round [726] log likelihood: -4328.354624 EM: Round [727] log likelihood: -4328.354512 EM: Round [728] log likelihood: -4328.354400 EM: Round [729] log likelihood: -4328.354290 EM: Round [730] log likelihood: -4328.354179 EM: Round [731] log likelihood: -4328.354069 EM: Round [732] log likelihood: -4328.353959 EM: Round [733] log likelihood: -4328.353850 EM: Round [734] log likelihood: -4328.353741 EM: Round [735] log likelihood: -4328.353633 EM: Round [736] log likelihood: -4328.353525 EM: Round [737] log likelihood: -4328.353418 EM: Round [738] log likelihood: -4328.353311 EM: Round [739] log likelihood: -4328.353204 EM: Round [740] log likelihood: -4328.353098 EM: Round [741] log likelihood: -4328.352993 EM: Round [742] log likelihood: -4328.352887 EM: Round [743] log likelihood: -4328.352783 EM: Round [744] log likelihood: -4328.352678 EM: Round [745] log likelihood: -4328.352574 EM: Round [746] log likelihood: -4328.352471 EM: Round [747] log likelihood: -4328.352368 EM: Round [748] log likelihood: -4328.352265 EM: Round [749] log likelihood: -4328.352163 EM: Round [750] log likelihood: -4328.352061 EM: Round [751] log likelihood: -4328.351960 EM: Round [752] log likelihood: -4328.351859 EM: Round [753] log likelihood: -4328.351758 EM: Round [754] log likelihood: -4328.351658 EM: Round [755] log likelihood: -4328.351558 EM: Stopping iterations at round 755 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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz: 267401418 Execution Time = 5.33 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_1.fastp.fastq.gz /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/fi_workdir/microH.dat Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fa --gtf /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gtf > /tmp/nxf.FBo812kcg8/fi_workdir/microH.dat Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.FBo812kcg8/fi_workdir/microH.dat /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_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.FBo812kcg8/fi_workdir/microH.dat /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.FBo812kcg8 --json_outfile /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.FBo812kcg8 --json_outfile /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.json --file_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 Running: touch /tmp/nxf.FBo812kcg8/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.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --html_output /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.json --input_file_prefix aih-tih-sc-1ffee4-R1_A23WJ53LT4_1 --html_output /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000284627.1] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000214837.8] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286065.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.FBo812kcg8/ctat_genome_lib_build_dir > /tmp/nxf.FBo812kcg8/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.FBo812kcg8/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory