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/b5/5313ef4ad2752d8c42685ad1008b33/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/5b2777bfb4db992854c0aa79553ba0/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/5b2777bfb4db992854c0aa79553ba0/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/d168738dce0981bffa4b5abf4afa96/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/d168738dce0981bffa4b5abf4afa96/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --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 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/cytoBand.txt Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed -parsing GTF file: /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok Running: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok Running: samtools faidx /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.pHsQaijzGO/fi_workdir --reads "/tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:57:50 ..... started STAR run Jun 08 10:57:50 ..... loading genome Jun 08 10:59:32 ... generating Suffix Array index Jun 08 11:03:25 ... completed Suffix Array index Jun 08 11:03:25 ..... processing annotations GTF Jun 08 11:03:25 ..... inserting junctions into the genome indices Jun 08 11:04:28 ..... started mapping Jun 08 12:07:33 ..... finished mapping Jun 08 12:07:35 ..... started sorting BAM Jun 08 12:07:35 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam Execution Time = 69.78 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.pHsQaijzGO/fi_workdir --reads "/tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups 12:07:43 : INFO : Done. Execution Time = 0.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf -parsing /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] [1300000] [1310000] -done parsing /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'per_id < 96' => 6430, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4, 'seq-similar region overlap' => 135, 'num genes matched < 2' => 22, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 24, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2, ' ** passed ** ' => 10675, 'low complexity anchor region' => 2, 'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 18, 'exons hit < 2' => 5, 'small anchor length' => 201, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 69, 'excessive soft clipping' => 7808, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 12, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1 }; -writing fusion junction support info. Execution Time = 0.68 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] -fusion SPANNING read extraction for scaff: ACCS--DCDC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] -fusion SPANNING read extraction for scaff: FRG1--FAT1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: GDAP2--AC133865.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: GDAP2--AC099786.3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] -fusion SPANNING read extraction for scaff: HK1--CAMK2G [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: INPP5E--SMAD2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] -fusion SPANNING read extraction for scaff: PARVA--PRRT1B [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: PCDHA4--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] -fusion SPANNING read extraction for scaff: PRSS27--TPSB2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 28484, 'lacks exon overlap' => 1995 }; Execution Time = 1.61 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -4699.296218 EM: Round [1] log likelihood: -4698.723866 EM: Round [2] log likelihood: -4698.202443 EM: Round [3] log likelihood: -4697.723412 EM: Round [4] log likelihood: -4697.281727 EM: Round [5] log likelihood: -4696.873324 EM: Round [6] log likelihood: -4696.494829 EM: Round [7] log likelihood: -4696.143375 EM: Round [8] log likelihood: -4695.816485 EM: Round [9] log likelihood: -4695.511987 EM: Round [10] log likelihood: -4695.227959 EM: Round [11] log likelihood: -4694.962684 EM: Round [12] log likelihood: -4694.714620 EM: Round [13] log likelihood: -4694.482375 EM: Round [14] log likelihood: -4694.264688 EM: Round [15] log likelihood: -4694.060414 EM: Round [16] log likelihood: -4693.868510 EM: Round [17] log likelihood: -4693.688027 EM: Round [18] log likelihood: -4693.518095 EM: Round [19] log likelihood: -4693.357923 EM: Round [20] log likelihood: -4693.206784 EM: Round [21] log likelihood: -4693.064013 EM: Round [22] log likelihood: -4692.929002 EM: Round [23] log likelihood: -4692.801194 EM: Round [24] log likelihood: -4692.680075 EM: Round [25] log likelihood: -4692.565175 EM: Round [26] log likelihood: -4692.456065 EM: Round [27] log likelihood: -4692.352345 EM: Round [28] log likelihood: -4692.253653 EM: Round [29] log likelihood: -4692.159652 EM: Round [30] log likelihood: -4692.070033 EM: Round [31] log likelihood: -4691.984512 EM: Round [32] log likelihood: -4691.902827 EM: Round [33] log likelihood: -4691.824736 EM: Round [34] log likelihood: -4691.750015 EM: Round [35] log likelihood: -4691.678458 EM: Round [36] log likelihood: -4691.609874 EM: Round [37] log likelihood: -4691.544088 EM: Round [38] log likelihood: -4691.480936 EM: Round [39] log likelihood: -4691.420267 EM: Round [40] log likelihood: -4691.361940 EM: Round [41] log likelihood: -4691.305826 EM: Round [42] log likelihood: -4691.251803 EM: Round [43] log likelihood: -4691.199760 EM: Round [44] log likelihood: -4691.149591 EM: Round [45] log likelihood: -4691.101199 EM: Round [46] log likelihood: -4691.054494 EM: Round [47] log likelihood: -4691.009391 EM: Round [48] log likelihood: -4690.965811 EM: Round [49] log likelihood: -4690.923679 EM: Round [50] log likelihood: -4690.882928 EM: Round [51] log likelihood: -4690.843492 EM: Round [52] log likelihood: -4690.805310 EM: Round [53] log likelihood: -4690.768325 EM: Round [54] log likelihood: -4690.732485 EM: Round [55] log likelihood: -4690.697738 EM: Round [56] log likelihood: -4690.664038 EM: Round [57] log likelihood: -4690.631340 EM: Round [58] log likelihood: -4690.599602 EM: Round [59] log likelihood: -4690.568785 EM: Round [60] log likelihood: -4690.538850 EM: Round [61] log likelihood: -4690.509763 EM: Round [62] log likelihood: -4690.481491 EM: Round [63] log likelihood: -4690.454001 EM: Round [64] log likelihood: -4690.427263 EM: Round [65] log likelihood: -4690.401250 EM: Round [66] log likelihood: -4690.375934 EM: Round [67] log likelihood: -4690.351290 EM: Round [68] log likelihood: -4690.327292 EM: Round [69] log likelihood: -4690.303919 EM: Round [70] log likelihood: -4690.281147 EM: Round [71] log likelihood: -4690.258956 EM: Round [72] log likelihood: -4690.237326 EM: Round [73] log likelihood: -4690.216237 EM: Round [74] log likelihood: -4690.195672 EM: Round [75] log likelihood: -4690.175612 EM: Round [76] log likelihood: -4690.156041 EM: Round [77] log likelihood: -4690.136943 EM: Round [78] log likelihood: -4690.118303 EM: Round [79] log likelihood: -4690.100106 EM: Round [80] log likelihood: -4690.082337 EM: Round [81] log likelihood: -4690.064984 EM: Round [82] log likelihood: -4690.048034 EM: Round [83] log likelihood: -4690.031473 EM: Round [84] log likelihood: -4690.015291 EM: Round [85] log likelihood: -4689.999476 EM: Round [86] log likelihood: -4689.984016 EM: Round [87] log likelihood: -4689.968901 EM: Round [88] log likelihood: -4689.954121 EM: Round [89] log likelihood: -4689.939666 EM: Round [90] log likelihood: -4689.925526 EM: Round [91] log likelihood: -4689.911693 EM: Round [92] log likelihood: -4689.898157 EM: Round [93] log likelihood: -4689.884911 EM: Round [94] log likelihood: -4689.871945 EM: Round [95] log likelihood: -4689.859252 EM: Round [96] log likelihood: -4689.846825 EM: Round [97] log likelihood: -4689.834656 EM: Round [98] log likelihood: -4689.822738 EM: Round [99] log likelihood: -4689.811064 EM: Round [100] log likelihood: -4689.799628 EM: Round [101] log likelihood: -4689.788422 EM: Round [102] log likelihood: -4689.777441 EM: Round [103] log likelihood: -4689.766679 EM: Round [104] log likelihood: -4689.756131 EM: Round [105] log likelihood: -4689.745789 EM: Round [106] log likelihood: -4689.735650 EM: Round [107] log likelihood: -4689.725707 EM: Round [108] log likelihood: -4689.715956 EM: Round [109] log likelihood: -4689.706391 EM: Round [110] log likelihood: -4689.697008 EM: Round [111] log likelihood: -4689.687803 EM: Round [112] log likelihood: -4689.678770 EM: Round [113] log likelihood: -4689.669905 EM: Round [114] log likelihood: -4689.661205 EM: Round [115] log likelihood: -4689.652665 EM: Round [116] log likelihood: -4689.644280 EM: Round [117] log likelihood: -4689.636048 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likelihood: -4688.965173 EM: Round [537] log likelihood: -4688.964948 EM: Round [538] log likelihood: -4688.964724 EM: Round [539] log likelihood: -4688.964502 EM: Round [540] log likelihood: -4688.964280 EM: Round [541] log likelihood: -4688.964061 EM: Round [542] log likelihood: -4688.963842 EM: Round [543] log likelihood: -4688.963625 EM: Round [544] log likelihood: -4688.963410 EM: Round [545] log likelihood: -4688.963195 EM: Round [546] log likelihood: -4688.962982 EM: Round [547] log likelihood: -4688.962770 EM: Round [548] log likelihood: -4688.962560 EM: Round [549] log likelihood: -4688.962351 EM: Round [550] log likelihood: -4688.962143 EM: Round [551] log likelihood: -4688.961936 EM: Round [552] log likelihood: -4688.961731 EM: Round [553] log likelihood: -4688.961527 EM: Round [554] log likelihood: -4688.961324 EM: Round [555] log likelihood: -4688.961122 EM: Round [556] log likelihood: -4688.960922 EM: Round [557] log likelihood: -4688.960723 EM: Round [558] log likelihood: -4688.960525 EM: Round [559] log likelihood: -4688.960329 EM: Round [560] log likelihood: -4688.960133 EM: Round [561] log likelihood: -4688.959939 EM: Round [562] log likelihood: -4688.959746 EM: Round [563] log likelihood: -4688.959554 EM: Round [564] log likelihood: -4688.959363 EM: Round [565] log likelihood: -4688.959174 EM: Round [566] log likelihood: -4688.958986 EM: Round [567] log likelihood: -4688.958798 EM: Round [568] log likelihood: -4688.958612 EM: Round [569] log likelihood: -4688.958428 EM: Round [570] log likelihood: -4688.958244 EM: Round [571] log likelihood: -4688.958061 EM: Round [572] log likelihood: -4688.957880 EM: Round [573] log likelihood: -4688.957699 EM: Round [574] log likelihood: -4688.957520 EM: Round [575] log likelihood: -4688.957342 EM: Round [576] log likelihood: -4688.957165 EM: Round [577] log likelihood: -4688.956989 EM: Round [578] log likelihood: -4688.956814 EM: Round [579] log likelihood: -4688.956640 EM: Round [580] log likelihood: -4688.956467 EM: Round [581] log likelihood: -4688.956295 EM: Round [582] log likelihood: -4688.956125 EM: Round [583] log likelihood: -4688.955955 EM: Round [584] log likelihood: -4688.955787 EM: Round [585] log likelihood: -4688.955619 EM: Round [586] log likelihood: -4688.955452 EM: Round [587] log likelihood: -4688.955287 EM: Round [588] log likelihood: -4688.955122 EM: Round [589] log likelihood: -4688.954959 EM: Round [590] log likelihood: -4688.954796 EM: Round [591] log likelihood: -4688.954635 EM: Round [592] log likelihood: -4688.954474 EM: Round [593] log likelihood: -4688.954315 EM: Round [594] log likelihood: -4688.954156 EM: Round [595] log likelihood: -4688.953999 EM: Round [596] log likelihood: -4688.953842 EM: Round [597] log likelihood: -4688.953686 EM: Round [598] log likelihood: -4688.953532 EM: Round [599] log likelihood: -4688.953378 EM: Round [600] log likelihood: -4688.953225 EM: Round [601] log likelihood: -4688.953073 EM: Round [602] log likelihood: -4688.952922 EM: Round [603] log likelihood: -4688.952772 EM: Round [604] log likelihood: -4688.952623 EM: Round [605] log likelihood: -4688.952475 EM: Round [606] log likelihood: -4688.952327 EM: Round [607] log likelihood: -4688.952181 EM: Round [608] log likelihood: -4688.952035 EM: Round [609] log likelihood: -4688.951891 EM: Round [610] log likelihood: -4688.951747 EM: Round [611] log likelihood: -4688.951604 EM: Round [612] log likelihood: -4688.951462 EM: Round [613] log likelihood: -4688.951321 EM: Round [614] log likelihood: -4688.951181 EM: Round [615] log likelihood: -4688.951041 EM: Round [616] log likelihood: -4688.950903 EM: Round [617] log likelihood: -4688.950765 EM: Round [618] log likelihood: -4688.950628 EM: Round [619] log likelihood: -4688.950492 EM: Round [620] log likelihood: -4688.950357 EM: Round [621] log likelihood: -4688.950222 EM: Round [622] log likelihood: -4688.950089 EM: Round [623] log likelihood: -4688.949956 EM: Round [624] log likelihood: -4688.949824 EM: Round [625] log likelihood: -4688.949693 EM: Round [626] log likelihood: -4688.949562 EM: Round [627] log likelihood: -4688.949433 EM: Round [628] log likelihood: -4688.949304 EM: Round [629] log likelihood: -4688.949176 EM: Round [630] log likelihood: -4688.949049 EM: Round [631] log likelihood: -4688.948922 EM: Round [632] log likelihood: -4688.948796 EM: Round [633] log likelihood: -4688.948671 EM: Round [634] log likelihood: -4688.948547 EM: Round [635] log likelihood: -4688.948424 EM: Round [636] log likelihood: -4688.948301 EM: Round [637] log likelihood: -4688.948179 EM: Round [638] log likelihood: -4688.948058 EM: Round [639] log likelihood: -4688.947938 EM: Round [640] log likelihood: -4688.947818 EM: Round [641] log likelihood: -4688.947699 EM: Round [642] log likelihood: -4688.947581 EM: Round [643] log likelihood: -4688.947463 EM: Round [644] log likelihood: -4688.947346 EM: Round [645] log likelihood: -4688.947230 EM: Round [646] log likelihood: -4688.947115 EM: Round [647] log likelihood: -4688.947000 EM: Round [648] log likelihood: -4688.946886 EM: Round [649] log likelihood: -4688.946773 EM: Round [650] log likelihood: -4688.946660 EM: Round [651] log likelihood: -4688.946548 EM: Round [652] log likelihood: -4688.946437 EM: Round [653] log likelihood: -4688.946326 EM: Round [654] log likelihood: -4688.946216 EM: Round [655] log likelihood: -4688.946107 EM: Round [656] log likelihood: -4688.945998 EM: Round [657] log likelihood: -4688.945890 EM: Round [658] log likelihood: -4688.945783 EM: Round [659] log likelihood: -4688.945676 EM: Round [660] log likelihood: -4688.945570 EM: Round [661] log likelihood: -4688.945465 EM: Round [662] log likelihood: -4688.945360 EM: Round [663] log likelihood: -4688.945256 EM: Round [664] log likelihood: -4688.945153 EM: Round [665] log likelihood: -4688.945050 EM: Round [666] log likelihood: -4688.944948 EM: Round [667] log likelihood: -4688.944846 EM: Round [668] log likelihood: -4688.944745 EM: Round [669] log likelihood: -4688.944645 EM: Round [670] log likelihood: -4688.944545 EM: Stopping iterations at round 670 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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam" Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords CMD: touch /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.32 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir -done, see /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -4126.677716 EM: Round [1] log likelihood: -4126.675592 EM: Round [2] log likelihood: -4126.675576 EM: Stopping iterations at round 2 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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 294060824 Execution Time = 5.57 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.pHsQaijzGO/fi_workdir/microH.dat Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.pHsQaijzGO/fi_workdir/microH.dat /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/fi_workdir/microH.dat /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.pHsQaijzGO --json_outfile /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.pHsQaijzGO --json_outfile /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 Running: touch /tmp/nxf.pHsQaijzGO/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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.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.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect 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 [ENSG00000280136.2] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.pHsQaijzGO/ctat_genome_lib_build_dir > /tmp/nxf.pHsQaijzGO/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.pHsQaijzGO/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory