Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/cfb0cbf07fdb22704dd83d50aaf440/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/2f5f01907f54ef0ca6a3a2b88694e7/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/2f5f01907f54ef0ca6a3a2b88694e7/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/09ccc4496613519b4fb75dbd2aa5c6/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/cfb0cbf07fdb22704dd83d50aaf440/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/cytoBand.txt Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed -parsing GTF file: /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.zW2b2UEleD/fi_workdir --reads "/tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:52:52 ..... started STAR run Jun 08 10:52:52 ..... loading genome Jun 08 10:54:34 ... generating Suffix Array index Jun 08 10:58:28 ... completed Suffix Array index Jun 08 10:58:28 ..... processing annotations GTF Jun 08 10:58:29 ..... inserting junctions into the genome indices Jun 08 10:59:29 ..... started mapping Jun 08 11:55:58 ..... finished mapping Jun 08 11:56:00 ..... started sorting BAM Jun 08 11:56:01 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam Execution Time = 63.19 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.zW2b2UEleD/fi_workdir --reads "/tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:56:13 : INFO : Done. Execution Time = 0.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf -parsing /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [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] [1320000] [1330000] [1340000] [1350000] [1360000] [1370000] [1380000] [1390000] [1400000] [1410000] [1420000] [1430000] [1440000] [1450000] [1460000] [1470000] [1480000] [1490000] [1500000] [1510000] [1520000] [1530000] [1540000] [1550000] [1560000] [1570000] [1580000] [1590000] [1600000] [1610000] [1620000] [1630000] [1640000] [1650000] [1660000] [1670000] [1680000] [1690000] [1700000] [1710000] [1720000] [1730000] [1740000] [1750000] [1760000] [1770000] [1780000] [1790000] [1800000] [1810000] [1820000] [1830000] [1840000] [1850000] [1860000] [1870000] [1880000] [1890000] [1900000] [1910000] [1920000] [1930000] [1940000] [1950000] [1960000] [1970000] [1980000] [1990000] [2000000] -done parsing /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 10 != num_counted_on_fusion_contigs 4 ' => 28, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 3, 'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 108, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 48, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 4, 'num_hits: 8 != num_counted_on_fusion_contigs 3 ' => 3, 'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 6, 'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 129, 'num_hits: 9 != num_counted_on_fusion_contigs 6 ' => 6, 'num_hits: 9 != num_counted_on_fusion_contigs 7 ' => 21, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 168, 'excessive soft clipping' => 10920, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 715, 'num_hits: 9 != num_counted_on_fusion_contigs 1 ' => 7, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4, 'num_hits: 10 != num_counted_on_fusion_contigs 2 ' => 4, 'num_hits: 10 != num_counted_on_fusion_contigs 1 ' => 4, 'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 19, 'seq-similar region overlap' => 81, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3, 'num_hits: 10 != num_counted_on_fusion_contigs 3 ' => 3, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 21, 'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 120, 'small anchor length' => 285, 'num_hits: 8 != num_counted_on_fusion_contigs 1 ' => 5, 'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 120, 'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 6, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 31, ' ** passed ** ' => 10479, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 15, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4, 'num genes matched < 2' => 19, 'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 78, 'per_id < 96' => 9526, 'num_hits: 9 != num_counted_on_fusion_contigs 4 ' => 20, 'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 56, 'num_hits: 10 != num_counted_on_fusion_contigs 5 ' => 10, 'exons hit < 2' => 10 }; -writing fusion junction support info. Execution Time = 1.08 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] -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] 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[419000] [420000] [421000] [422000] [423000] [424000] [425000] [426000] [427000] [428000] [429000] [430000] [431000] [432000] [433000] [434000] [435000] [436000] [437000] [438000] [439000] [440000] [441000] [442000] [443000] [444000] [445000] [446000] [447000] [448000] [449000] [450000] [451000] [452000] [453000] [454000] [455000] [456000] [457000] [458000] [459000] [460000] [461000] [462000] [463000] [464000] [465000] [466000] [467000] [468000] [469000] [470000] [471000] [472000] [473000] [474000] [475000] [476000] [477000] [478000] [479000] [480000] [481000] [482000] [483000] [484000] [485000] [486000] [487000] [488000] [489000] [490000] [491000] [492000] [493000] [494000] [495000] [496000] [497000] [498000] [499000] [500000] [501000] [502000] [503000] [504000] [505000] [506000] [507000] [508000] [509000] [510000] [511000] [512000] [513000] [514000] [515000] [516000] [517000] [518000] [519000] [520000] [521000] [522000] [523000] [524000] [525000] [526000] [527000] [528000] [529000] [530000] [531000] [532000] [533000] [534000] [535000] [536000] [537000] [538000] [539000] [540000] [541000] [542000] [543000] [544000] [545000] [546000] [547000] [548000] [549000] [550000] [551000] [552000] [553000] [554000] [555000] [556000] [557000] [558000] [559000] [560000] [561000] [562000] [563000] [564000] [565000] [566000] [567000] [568000] [569000] [570000] [571000] [572000] -fusion SPANNING read extraction for scaff: CCDC198--NPIPB12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] -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] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] -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] [60000] -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] -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] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11 [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] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -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] -fusion SPANNING read extraction for scaff: PCDHGA2--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] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -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] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11 [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] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -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] -fusion SPANNING read extraction for scaff: PCDHGA5--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] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGA6--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] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -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] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -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] -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] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] -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] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] -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] [119000] [120000] [121000] [122000] [123000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -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' => 37644, 'lacks exon overlap' => 8697 }; Execution Time = 2.74 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -4058.052681 EM: Round [1] log likelihood: -4057.025097 EM: Round [2] log likelihood: -4056.128091 EM: Round [3] log likelihood: -4055.311057 EM: Round [4] log likelihood: -4054.562860 EM: Round [5] log likelihood: -4053.874942 EM: Round [6] log likelihood: -4053.240511 EM: Round [7] log likelihood: -4052.654009 EM: Round [8] log likelihood: -4052.110747 EM: Round [9] log likelihood: -4051.606677 EM: Round [10] log likelihood: -4051.138235 EM: Round [11] log likelihood: -4050.702242 EM: Round [12] log likelihood: -4050.295839 EM: Round [13] log likelihood: -4049.916441 EM: Round [14] log likelihood: -4049.561707 EM: Round [15] log likelihood: -4049.229519 EM: Round [16] log likelihood: -4048.917954 EM: Round [17] log likelihood: -4048.625276 EM: Round [18] log likelihood: -4048.349915 EM: Round [19] log likelihood: -4048.090455 EM: Round [20] log likelihood: -4047.845620 EM: Round [21] log likelihood: -4047.614259 EM: Round [22] log likelihood: -4047.395335 EM: Round [23] log likelihood: -4047.187916 EM: Round [24] log likelihood: -4046.991160 EM: Round [25] log likelihood: -4046.804309 EM: Round [26] log likelihood: -4046.626679 EM: Round [27] log likelihood: -4046.457649 EM: Round [28] log likelihood: -4046.296659 EM: Round [29] log likelihood: -4046.143200 EM: Round [30] log likelihood: -4045.996808 EM: Round [31] log likelihood: -4045.857061 EM: Round [32] log likelihood: -4045.723572 EM: Round [33] log likelihood: -4045.595987 EM: Round [34] log likelihood: -4045.473980 EM: Round [35] log likelihood: -4045.357251 EM: Round [36] log likelihood: -4045.245523 EM: Round [37] log likelihood: -4045.138538 EM: Round [38] log likelihood: -4045.036056 EM: Round [39] log likelihood: -4044.937856 EM: Round [40] log likelihood: -4044.843729 EM: Round [41] log likelihood: -4044.753480 EM: Round [42] log likelihood: -4044.666927 EM: Round [43] log likelihood: -4044.583897 EM: Round [44] log likelihood: -4044.504229 EM: Round [45] log likelihood: -4044.427771 EM: Round [46] log likelihood: -4044.354377 EM: Round [47] log likelihood: -4044.283913 EM: Round [48] log likelihood: -4044.216247 EM: Round [49] log likelihood: -4044.151259 EM: Round [50] log likelihood: -4044.088831 EM: Round [51] log likelihood: -4044.028853 EM: Round [52] log likelihood: -4043.971220 EM: Round [53] log likelihood: -4043.915831 EM: Round [54] log likelihood: -4043.862592 EM: Round [55] log likelihood: -4043.811411 EM: Round [56] log likelihood: -4043.762202 EM: Round [57] log likelihood: -4043.714882 EM: Round [58] log likelihood: -4043.669373 EM: Round [59] log likelihood: -4043.625599 EM: Round [60] log likelihood: -4043.583488 EM: Round [61] log likelihood: -4043.542971 EM: Round [62] log likelihood: -4043.503984 EM: Round [63] log likelihood: -4043.466463 EM: Round [64] log likelihood: -4043.430348 EM: Round [65] log likelihood: -4043.395583 EM: Round [66] log likelihood: -4043.362112 EM: Round [67] log likelihood: -4043.329882 EM: Round [68] log likelihood: -4043.298845 EM: Round [69] log likelihood: -4043.268953 EM: Round [70] log likelihood: -4043.240158 EM: Round [71] log likelihood: -4043.212418 EM: Round [72] log likelihood: -4043.185690 EM: Round [73] log likelihood: -4043.159934 EM: Round [74] log likelihood: -4043.135112 EM: Round [75] log likelihood: -4043.111188 EM: Round [76] log likelihood: -4043.088125 EM: Round [77] log likelihood: -4043.065890 EM: Round [78] log likelihood: -4043.044451 EM: Round [79] log likelihood: -4043.023777 EM: Round [80] log likelihood: -4043.003839 EM: Round [81] log likelihood: -4042.984607 EM: Round [82] log likelihood: -4042.966054 EM: Round [83] log likelihood: -4042.948156 EM: Round [84] log likelihood: -4042.930886 EM: Round [85] log likelihood: -4042.914221 EM: Round [86] log likelihood: -4042.898138 EM: Round [87] log likelihood: -4042.882614 EM: Round [88] log likelihood: -4042.867630 EM: Round [89] log likelihood: -4042.853164 EM: Round [90] log likelihood: -4042.839197 EM: Round [91] log likelihood: -4042.825710 EM: Round [92] log likelihood: -4042.812687 EM: Round [93] log likelihood: -4042.800109 EM: Round [94] log likelihood: -4042.787960 EM: Round [95] log likelihood: -4042.776224 EM: Round [96] log likelihood: -4042.764887 EM: Round [97] log likelihood: -4042.753934 EM: Round [98] log likelihood: -4042.743350 EM: Round [99] log likelihood: -4042.733123 EM: Round [100] log likelihood: -4042.723240 EM: Round [101] log likelihood: -4042.713687 EM: Round [102] log likelihood: -4042.704454 EM: Round [103] log likelihood: -4042.695529 EM: Round [104] log likelihood: -4042.686901 EM: Round [105] log likelihood: -4042.678559 EM: Round [106] log likelihood: -4042.670493 EM: Round [107] log likelihood: -4042.662694 EM: Round [108] log likelihood: -4042.655153 EM: Round [109] log likelihood: -4042.647859 EM: Round [110] log likelihood: -4042.640804 EM: Round [111] log likelihood: -4042.633981 EM: Round [112] log likelihood: -4042.627381 EM: Round [113] log likelihood: -4042.620996 EM: Round [114] log likelihood: -4042.614820 EM: Round [115] log likelihood: -4042.608844 EM: Round [116] log likelihood: -4042.603061 EM: Round [117] log likelihood: -4042.597467 EM: Round [118] log likelihood: -4042.592052 EM: Round [119] log likelihood: -4042.586813 EM: Round [120] log likelihood: -4042.581742 EM: Round [121] log likelihood: -4042.576835 EM: Round [122] log likelihood: -4042.572085 EM: Round [123] log likelihood: -4042.567487 EM: Round [124] log likelihood: -4042.563036 EM: Round [125] log likelihood: -4042.558728 EM: Round [126] log likelihood: -4042.554556 EM: Round [127] log likelihood: -4042.550518 EM: Round [128] log likelihood: -4042.546608 EM: Round [129] log likelihood: -4042.542822 EM: Round [130] log likelihood: -4042.539157 EM: Round [131] log likelihood: -4042.535607 EM: Round [132] log likelihood: -4042.532169 EM: Round [133] log likelihood: -4042.528841 EM: Round [134] log likelihood: -4042.525617 EM: Round [135] log likelihood: -4042.522494 EM: Round [136] log likelihood: -4042.519470 EM: Round [137] log likelihood: -4042.516541 EM: Round [138] log likelihood: -4042.513703 EM: Round [139] log likelihood: -4042.510955 EM: Round [140] log likelihood: -4042.508293 EM: Round [141] log likelihood: -4042.505713 EM: Round [142] log likelihood: -4042.503215 EM: Round [143] log likelihood: -4042.500794 EM: Round [144] log likelihood: -4042.498449 EM: Round [145] log likelihood: -4042.496177 EM: Round [146] log likelihood: -4042.493975 EM: Round [147] log likelihood: -4042.491842 EM: Round [148] log likelihood: -4042.489775 EM: Round [149] log likelihood: -4042.487772 EM: Round [150] log likelihood: -4042.485831 EM: Round [151] log likelihood: -4042.483950 EM: Round [152] log likelihood: -4042.482127 EM: Round [153] log likelihood: -4042.480361 EM: Round [154] log likelihood: -4042.478649 EM: Round [155] log likelihood: -4042.476990 EM: Round [156] log likelihood: -4042.475382 EM: Round [157] log likelihood: -4042.473823 EM: Round [158] log likelihood: -4042.472313 EM: Round [159] log likelihood: -4042.470849 EM: Round [160] log likelihood: -4042.469429 EM: Round [161] log likelihood: -4042.468054 EM: Round [162] log likelihood: -4042.466720 EM: Round [163] log likelihood: -4042.465427 EM: Round [164] log likelihood: -4042.464174 EM: Round [165] log likelihood: -4042.462959 EM: Round [166] log likelihood: -4042.461782 EM: Round [167] log likelihood: -4042.460640 EM: Round [168] log likelihood: -4042.459533 EM: Round [169] log likelihood: -4042.458460 EM: Round [170] log likelihood: -4042.457419 EM: Round [171] log likelihood: -4042.456411 EM: Round [172] log likelihood: -4042.455433 EM: Round [173] log likelihood: -4042.454484 EM: Round [174] log likelihood: -4042.453565 EM: Round [175] log likelihood: -4042.452673 EM: Round [176] log likelihood: -4042.451809 EM: Round [177] log likelihood: -4042.450970 EM: Round [178] log likelihood: -4042.450158 EM: Round [179] log likelihood: -4042.449369 EM: Round [180] log likelihood: -4042.448605 EM: Round [181] log likelihood: -4042.447864 EM: Round [182] log likelihood: -4042.447145 EM: Round [183] log likelihood: -4042.446448 EM: Round [184] log likelihood: -4042.445772 EM: Round [185] log likelihood: -4042.445116 EM: Round [186] log likelihood: -4042.444480 EM: Round [187] log likelihood: -4042.443864 EM: Round [188] log likelihood: -4042.443266 EM: Round [189] log likelihood: -4042.442686 EM: Round [190] log likelihood: -4042.442123 EM: Round [191] log likelihood: -4042.441578 EM: Round [192] log likelihood: -4042.441048 EM: Round [193] log likelihood: -4042.440535 EM: Round [194] log likelihood: -4042.440037 EM: Round [195] log likelihood: -4042.439554 EM: Round [196] log likelihood: -4042.439086 EM: Round [197] log likelihood: -4042.438632 EM: Round [198] log likelihood: -4042.438191 EM: Round [199] log likelihood: -4042.437763 EM: Round [200] log likelihood: -4042.437349 EM: Round [201] log likelihood: -4042.436946 EM: Round [202] log likelihood: -4042.436556 EM: Round [203] log likelihood: -4042.436178 EM: Round [204] log likelihood: -4042.435810 EM: Round [205] log likelihood: -4042.435454 EM: Round [206] log likelihood: -4042.435109 EM: Round [207] log likelihood: -4042.434773 EM: Round [208] log likelihood: -4042.434448 EM: Round [209] log likelihood: -4042.434133 EM: Round [210] log likelihood: -4042.433826 EM: Round [211] log likelihood: -4042.433529 EM: Round [212] log likelihood: -4042.433241 EM: Round [213] log likelihood: -4042.432962 EM: Round [214] log likelihood: -4042.432691 EM: Round [215] log likelihood: -4042.432427 EM: Round [216] log likelihood: -4042.432172 EM: Round [217] log likelihood: -4042.431924 EM: Round [218] log likelihood: -4042.431684 EM: Round [219] log likelihood: -4042.431451 EM: Round [220] log likelihood: -4042.431225 EM: Round [221] log likelihood: -4042.431005 EM: Round [222] log likelihood: -4042.430792 EM: Round [223] log likelihood: -4042.430585 EM: Round [224] log likelihood: -4042.430385 EM: Round [225] log likelihood: -4042.430190 EM: Round [226] log likelihood: -4042.430001 EM: Round [227] log likelihood: -4042.429818 EM: Round [228] log likelihood: -4042.429640 EM: Round [229] log likelihood: -4042.429468 EM: Round [230] log likelihood: -4042.429300 EM: Round [231] log likelihood: -4042.429138 EM: Round [232] log likelihood: -4042.428980 EM: Round [233] log likelihood: -4042.428827 EM: Round [234] log likelihood: -4042.428679 EM: Round [235] log likelihood: -4042.428535 EM: Round [236] log likelihood: -4042.428395 EM: Round [237] log likelihood: -4042.428259 EM: Round [238] log likelihood: -4042.428128 EM: Round [239] log likelihood: -4042.428000 EM: Round [240] log likelihood: -4042.427876 EM: Round [241] log likelihood: -4042.427755 EM: Round [242] log likelihood: -4042.427639 EM: Round [243] log likelihood: -4042.427525 EM: Round [244] log likelihood: -4042.427415 EM: Round [245] log likelihood: -4042.427308 EM: Round [246] log likelihood: -4042.427205 EM: Round [247] log likelihood: -4042.427104 EM: Round [248] log likelihood: -4042.427007 EM: Stopping iterations at round 248 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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.55 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir -done, see /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -2875.390290 EM: Round [1] log likelihood: -2875.354583 EM: Round [2] log likelihood: -2875.354583 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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 294354607 Execution Time = 5.36 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.zW2b2UEleD/fi_workdir/microH.dat Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.zW2b2UEleD/fi_workdir/microH.dat /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/fi_workdir/microH.dat /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.zW2b2UEleD --json_outfile /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.zW2b2UEleD --json_outfile /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 Running: touch /tmp/nxf.zW2b2UEleD/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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_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.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.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] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.zW2b2UEleD/ctat_genome_lib_build_dir > /tmp/nxf.zW2b2UEleD/1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.zW2b2UEleD/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory