Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/2c92445f4b2a4ba13847c1b13acd00/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_2.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/c4/b99b2f9c16ab4e1a228c4b954ef28c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/b99b2f9c16ab4e1a228c4b954ef28c/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/cf405f2d0dec0548ddb33fd1161965/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/2c92445f4b2a4ba13847c1b13acd00/1173_GZ1_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_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.EWpmWH8u8E/1173_GZ1_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_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.EWpmWH8u8E/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.EWpmWH8u8E/cytoBand.txt Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed -parsing GTF file: /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok Running: bgzip -f /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok Running: samtools faidx /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.EWpmWH8u8E/fi_workdir --reads "/tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:28:17 ..... started STAR run Jun 08 10:28:17 ..... loading genome Jun 08 10:29:56 ... generating Suffix Array index Jun 08 10:33:39 ... completed Suffix Array index Jun 08 10:33:39 ..... processing annotations GTF Jun 08 10:33:39 ..... inserting junctions into the genome indices Jun 08 10:34:39 ..... started mapping Jun 08 11:26:14 ..... finished mapping Jun 08 11:26:16 ..... started sorting BAM Jun 08 11:26:16 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam Execution Time = 57.99 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.EWpmWH8u8E/fi_workdir --reads "/tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups 11:26:18 : INFO : Done. Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf -parsing /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_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] -done parsing /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 25, ' ** passed ** ' => 7550, 'small anchor length' => 180, 'per_id < 96' => 1551, 'seq-similar region overlap' => 188, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 18, 'excessive soft clipping' => 2132, 'num genes matched < 2' => 2 }; -writing fusion junction support info. Execution Time = 0.21 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_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] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -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--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [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: PCDHGB2--PCDHGA11 [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: 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] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] -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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [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] -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] -fusion SPANNING read extraction for scaff: TLK2--LINC01347 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -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] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 43027, 'lacks exon overlap' => 875 }; Execution Time = 0.41 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -1584.148289 EM: Round [1] log likelihood: -1584.073883 EM: Round [2] log likelihood: -1584.039919 EM: Round [3] log likelihood: -1584.008277 EM: Round [4] log likelihood: -1583.978302 EM: Round [5] log likelihood: -1583.949876 EM: Round [6] log likelihood: -1583.922899 EM: Round [7] log likelihood: -1583.897279 EM: Round [8] log likelihood: -1583.872932 EM: Round [9] log likelihood: -1583.849781 EM: Round [10] log likelihood: -1583.827753 EM: Round [11] log likelihood: -1583.806783 EM: Round [12] log likelihood: -1583.786810 EM: Round [13] log likelihood: -1583.767777 EM: Round [14] log likelihood: -1583.749631 EM: Round [15] log likelihood: -1583.732325 EM: Round [16] log likelihood: -1583.715811 EM: Round [17] log likelihood: -1583.700049 EM: Round [18] log likelihood: -1583.684998 EM: Round [19] log likelihood: -1583.670621 EM: Round [20] log likelihood: -1583.656883 EM: Round [21] log likelihood: -1583.643752 EM: Round [22] log likelihood: -1583.631198 EM: Round [23] log likelihood: -1583.619191 EM: Round [24] log likelihood: -1583.607705 EM: Round [25] log likelihood: -1583.596715 EM: Round [26] log likelihood: -1583.586195 EM: Round [27] log likelihood: -1583.576125 EM: Round [28] log likelihood: -1583.566483 EM: Round [29] log likelihood: -1583.557248 EM: Round [30] log likelihood: -1583.548401 EM: Round [31] log likelihood: -1583.539925 EM: Round [32] log likelihood: -1583.531803 EM: Round [33] log likelihood: -1583.524018 EM: Round [34] log likelihood: -1583.516556 EM: Round [35] log likelihood: -1583.509401 EM: Round [36] log likelihood: -1583.502541 EM: Round [37] log likelihood: -1583.495961 EM: Round [38] log likelihood: -1583.489650 EM: Round [39] log likelihood: -1583.483596 EM: Round [40] log likelihood: -1583.477788 EM: Round [41] log likelihood: -1583.472215 EM: Round [42] log likelihood: -1583.466866 EM: Round [43] log likelihood: -1583.461733 EM: Round [44] log likelihood: -1583.456807 EM: Round [45] log likelihood: -1583.452077 EM: Round [46] log likelihood: -1583.447536 EM: Round [47] log likelihood: -1583.443177 EM: Round [48] log likelihood: -1583.438991 EM: Round [49] log likelihood: -1583.434971 EM: Round [50] log likelihood: -1583.431111 EM: Round [51] log likelihood: -1583.427403 EM: Round [52] log likelihood: -1583.423841 EM: Round [53] log likelihood: -1583.420420 EM: Round [54] log likelihood: -1583.417134 EM: Round [55] log likelihood: -1583.413977 EM: Round [56] log likelihood: -1583.410943 EM: Round [57] log likelihood: -1583.408028 EM: Round [58] log likelihood: -1583.405228 EM: Round [59] log likelihood: -1583.402536 EM: Round [60] log likelihood: -1583.399950 EM: Round [61] log likelihood: -1583.397464 EM: Round [62] log likelihood: -1583.395076 EM: Round [63] log likelihood: -1583.392780 EM: Round [64] log likelihood: -1583.390573 EM: Round [65] log likelihood: -1583.388451 EM: Round [66] log likelihood: -1583.386412 EM: Round [67] log likelihood: -1583.384452 EM: Round [68] log likelihood: -1583.382568 EM: Round [69] log likelihood: -1583.380756 EM: Round [70] log likelihood: -1583.379014 EM: Round [71] log likelihood: -1583.377339 EM: Round [72] log likelihood: -1583.375729 EM: Round [73] log likelihood: -1583.374181 EM: Round [74] log likelihood: -1583.372693 EM: Round [75] log likelihood: -1583.371261 EM: Round [76] log likelihood: -1583.369885 EM: Round [77] log likelihood: -1583.368561 EM: Round [78] log likelihood: -1583.367289 EM: Round [79] log likelihood: -1583.366065 EM: Round [80] log likelihood: -1583.364888 EM: Round [81] log likelihood: -1583.363756 EM: Round [82] log likelihood: -1583.362667 EM: Round [83] log likelihood: -1583.361620 EM: Round [84] log likelihood: -1583.360613 EM: Round [85] log likelihood: -1583.359644 EM: Round [86] log likelihood: -1583.358713 EM: Round [87] log likelihood: -1583.357817 EM: Round [88] log likelihood: -1583.356955 EM: Round [89] log likelihood: -1583.356126 EM: Round [90] log likelihood: -1583.355329 EM: Round [91] log likelihood: -1583.354562 EM: Round [92] log likelihood: -1583.353824 EM: Round [93] log likelihood: -1583.353115 EM: Round [94] log likelihood: -1583.352432 EM: Round [95] log likelihood: -1583.351775 EM: Round [96] log likelihood: -1583.351144 EM: Round [97] log likelihood: -1583.350536 EM: Round [98] log likelihood: -1583.349952 EM: Round [99] log likelihood: -1583.349389 EM: Round [100] log likelihood: -1583.348848 EM: Round [101] log likelihood: -1583.348328 EM: Round [102] log likelihood: -1583.347827 EM: Round [103] log likelihood: -1583.347346 EM: Round [104] log likelihood: -1583.346883 EM: Round [105] log likelihood: -1583.346437 EM: Round [106] log likelihood: -1583.346008 EM: Round [107] log likelihood: -1583.345595 EM: Round [108] log likelihood: -1583.345199 EM: Round [109] log likelihood: -1583.344817 EM: Round [110] log likelihood: -1583.344449 EM: Round [111] log likelihood: -1583.344096 EM: Round [112] log likelihood: -1583.343756 EM: Round [113] log likelihood: -1583.343429 EM: Round [114] log likelihood: -1583.343114 EM: Round [115] log likelihood: -1583.342811 EM: Round [116] log likelihood: -1583.342520 EM: Round [117] log likelihood: -1583.342239 EM: Round [118] log likelihood: -1583.341970 EM: Round [119] log likelihood: -1583.341710 EM: Round [120] log likelihood: -1583.341460 EM: Round [121] log likelihood: -1583.341220 EM: Round [122] log likelihood: -1583.340989 EM: Round [123] log likelihood: -1583.340767 EM: Round [124] log likelihood: -1583.340553 EM: Round [125] log likelihood: -1583.340347 EM: Round [126] log likelihood: -1583.340149 EM: Round [127] log likelihood: -1583.339958 EM: Round [128] log likelihood: -1583.339775 EM: Round [129] log likelihood: -1583.339598 EM: Round [130] log likelihood: -1583.339429 EM: Round [131] log likelihood: -1583.339265 EM: Round [132] log likelihood: -1583.339108 EM: Round [133] log likelihood: -1583.338957 EM: Round [134] log likelihood: -1583.338811 EM: Round [135] log likelihood: -1583.338671 EM: Round [136] log likelihood: -1583.338537 EM: Round [137] log likelihood: -1583.338407 EM: Round [138] log likelihood: -1583.338282 EM: Round [139] log likelihood: -1583.338162 EM: Round [140] log likelihood: -1583.338047 EM: Round [141] log likelihood: -1583.337936 EM: Round [142] log likelihood: -1583.337829 EM: Round [143] log likelihood: -1583.337726 EM: Round [144] log likelihood: -1583.337627 EM: Stopping iterations at round 144 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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam" Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords CMD: touch /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.10 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/fi_workdir/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir -done, see /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -1464.916540 EM: Round [1] log likelihood: -1464.877460 EM: Round [2] log likelihood: -1464.876909 EM: Round [3] log likelihood: -1464.876901 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 280329213 Execution Time = 5.06 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.EWpmWH8u8E/fi_workdir/microH.dat Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.EWpmWH8u8E/fi_workdir/microH.dat /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/fi_workdir/microH.dat /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.EWpmWH8u8E --json_outfile /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_GZ1_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.EWpmWH8u8E --json_outfile /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2 Running: touch /tmp/nxf.EWpmWH8u8E/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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.00 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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/1173_GZ1_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 [ENSG00000214837.8] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.EWpmWH8u8E/ctat_genome_lib_build_dir > /tmp/nxf.EWpmWH8u8E/1173_GZ1_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.EWpmWH8u8E/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory