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/7a/eea927ce9804024e9c2a7549b0dd03/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/82da9e23cc82e629feba65aab3575d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/eea927ce9804024e9c2a7549b0dd03/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/82da9e23cc82e629feba65aab3575d/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/ae870c6c339208a20a71e4c54d691e/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.uEBBjWs2L5/1173_NMN_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_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusionreport.tsv --gtf /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.uEBBjWs2L5/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.uEBBjWs2L5/cytoBand.txt Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed -parsing GTF file: /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.bedsort.ok Running: bgzip -f /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.sorted.bed.gz Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.bed.tabix.ok Running: samtools faidx /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.uEBBjWs2L5/fi_workdir --reads "/tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:26:08 ..... started STAR run Jun 08 10:26:08 ..... loading genome Jun 08 10:27:50 ... generating Suffix Array index Jun 08 10:31:33 ... completed Suffix Array index Jun 08 10:31:33 ..... processing annotations GTF Jun 08 10:31:34 ..... inserting junctions into the genome indices Jun 08 10:32:34 ..... started mapping Jun 08 11:13:54 ..... finished mapping Jun 08 11:13:55 ..... started sorting BAM Jun 08 11:13:56 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam Execution Time = 47.82 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa --max_mate_dist 100000 -G /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --CPU 8 --out_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star --out_dir /tmp/nxf.uEBBjWs2L5/fi_workdir --reads "/tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz" Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups 11:14:05 : INFO : Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam -o /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf -parsing /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] [1300000] [1310000] [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] -done parsing /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'per_id < 96' => 6427, 'small anchor length' => 28, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 21, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 36, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 77, ' ** passed ** ' => 8393, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2464, 'num genes matched < 2' => 12, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 9, 'seq-similar region overlap' => 264, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 14, 'exons hit < 2' => 2, 'excessive soft clipping' => 9696, 'low complexity anchor region' => 10, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8 }; -writing fusion junction support info. Execution Time = 0.91 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_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] -fusion SPANNING read extraction for scaff: AC068769.1--KLHL6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: CDK14--KCNAB1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: CRY1--RPAP3 [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: EFL1--GOLGA6L11P [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] -fusion SPANNING read extraction for scaff: GOLGA6L10--GOLGA2P6 [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: HIBADH--CPVL [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] -fusion SPANNING read extraction for scaff: MARK2--PPM1D [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] -fusion SPANNING read extraction for scaff: NELFB--TRAF2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] -fusion SPANNING read extraction for scaff: NFIB--AL035252.5 [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] -fusion SPANNING read extraction for scaff: NOLC1--PPRC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHA11--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] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8 [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: PCDHGA6--PCDHGB6 [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] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4 [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: PCDHGA6--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] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] -fusion SPANNING read extraction for scaff: PCDHGA6--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] [33000] [34000] [35000] [36000] [37000] [38000] -fusion SPANNING read extraction for scaff: PCDHGA6--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] -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] [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] -fusion SPANNING read extraction for scaff: PPP5C--TSHZ2 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: PTPN20--BMS1P7 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: RIMS4--PGBD4P2 [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: STON1--GTF2A1L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] -fusion SPANNING read extraction for scaff: TLK2--LINC01347 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] -fusion SPANNING read extraction for scaff: TSHZ2--HIF3A [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 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: USP2-AS1--MFRP [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] -fusion SPANNING read extraction for scaff: VPS13A--PCSK5 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 10424, 'seq similar region alignment' => 46864 }; Execution Time = 2.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -8307.068619 EM: Round [1] log likelihood: -8307.045433 EM: Round [2] log likelihood: -8307.024071 EM: Round [3] log likelihood: -8307.003425 EM: Round [4] log likelihood: -8306.983423 EM: Round [5] log likelihood: -8306.964034 EM: Round [6] log likelihood: -8306.945236 EM: Round [7] log likelihood: -8306.927004 EM: Round [8] log likelihood: -8306.909316 EM: Round [9] log likelihood: -8306.892152 EM: Round [10] log likelihood: -8306.875491 EM: Round [11] log likelihood: -8306.859315 EM: Round [12] log likelihood: -8306.843605 EM: Round [13] log likelihood: -8306.828344 EM: Round [14] log likelihood: -8306.813517 EM: Round [15] log likelihood: -8306.799107 EM: Round [16] log likelihood: -8306.785100 EM: Round [17] log likelihood: -8306.771482 EM: Round [18] log likelihood: -8306.758239 EM: Round [19] log likelihood: -8306.745358 EM: Round [20] log likelihood: -8306.732827 EM: Round [21] log likelihood: -8306.720635 EM: Round [22] log likelihood: -8306.708770 EM: Round [23] log likelihood: -8306.697222 EM: Round [24] log likelihood: -8306.685979 EM: Round [25] log likelihood: -8306.675032 EM: Round [26] log likelihood: -8306.664372 EM: Round [27] log likelihood: -8306.653990 EM: Round [28] log likelihood: -8306.643876 EM: Round [29] log likelihood: -8306.634023 EM: Round [30] log likelihood: -8306.624422 EM: Round [31] log likelihood: -8306.615066 EM: Round [32] log likelihood: -8306.605946 EM: Round [33] log likelihood: -8306.597057 EM: Round [34] log likelihood: -8306.588391 EM: Round [35] log likelihood: -8306.579941 EM: Round [36] log likelihood: -8306.571701 EM: Round [37] log likelihood: -8306.563664 EM: Round [38] log likelihood: -8306.555826 EM: Round [39] log likelihood: -8306.548180 EM: Round [40] log likelihood: -8306.540720 EM: Round [41] log likelihood: -8306.533441 EM: Round [42] log likelihood: -8306.526339 EM: Round [43] log likelihood: -8306.519407 EM: Round [44] log likelihood: -8306.512642 EM: Round [45] log likelihood: -8306.506039 EM: Round [46] log likelihood: -8306.499592 EM: Round [47] log likelihood: -8306.493299 EM: Round [48] log likelihood: -8306.487154 EM: Round [49] log likelihood: -8306.481153 EM: Round [50] log likelihood: -8306.475294 EM: Round [51] log likelihood: -8306.469570 EM: Round [52] log likelihood: -8306.463980 EM: Round [53] log likelihood: -8306.458520 EM: Round [54] log likelihood: -8306.453186 EM: Round [55] log likelihood: -8306.447974 EM: Round [56] log likelihood: -8306.442882 EM: Round [57] log likelihood: -8306.437906 EM: Round [58] log likelihood: -8306.433044 EM: Round [59] log likelihood: -8306.428292 EM: Round [60] log likelihood: -8306.423647 EM: Round [61] log likelihood: -8306.419108 EM: Round [62] log likelihood: -8306.414670 EM: Round [63] log likelihood: -8306.410332 EM: Round [64] log likelihood: -8306.406090 EM: Round [65] log likelihood: -8306.401943 EM: Round [66] log likelihood: -8306.397888 EM: Round [67] log likelihood: -8306.393923 EM: Round [68] log likelihood: -8306.390045 EM: Round [69] log likelihood: -8306.386253 EM: Round [70] log likelihood: -8306.382543 EM: Round [71] log likelihood: -8306.378915 EM: Round [72] log likelihood: -8306.375366 EM: Round [73] log likelihood: -8306.371894 EM: Round [74] log likelihood: -8306.368497 EM: Round [75] log likelihood: -8306.365173 EM: Round [76] log likelihood: -8306.361921 EM: Round [77] log likelihood: -8306.358739 EM: Round [78] log likelihood: -8306.355625 EM: Round [79] log likelihood: -8306.352577 EM: Round [80] log likelihood: -8306.349595 EM: Round [81] log likelihood: -8306.346675 EM: Round [82] log likelihood: -8306.343818 EM: Round [83] log likelihood: -8306.341020 EM: Round [84] log likelihood: -8306.338282 EM: Round [85] log likelihood: -8306.335601 EM: Round [86] log likelihood: -8306.332976 EM: Round [87] log likelihood: -8306.330406 EM: Round [88] log likelihood: -8306.327890 EM: Round [89] log likelihood: -8306.325425 EM: Round [90] log likelihood: -8306.323012 EM: Round [91] log likelihood: -8306.320648 EM: Round [92] log likelihood: -8306.318334 EM: Round [93] log likelihood: -8306.316066 EM: Round [94] log likelihood: -8306.313845 EM: Round [95] log likelihood: -8306.311669 EM: Round [96] log likelihood: -8306.309538 EM: Round [97] log likelihood: -8306.307450 EM: Round [98] log likelihood: -8306.305404 EM: Round [99] log likelihood: -8306.303399 EM: Round [100] log likelihood: -8306.301435 EM: Round [101] log likelihood: -8306.299510 EM: Round [102] log likelihood: -8306.297623 EM: Round [103] log likelihood: -8306.295775 EM: Round [104] log likelihood: -8306.293963 EM: Round [105] log likelihood: -8306.292186 EM: Round [106] log likelihood: -8306.290445 EM: Round [107] log likelihood: -8306.288739 EM: Round [108] log likelihood: -8306.287066 EM: Round [109] log likelihood: -8306.285425 EM: Round [110] log likelihood: -8306.283817 EM: Round [111] log likelihood: -8306.282240 EM: Round [112] log likelihood: -8306.280694 EM: Round [113] log likelihood: -8306.279177 EM: Round [114] log likelihood: -8306.277690 EM: Round [115] log likelihood: -8306.276232 EM: Round [116] log likelihood: -8306.274802 EM: Round [117] log likelihood: -8306.273398 EM: Round [118] log likelihood: -8306.272022 EM: Round [119] log likelihood: -8306.270672 EM: Round [120] log likelihood: -8306.269348 EM: Round [121] log likelihood: -8306.268048 EM: Round [122] log likelihood: -8306.266773 EM: Round [123] log likelihood: -8306.265522 EM: Round [124] log likelihood: -8306.264295 EM: Round [125] log likelihood: -8306.263090 EM: Round [126] log likelihood: -8306.261908 EM: Round [127] log likelihood: -8306.260747 EM: Round [128] log likelihood: -8306.259608 EM: Round [129] log likelihood: -8306.258490 EM: Round [130] log likelihood: -8306.257393 EM: Round [131] log likelihood: -8306.256316 EM: Round [132] log likelihood: -8306.255258 EM: Round [133] log likelihood: -8306.254220 EM: Round [134] log likelihood: -8306.253200 EM: Round [135] log likelihood: -8306.252199 EM: Round [136] log likelihood: -8306.251216 EM: Round [137] log likelihood: -8306.250250 EM: Round [138] log likelihood: -8306.249302 EM: Round [139] log likelihood: -8306.248371 EM: Round [140] log likelihood: -8306.247456 EM: Round [141] log likelihood: -8306.246557 EM: Round [142] log likelihood: -8306.245674 EM: Round [143] log likelihood: -8306.244807 EM: Round [144] log likelihood: -8306.243955 EM: Round [145] log likelihood: -8306.243118 EM: Round [146] log likelihood: -8306.242295 EM: Round [147] log likelihood: -8306.241487 EM: Round [148] log likelihood: -8306.240692 EM: Round [149] log likelihood: -8306.239911 EM: Round [150] log likelihood: -8306.239144 EM: Round [151] log likelihood: -8306.238389 EM: Round [152] log likelihood: -8306.237647 EM: Round [153] log likelihood: -8306.236918 EM: Round [154] log likelihood: -8306.236202 EM: Round [155] log likelihood: -8306.235497 EM: Round [156] log likelihood: -8306.234804 EM: Round [157] log likelihood: -8306.234122 EM: Round [158] log likelihood: -8306.233452 EM: Round [159] log likelihood: -8306.232793 EM: Round [160] log likelihood: -8306.232145 EM: Round [161] log likelihood: -8306.231507 EM: Round [162] log likelihood: -8306.230880 EM: Round [163] log likelihood: -8306.230263 EM: Round [164] log likelihood: -8306.229656 EM: Round [165] log likelihood: -8306.229059 EM: Round [166] log likelihood: -8306.228471 EM: Round [167] log likelihood: -8306.227893 EM: Round [168] log likelihood: -8306.227324 EM: Round [169] log likelihood: -8306.226764 EM: Round [170] log likelihood: -8306.226212 EM: Round [171] log likelihood: -8306.225670 EM: Round [172] log likelihood: -8306.225136 EM: Round [173] log likelihood: -8306.224610 EM: Round [174] log likelihood: -8306.224092 EM: Round [175] log likelihood: -8306.223583 EM: Round [176] log likelihood: -8306.223081 EM: Round [177] log likelihood: -8306.222587 EM: Round [178] log likelihood: -8306.222100 EM: Round [179] log likelihood: -8306.221621 EM: Round [180] log likelihood: -8306.221149 EM: Round [181] log likelihood: -8306.220684 EM: Round [182] log likelihood: -8306.220226 EM: Round [183] log likelihood: -8306.219775 EM: Round [184] log likelihood: -8306.219331 EM: Round [185] log likelihood: -8306.218893 EM: Round [186] log likelihood: -8306.218461 EM: Round [187] log likelihood: -8306.218036 EM: Round [188] log likelihood: -8306.217617 EM: Round [189] log likelihood: -8306.217204 EM: Round [190] log likelihood: -8306.216797 EM: Round [191] log likelihood: -8306.216396 EM: Round [192] log likelihood: -8306.216001 EM: Round [193] log likelihood: -8306.215611 EM: Round [194] log likelihood: -8306.215226 EM: Round [195] log likelihood: -8306.214847 EM: Round [196] log likelihood: -8306.214474 EM: Round [197] log likelihood: -8306.214105 EM: Round [198] log likelihood: -8306.213742 EM: Round [199] log likelihood: -8306.213383 EM: Round [200] log likelihood: -8306.213030 EM: Round [201] log likelihood: -8306.212681 EM: Round [202] log likelihood: -8306.212337 EM: Round [203] log likelihood: -8306.211998 EM: Round [204] log likelihood: -8306.211663 EM: Round [205] log likelihood: -8306.211333 EM: Round [206] log likelihood: -8306.211007 EM: Round [207] log likelihood: -8306.210686 EM: Round [208] log likelihood: -8306.210368 EM: Round [209] log likelihood: -8306.210055 EM: Round [210] log likelihood: -8306.209746 EM: Round [211] log likelihood: -8306.209441 EM: Round [212] log likelihood: -8306.209140 EM: Round [213] log likelihood: -8306.208842 EM: Round [214] log likelihood: -8306.208549 EM: Round [215] log likelihood: -8306.208259 EM: Round [216] log likelihood: -8306.207973 EM: Round [217] log likelihood: -8306.207690 EM: Round [218] log likelihood: -8306.207411 EM: Round [219] log likelihood: -8306.207136 EM: Round [220] log likelihood: -8306.206863 EM: Round [221] log likelihood: -8306.206595 EM: Round [222] log likelihood: -8306.206329 EM: Round [223] log likelihood: -8306.206067 EM: Round [224] log likelihood: -8306.205807 EM: Round [225] log likelihood: -8306.205551 EM: Round [226] log likelihood: -8306.205298 EM: Round [227] log likelihood: -8306.205048 EM: Round [228] log likelihood: -8306.204801 EM: Round [229] log likelihood: -8306.204557 EM: Round [230] log likelihood: -8306.204316 EM: Round [231] log likelihood: -8306.204077 EM: Round [232] log likelihood: -8306.203842 EM: Round [233] log likelihood: -8306.203609 EM: Round [234] log likelihood: -8306.203378 EM: Round [235] log likelihood: -8306.203151 EM: Round [236] log likelihood: -8306.202925 EM: Round [237] log likelihood: -8306.202703 EM: Round [238] log likelihood: -8306.202483 EM: Round [239] log likelihood: -8306.202265 EM: Round [240] log likelihood: -8306.202050 EM: Round [241] log likelihood: -8306.201837 EM: Round [242] log likelihood: -8306.201626 EM: Round [243] log likelihood: -8306.201418 EM: Round [244] log likelihood: -8306.201212 EM: Round [245] log likelihood: -8306.201008 EM: Round [246] log likelihood: -8306.200807 EM: Round [247] log likelihood: -8306.200607 EM: Round [248] log likelihood: -8306.200410 EM: Round [249] log likelihood: -8306.200215 EM: Round [250] log likelihood: -8306.200022 EM: Round [251] log likelihood: -8306.199830 EM: Round [252] log likelihood: -8306.199641 EM: Round [253] log likelihood: -8306.199454 EM: Round [254] log likelihood: -8306.199269 EM: Round [255] log likelihood: -8306.199085 EM: Round [256] log likelihood: -8306.198904 EM: Round [257] log likelihood: -8306.198724 EM: Round [258] log likelihood: -8306.198546 EM: Round [259] log likelihood: -8306.198370 EM: Round [260] log likelihood: -8306.198196 EM: Round [261] log likelihood: -8306.198023 EM: Round [262] log likelihood: -8306.197852 EM: Round [263] log likelihood: -8306.197683 EM: Round [264] log likelihood: -8306.197515 EM: Round [265] log likelihood: -8306.197349 EM: Round [266] log likelihood: -8306.197185 EM: Round [267] log likelihood: -8306.197022 EM: Round [268] log likelihood: -8306.196861 EM: Round [269] log likelihood: -8306.196701 EM: Round [270] log likelihood: -8306.196543 EM: Round [271] log likelihood: -8306.196386 EM: Round [272] log likelihood: -8306.196231 EM: Round [273] log likelihood: -8306.196077 EM: Round [274] log likelihood: -8306.195925 EM: Round [275] log likelihood: -8306.195774 EM: Round [276] log likelihood: -8306.195625 EM: Round [277] log likelihood: -8306.195476 EM: Round [278] log likelihood: -8306.195330 EM: Round [279] log likelihood: -8306.195184 EM: Round [280] log likelihood: -8306.195040 EM: Round [281] log likelihood: -8306.194897 EM: Round [282] log likelihood: -8306.194755 EM: Round [283] log likelihood: -8306.194615 EM: Round [284] log likelihood: -8306.194476 EM: Round [285] log likelihood: -8306.194338 EM: Round [286] log likelihood: -8306.194201 EM: Round [287] log likelihood: -8306.194066 EM: Round [288] log likelihood: -8306.193932 EM: Round [289] log likelihood: -8306.193798 EM: Round [290] log likelihood: -8306.193666 EM: Round [291] log likelihood: -8306.193536 EM: Round [292] log likelihood: -8306.193406 EM: Round [293] log likelihood: -8306.193277 EM: Round [294] log likelihood: -8306.193150 EM: Round [295] log likelihood: -8306.193023 EM: Round [296] log likelihood: -8306.192898 EM: Round [297] log likelihood: -8306.192773 EM: Round [298] log likelihood: -8306.192650 EM: Round [299] log likelihood: -8306.192528 EM: Round [300] log likelihood: -8306.192406 EM: Round [301] log likelihood: -8306.192286 EM: Round [302] log likelihood: -8306.192167 EM: Round [303] log likelihood: -8306.192048 EM: Round [304] log likelihood: -8306.191931 EM: Round [305] log likelihood: -8306.191814 EM: Round [306] log likelihood: -8306.191699 EM: Round [307] log likelihood: -8306.191584 EM: Round [308] log likelihood: -8306.191471 EM: Round [309] log likelihood: -8306.191358 EM: Round [310] log likelihood: -8306.191246 EM: Round [311] log likelihood: -8306.191135 EM: Round [312] log likelihood: -8306.191025 EM: Round [313] log likelihood: -8306.190916 EM: Round [314] log likelihood: -8306.190807 EM: Round [315] log likelihood: -8306.190700 EM: Round [316] log likelihood: -8306.190593 EM: Round [317] log likelihood: -8306.190487 EM: Round [318] log likelihood: -8306.190382 EM: Round [319] log likelihood: -8306.190278 EM: Round [320] log likelihood: -8306.190174 EM: Round [321] log likelihood: -8306.190072 EM: Round [322] log likelihood: -8306.189970 EM: Round [323] log likelihood: -8306.189868 EM: Round [324] log likelihood: -8306.189768 EM: Round [325] log likelihood: -8306.189668 EM: Stopping iterations at round 325 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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam" Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa - | samtools sort -@ 8 - -o /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam || : Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords CMD: touch /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.FusionJuncSpan Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.gff3 > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.Pfam.bed Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.gff3 > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.igv.seqsimilar.bed Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa > /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/fi_workdir/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir -done, see /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -7904.799434 EM: Round [1] log likelihood: -7904.798257 EM: Round [2] log likelihood: -7904.798207 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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 257771495 Execution Time = 4.62 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fa --gtf /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gtf > /tmp/nxf.uEBBjWs2L5/fi_workdir/microH.dat Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.uEBBjWs2L5/fi_workdir/microH.dat /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/fi_workdir/microH.dat /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.uEBBjWs2L5 --json_outfile /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_NMN_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.uEBBjWs2L5 --json_outfile /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --file_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2 Running: touch /tmp/nxf.uEBBjWs2L5/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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.json --input_file_prefix 1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2 --html_output /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.fusion_inspector_web.html Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/1173_NMN_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.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000286472.1] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000214837.8] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000270025.2] WARNING, no entry stored in dbm for [ENSG00000241621.1] WARNING, no entry stored in dbm for [ENSG00000245248.8] WARNING, no entry stored in dbm for [ENSG00000245248.8] WARNING, no entry stored in dbm for [ENSG00000223698.3] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.uEBBjWs2L5/ctat_genome_lib_build_dir > /tmp/nxf.uEBBjWs2L5/1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.uEBBjWs2L5/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory