Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/419c116728119ba56d078a1b40bf28/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_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/35/125125eb9e288fcb0be5230262a36e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/125125eb9e288fcb0be5230262a36e/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/419c116728119ba56d078a1b40bf28/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/3c7d07aaba0594e37b01d73884e753/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusionreport.tsv --gtf /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.eDQ4yJzzvU/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.eDQ4yJzzvU/cytoBand.txt Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed -parsing GTF file: /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.eDQ4yJzzvU/fi_workdir --reads "/tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 09:55:08 ..... started STAR run Jun 08 09:55:08 ..... loading genome Jun 08 09:56:53 ... generating Suffix Array index Jun 08 10:00:48 ... completed Suffix Array index Jun 08 10:00:49 ..... processing annotations GTF Jun 08 10:00:49 ..... inserting junctions into the genome indices Jun 08 10:01:50 ..... started mapping Jun 08 10:54:58 ..... finished mapping Jun 08 10:55:00 ..... started sorting BAM Jun 08 10:55:00 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam Execution Time = 59.88 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --CPU 8 --out_prefix 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star --out_dir /tmp/nxf.eDQ4yJzzvU/fi_workdir --reads "/tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups 10:55:04 : INFO : Done. Execution Time = 0.05 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf -parsing /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] -done parsing /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'excessive soft clipping' => 3313, 'num genes matched < 2' => 10, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8, 'seq-similar region overlap' => 18, 'low complexity anchor region' => 18, ' ** passed ** ' => 6377, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9, 'small anchor length' => 152, 'per_id < 96' => 2906, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 32 }; -writing fusion junction support info. Execution Time = 0.42 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: AC092666.2--ACTR3B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHA7--PCDHAC2 [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: PCDHA7--PCDHA13 [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: PCDHGA5--PCDHGA8 [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: PCDHGA5--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3 [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: PCDHGA5--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] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] -fusion SPANNING read extraction for scaff: PCDHGA5--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] [28000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11 [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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [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] -fusion SPANNING read extraction for scaff: TCEAL4--MTRNR2L12 [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] -fusion SPANNING read extraction for scaff: TLK2--LINC01347 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: 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] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 968, 'seq similar region alignment' => 5619 }; Execution Time = 0.90 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -3519.248944 EM: Round [1] log likelihood: -3518.563840 EM: Round [2] log likelihood: -3518.472049 EM: Round [3] log likelihood: -3518.406234 EM: Round [4] log likelihood: -3518.341434 EM: Round [5] log likelihood: -3518.276635 EM: Round [6] log likelihood: -3518.211837 EM: Round [7] log likelihood: -3518.147089 EM: Round [8] log likelihood: -3518.082441 EM: Round [9] log likelihood: -3518.017947 EM: Round [10] log likelihood: -3517.953661 EM: Round [11] log likelihood: -3517.889637 EM: Round [12] log likelihood: -3517.825929 EM: Round [13] log likelihood: -3517.762591 EM: Round [14] log likelihood: -3517.699676 EM: Round [15] log likelihood: -3517.637236 EM: Round [16] log likelihood: -3517.575319 EM: Round [17] log likelihood: -3517.513974 EM: Round [18] log likelihood: -3517.453247 EM: Round [19] log likelihood: -3517.393180 EM: Round [20] log likelihood: -3517.333815 EM: Round [21] log likelihood: -3517.275187 EM: Round [22] log likelihood: -3517.217334 EM: Round [23] log likelihood: -3517.160285 EM: Round [24] log likelihood: -3517.104072 EM: Round [25] log likelihood: -3517.048718 EM: Round [26] log likelihood: -3516.994248 EM: Round [27] log likelihood: -3516.940682 EM: Round [28] log likelihood: -3516.888036 EM: Round [29] log likelihood: -3516.836326 EM: Round [30] log likelihood: -3516.785563 EM: Round [31] log likelihood: -3516.735756 EM: Round [32] log likelihood: -3516.686913 EM: Round [33] log likelihood: -3516.639037 EM: Round [34] log likelihood: -3516.592131 EM: Round [35] log likelihood: -3516.546196 EM: Round [36] log likelihood: -3516.501229 EM: Round [37] log likelihood: -3516.457227 EM: Round [38] log likelihood: -3516.414184 EM: Round [39] log likelihood: -3516.372094 EM: Round [40] log likelihood: -3516.330949 EM: Round [41] log likelihood: -3516.290739 EM: Round [42] log likelihood: -3516.251453 EM: Round [43] log likelihood: -3516.213080 EM: Round [44] log likelihood: -3516.175607 EM: Round [45] log likelihood: -3516.139021 EM: Round [46] log likelihood: -3516.103307 EM: Round [47] log likelihood: -3516.068450 EM: Round [48] log likelihood: -3516.034436 EM: Round [49] log likelihood: -3516.001249 EM: Round [50] log likelihood: -3515.968872 EM: Round [51] log likelihood: -3515.937288 EM: Round [52] log likelihood: -3515.906482 EM: Round [53] log likelihood: -3515.876436 EM: Round [54] log likelihood: -3515.847133 EM: Round [55] log likelihood: -3515.818557 EM: Round [56] log likelihood: -3515.790691 EM: Round [57] log likelihood: -3515.763516 EM: Round [58] log likelihood: -3515.737018 EM: Round [59] log likelihood: -3515.711178 EM: Round [60] log likelihood: -3515.685980 EM: Round [61] log likelihood: -3515.661408 EM: Round [62] log likelihood: -3515.637445 EM: Round [63] log likelihood: -3515.614076 EM: Round [64] log likelihood: -3515.591285 EM: Round [65] log likelihood: -3515.569057 EM: Round [66] log likelihood: -3515.547375 EM: Round [67] log likelihood: -3515.526226 EM: Round [68] log likelihood: -3515.505594 EM: Round [69] log likelihood: -3515.485466 EM: Round [70] log likelihood: -3515.465827 EM: Round [71] log likelihood: -3515.446664 EM: Round [72] log likelihood: -3515.427963 EM: Round [73] log likelihood: -3515.409712 EM: Round [74] log likelihood: -3515.391897 EM: Round [75] log likelihood: -3515.374507 EM: Round [76] log likelihood: -3515.357529 EM: Round [77] log likelihood: -3515.340952 EM: Round [78] log likelihood: -3515.324764 EM: Round [79] log likelihood: -3515.308954 EM: Round [80] log likelihood: -3515.293512 EM: Round [81] log likelihood: -3515.278426 EM: Round [82] log likelihood: -3515.263688 EM: Round [83] log likelihood: -3515.249287 EM: Round [84] log likelihood: -3515.235213 EM: Round [85] log likelihood: -3515.221458 EM: Round [86] log likelihood: -3515.208012 EM: Round [87] log likelihood: -3515.194866 EM: Round [88] log likelihood: -3515.182013 EM: Round [89] log likelihood: -3515.169443 EM: Round [90] log likelihood: -3515.157150 EM: Round [91] log likelihood: -3515.145126 EM: Round [92] log likelihood: -3515.133362 EM: Round [93] log likelihood: -3515.121852 EM: Round [94] log likelihood: -3515.110589 EM: Round [95] log likelihood: -3515.099566 EM: Round [96] log likelihood: -3515.088777 EM: Round [97] log likelihood: -3515.078215 EM: Round [98] log likelihood: -3515.067875 EM: Round [99] log likelihood: -3515.057749 EM: Round [100] log likelihood: -3515.047833 EM: Round [101] log likelihood: -3515.038121 EM: Round [102] log likelihood: -3515.028608 EM: Round [103] log likelihood: -3515.019288 EM: Round [104] log likelihood: -3515.010157 EM: Round [105] log likelihood: -3515.001209 EM: Round [106] log likelihood: -3514.992440 EM: Round [107] log likelihood: -3514.983845 EM: Round [108] log likelihood: -3514.975420 EM: Round [109] log likelihood: -3514.967161 EM: Round [110] log likelihood: -3514.959063 EM: Round [111] log likelihood: -3514.951123 EM: Round [112] log likelihood: -3514.943336 EM: Round [113] log likelihood: -3514.935699 EM: Round [114] log likelihood: -3514.928207 EM: Round [115] log likelihood: -3514.920859 EM: Round [116] log likelihood: -3514.913650 EM: Round [117] log likelihood: -3514.906576 EM: Round [118] log likelihood: -3514.899635 EM: Round [119] log likelihood: -3514.892824 EM: Round [120] log likelihood: -3514.886139 EM: Round [121] log likelihood: -3514.879577 EM: Round [122] log likelihood: -3514.873136 EM: Round [123] log likelihood: -3514.866813 EM: Round [124] log likelihood: -3514.860606 EM: Round [125] log likelihood: -3514.854511 EM: Round [126] log likelihood: -3514.848526 EM: Round [127] log likelihood: -3514.842649 EM: Round [128] log likelihood: -3514.836877 EM: Round [129] log likelihood: -3514.831207 EM: Round [130] log likelihood: -3514.825639 EM: Round [131] log likelihood: -3514.820169 EM: Round [132] log likelihood: -3514.814796 EM: Round [133] log likelihood: -3514.809517 EM: Round [134] log likelihood: -3514.804330 EM: Round [135] log likelihood: -3514.799233 EM: Round [136] log likelihood: -3514.794225 EM: Round [137] log likelihood: -3514.789304 EM: Round [138] log likelihood: -3514.784468 EM: Round [139] log likelihood: -3514.779714 EM: Round [140] log likelihood: -3514.775042 EM: Round [141] log likelihood: -3514.770450 EM: Round [142] log likelihood: -3514.765936 EM: Round [143] log likelihood: -3514.761498 EM: Round [144] log likelihood: -3514.757136 EM: Round [145] log likelihood: -3514.752847 EM: Round [146] log likelihood: -3514.748630 EM: Round [147] log likelihood: -3514.744483 EM: Round [148] log likelihood: -3514.740406 EM: Round [149] log likelihood: -3514.736397 EM: Round [150] log likelihood: -3514.732455 EM: Round [151] log likelihood: -3514.728577 EM: Round [152] log likelihood: -3514.724764 EM: Round [153] log likelihood: -3514.721014 EM: Round [154] log likelihood: -3514.717326 EM: Round [155] log likelihood: -3514.713698 EM: Round [156] log likelihood: -3514.710129 EM: Round [157] log likelihood: -3514.706618 EM: Round [158] log likelihood: -3514.703165 EM: Round [159] log likelihood: -3514.699768 EM: Round [160] log likelihood: -3514.696426 EM: Round [161] log likelihood: -3514.693138 EM: Round [162] log likelihood: -3514.689904 EM: Round [163] log likelihood: -3514.686721 EM: Round [164] log likelihood: -3514.683589 EM: Round [165] log likelihood: -3514.680508 EM: Round [166] log likelihood: -3514.677476 EM: Round [167] log likelihood: -3514.674493 EM: Round [168] log likelihood: -3514.671557 EM: Round [169] log likelihood: -3514.668668 EM: Round [170] log likelihood: -3514.665825 EM: Round [171] log likelihood: -3514.663028 EM: Round [172] log likelihood: -3514.660274 EM: Round [173] log likelihood: -3514.657564 EM: Round [174] log likelihood: -3514.654897 EM: Round [175] log likelihood: -3514.652272 EM: Round [176] log likelihood: -3514.649688 EM: Round [177] log likelihood: -3514.647145 EM: Round [178] log likelihood: -3514.644642 EM: Round [179] log likelihood: -3514.642178 EM: Round [180] log likelihood: -3514.639753 EM: Round [181] log likelihood: -3514.637366 EM: Round [182] log likelihood: -3514.635016 EM: Round [183] log likelihood: -3514.632702 EM: Round [184] log likelihood: -3514.630425 EM: Round [185] log likelihood: -3514.628183 EM: Round [186] log likelihood: -3514.625976 EM: Round [187] log likelihood: -3514.623803 EM: Round [188] log likelihood: -3514.621664 EM: Round [189] log likelihood: -3514.619557 EM: Round [190] log likelihood: -3514.617484 EM: Round [191] log likelihood: -3514.615442 EM: Round [192] log likelihood: -3514.613432 EM: Round [193] log likelihood: -3514.611453 EM: Round [194] log likelihood: -3514.609505 EM: Round [195] log likelihood: -3514.607586 EM: Round [196] log likelihood: -3514.605697 EM: Round [197] log likelihood: -3514.603837 EM: Round [198] log likelihood: -3514.602005 EM: Round [199] log likelihood: -3514.600202 EM: Round [200] log likelihood: -3514.598426 EM: Round [201] log likelihood: -3514.596677 EM: Round [202] log likelihood: -3514.594955 EM: Round [203] log likelihood: -3514.593259 EM: Round [204] log likelihood: -3514.591589 EM: Round [205] log likelihood: -3514.589945 EM: Round [206] log likelihood: -3514.588325 EM: Round [207] log likelihood: -3514.586731 EM: Round [208] log likelihood: -3514.585160 EM: Round [209] log likelihood: -3514.583613 EM: Round [210] log likelihood: -3514.582090 EM: Round [211] log likelihood: -3514.580590 EM: Round [212] log likelihood: -3514.579112 EM: Round [213] log likelihood: -3514.577657 EM: Round [214] log likelihood: -3514.576224 EM: Round [215] log likelihood: -3514.574813 EM: Round [216] log likelihood: -3514.573423 EM: Round [217] log likelihood: -3514.572054 EM: Round [218] log likelihood: -3514.570706 EM: Round [219] log likelihood: -3514.569378 EM: Round [220] log likelihood: -3514.568070 EM: Round [221] log likelihood: -3514.566781 EM: Round [222] log likelihood: -3514.565512 EM: Round [223] log likelihood: -3514.564262 EM: Round [224] log likelihood: -3514.563031 EM: Round [225] log likelihood: -3514.561819 EM: Round [226] log likelihood: -3514.560624 EM: Round [227] log likelihood: -3514.559448 EM: Round [228] log likelihood: -3514.558289 EM: Round [229] log likelihood: -3514.557148 EM: Round [230] log likelihood: -3514.556023 EM: Round [231] log likelihood: -3514.554916 EM: Round [232] log likelihood: -3514.553825 EM: Round [233] log likelihood: -3514.552751 EM: Round [234] log likelihood: -3514.551692 EM: Round [235] log likelihood: -3514.550649 EM: Round [236] log likelihood: -3514.549622 EM: Round [237] log likelihood: -3514.548610 EM: Round [238] log likelihood: -3514.547614 EM: Round [239] log likelihood: -3514.546632 EM: Round [240] log likelihood: -3514.545665 EM: Round [241] log likelihood: -3514.544712 EM: Round [242] log likelihood: -3514.543774 EM: Round [243] log likelihood: -3514.542849 EM: Round [244] log likelihood: -3514.541938 EM: Round [245] log likelihood: -3514.541041 EM: Round [246] log likelihood: -3514.540157 EM: Round [247] log likelihood: -3514.539286 EM: Round [248] log likelihood: -3514.538428 EM: Round [249] log likelihood: -3514.537583 EM: Round [250] log likelihood: -3514.536751 EM: Round [251] log likelihood: -3514.535931 EM: Round [252] log likelihood: -3514.535123 EM: Round [253] log likelihood: -3514.534327 EM: Round [254] log likelihood: -3514.533542 EM: Round [255] log likelihood: -3514.532770 EM: Round [256] log likelihood: -3514.532009 EM: Round [257] log likelihood: -3514.531259 EM: Round [258] log likelihood: -3514.530520 EM: Round [259] log likelihood: -3514.529792 EM: Round [260] log likelihood: -3514.529075 EM: Round [261] log likelihood: -3514.528369 EM: Round [262] log likelihood: -3514.527673 EM: Round [263] log likelihood: -3514.526987 EM: Round [264] log likelihood: -3514.526311 EM: Round [265] log likelihood: -3514.525646 EM: Round [266] log likelihood: -3514.524990 EM: Round [267] log likelihood: -3514.524344 EM: Round [268] log likelihood: -3514.523707 EM: Round [269] log likelihood: -3514.523080 EM: Round [270] log likelihood: -3514.522462 EM: Round [271] log likelihood: -3514.521854 EM: Round [272] log likelihood: -3514.521254 EM: Round [273] log likelihood: -3514.520663 EM: Round [274] log likelihood: -3514.520081 EM: Round [275] log likelihood: -3514.519507 EM: Round [276] log likelihood: -3514.518942 EM: Round [277] log likelihood: -3514.518385 EM: Round [278] log likelihood: -3514.517836 EM: Round [279] log likelihood: -3514.517296 EM: Round [280] log likelihood: -3514.516763 EM: Round [281] log likelihood: -3514.516238 EM: Round [282] log likelihood: -3514.515721 EM: Round [283] log likelihood: -3514.515212 EM: Round [284] log likelihood: -3514.514710 EM: Round [285] log likelihood: -3514.514215 EM: Round [286] log likelihood: -3514.513728 EM: Round [287] log likelihood: -3514.513247 EM: Round [288] log likelihood: -3514.512774 EM: Round [289] log likelihood: -3514.512308 EM: Round [290] log likelihood: -3514.511849 EM: Round [291] log likelihood: -3514.511396 EM: Round [292] log likelihood: -3514.510950 EM: Round [293] log likelihood: -3514.510511 EM: Round [294] log likelihood: -3514.510078 EM: Round [295] log likelihood: -3514.509651 EM: Round [296] log likelihood: -3514.509231 EM: Round [297] log likelihood: -3514.508817 EM: Round [298] log likelihood: -3514.508409 EM: Round [299] log likelihood: -3514.508007 EM: Round [300] log likelihood: -3514.507610 EM: Round [301] log likelihood: -3514.507220 EM: Round [302] log likelihood: -3514.506835 EM: Round [303] log likelihood: -3514.506456 EM: Round [304] log likelihood: -3514.506083 EM: Round [305] log likelihood: -3514.505715 EM: Round [306] log likelihood: -3514.505352 EM: Round [307] log likelihood: -3514.504995 EM: Round [308] log likelihood: -3514.504643 EM: Round [309] log likelihood: -3514.504296 EM: Round [310] log likelihood: -3514.503954 EM: Round [311] log likelihood: -3514.503617 EM: Round [312] log likelihood: -3514.503285 EM: Round [313] log likelihood: -3514.502958 EM: Round [314] log likelihood: -3514.502636 EM: Round [315] log likelihood: -3514.502318 EM: Round [316] log likelihood: -3514.502005 EM: Round [317] log likelihood: -3514.501697 EM: Round [318] log likelihood: -3514.501393 EM: Round [319] log likelihood: -3514.501094 EM: Round [320] log likelihood: -3514.500799 EM: Round [321] log likelihood: -3514.500508 EM: Round [322] log likelihood: -3514.500222 EM: Round [323] log likelihood: -3514.499939 EM: Round [324] log likelihood: -3514.499661 EM: Round [325] log likelihood: -3514.499387 EM: Round [326] log likelihood: -3514.499117 EM: Round [327] log likelihood: -3514.498851 EM: Round [328] log likelihood: -3514.498589 EM: Round [329] log likelihood: -3514.498330 EM: Round [330] log likelihood: -3514.498075 EM: Round [331] log likelihood: -3514.497825 EM: Round [332] log likelihood: -3514.497577 EM: Round [333] log likelihood: -3514.497334 EM: Round [334] log likelihood: -3514.497093 EM: Round [335] log likelihood: -3514.496857 EM: Round [336] log likelihood: -3514.496624 EM: Round [337] log likelihood: -3514.496394 EM: Round [338] log likelihood: -3514.496168 EM: Round [339] log likelihood: -3514.495944 EM: Round [340] log likelihood: -3514.495725 EM: Round [341] log likelihood: -3514.495508 EM: Round [342] log likelihood: -3514.495294 EM: Round [343] log likelihood: -3514.495084 EM: Round [344] log likelihood: -3514.494877 EM: Round [345] log likelihood: -3514.494673 EM: Round [346] log likelihood: -3514.494471 EM: Round [347] log likelihood: -3514.494273 EM: Round [348] log likelihood: -3514.494077 EM: Round [349] log likelihood: -3514.493885 EM: Round [350] log likelihood: -3514.493695 EM: Round [351] log likelihood: -3514.493508 EM: Round [352] log likelihood: -3514.493324 EM: Round [353] log likelihood: -3514.493142 EM: Round [354] log likelihood: -3514.492963 EM: Round [355] log likelihood: -3514.492787 EM: Round [356] log likelihood: -3514.492613 EM: Round [357] log likelihood: -3514.492441 EM: Round [358] log likelihood: -3514.492273 EM: Round [359] log likelihood: -3514.492106 EM: Round [360] log likelihood: -3514.491942 EM: Round [361] log likelihood: -3514.491781 EM: Round [362] log likelihood: -3514.491622 EM: Round [363] log likelihood: -3514.491465 EM: Round [364] log likelihood: -3514.491310 EM: Round [365] log likelihood: -3514.491158 EM: Round [366] log likelihood: -3514.491008 EM: Round [367] log likelihood: -3514.490860 EM: Round [368] log likelihood: -3514.490714 EM: Round [369] log likelihood: -3514.490571 EM: Round [370] log likelihood: -3514.490429 EM: Round [371] log likelihood: -3514.490290 EM: Round [372] log likelihood: -3514.490152 EM: Round [373] log likelihood: -3514.490017 EM: Round [374] log likelihood: -3514.489883 EM: Round [375] log likelihood: -3514.489752 EM: Round [376] log likelihood: -3514.489622 EM: Round [377] log likelihood: -3514.489494 EM: Round [378] log likelihood: -3514.489368 EM: Round [379] log likelihood: -3514.489244 EM: Round [380] log likelihood: -3514.489122 EM: Round [381] log likelihood: -3514.489001 EM: Round [382] log likelihood: -3514.488883 EM: Round [383] log likelihood: -3514.488766 EM: Round [384] log likelihood: -3514.488650 EM: Round [385] log likelihood: -3514.488537 EM: Round [386] log likelihood: -3514.488425 EM: Round [387] log likelihood: -3514.488314 EM: Round [388] log likelihood: -3514.488206 EM: Round [389] log likelihood: -3514.488099 EM: Round [390] log likelihood: -3514.487993 EM: Round [391] log likelihood: -3514.487889 EM: Round [392] log likelihood: -3514.487786 EM: Round [393] log likelihood: -3514.487685 EM: Round [394] log likelihood: -3514.487586 EM: Stopping iterations at round 394 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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" [bam_sort_core] merging from 0 files and 8 in-memory blocks... Execution Time = 0.00 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam" Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Execution Time = 0.01 minutes. CMD: samtools index /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.16 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.gff3 > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.Pfam.bed Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa > /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.eDQ4yJzzvU/fi_workdir/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir -done, see /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -2768.914917 EM: Round [1] log likelihood: -2768.294182 EM: Round [2] log likelihood: -2768.266923 EM: Round [3] log likelihood: -2768.265768 EM: Round [4] log likelihood: -2768.265720 EM: Stopping iterations at round 4 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.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 233665214 Execution Time = 4.11 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fa --gtf /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.gtf > /tmp/nxf.eDQ4yJzzvU/fi_workdir/microH.dat Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.eDQ4yJzzvU/fi_workdir/microH.dat /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.eDQ4yJzzvU/fi_workdir/microH.dat /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.eDQ4yJzzvU --json_outfile /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.eDQ4yJzzvU --json_outfile /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --file_prefix 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1 Running: touch /tmp/nxf.eDQ4yJzzvU/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.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.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.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.json --input_file_prefix 1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1 --html_output /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000276538.1] 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] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.eDQ4yJzzvU/ctat_genome_lib_build_dir > /tmp/nxf.eDQ4yJzzvU/1173_M2F_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.eDQ4yJzzvU/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory