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/4d/b6087a7887f23d5d525d4ce2cc2321/tih_rna_sample_00616_B23MVV7LT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/7d3709e8501e1ea3e0efe636af4f9d/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/b6087a7887f23d5d525d4ce2cc2321/tih_rna_sample_00616_B23MVV7LT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/7d3709e8501e1ea3e0efe636af4f9d/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/f0befb752a3c721643fa16f1596928/tih_rna_sample_00616_B23MVV7LT4_1.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00616_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions tih_rna_sample_00616_B23MVV7LT4_1.fusionreport.tsv --gtf /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fa Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf > /tmp/nxf.ILSmsIZhgf/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf > /tmp/nxf.ILSmsIZhgf/cytoBand.txt Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed -parsing GTF file: /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.bed.bedsort.ok Running: bgzip -f /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed.sorted.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.bed.sorted.bed.gz Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.bed.tabix.ok Running: samtools faidx /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00616_B23MVV7LT4_1.star --out_dir /tmp/nxf.ILSmsIZhgf/fi_workdir --reads "/tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' Jun 08 10:30:08 ..... started STAR run Jun 08 10:30:08 ..... loading genome Jun 08 10:31:54 ... generating Suffix Array index Jun 08 10:35:48 ... completed Suffix Array index Jun 08 10:35:48 ..... processing annotations GTF Jun 08 10:35:48 ..... inserting junctions into the genome indices Jun 08 10:36:49 ..... started mapping Jun 08 11:53:51 ..... finished mapping Jun 08 11:53:53 ..... started sorting BAM Jun 08 11:53:54 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00616_B23MVV7LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00616_B23MVV7LT4_1.star.sortedByCoord.out.bam Execution Time = 83.80 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf --CPU 8 --out_prefix tih_rna_sample_00616_B23MVV7LT4_1.star --out_dir /tmp/nxf.ILSmsIZhgf/fi_workdir --reads "/tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_2.fastp.fastq.gz" Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups 11:54:07 : INFO : Done. Execution Time = 0.17 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf -parsing /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] [1300000] [1310000] [1320000] [1330000] [1340000] [1350000] [1360000] [1370000] [1380000] [1390000] [1400000] [1410000] [1420000] [1430000] [1440000] [1450000] [1460000] [1470000] [1480000] [1490000] [1500000] [1510000] [1520000] [1530000] [1540000] [1550000] [1560000] [1570000] [1580000] [1590000] -done parsing /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'low complexity anchor region' => 51, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 68, 'small anchor length' => 297, 'num genes matched < 2' => 5, 'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 54, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 22, 'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 12, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 1, 'excessive soft clipping' => 5732, 'seq-similar region overlap' => 638, 'per_id < 96' => 4531, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6, 'num_hits: 9 != num_counted_on_fusion_contigs 7 ' => 7, 'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 4, ' ** passed ** ' => 28341, 'num_hits: 7 != num_counted_on_fusion_contigs 1 ' => 67 }; -writing fusion junction support info. Execution Time = 0.87 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9 [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: PCDHGA2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [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] -fusion SPANNING read extraction for scaff: PCDHGA2--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] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9 [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: PCDHGA3--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [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] -fusion SPANNING read extraction for scaff: PCDHGA3--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] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9 [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: PCDHGA4--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [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] -fusion SPANNING read extraction for scaff: PCDHGA4--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] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -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] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [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] -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] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -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--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -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] -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] [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] -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] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] -fusion SPANNING read extraction for scaff: SNX29P1--AC138894.4 [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] -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] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] -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] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 89586, 'lacks exon overlap' => 760 }; Execution Time = 1.90 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -8115.593801 EM: Round [1] log likelihood: -8096.929598 EM: Round [2] log likelihood: -8084.777904 EM: Round [3] log likelihood: -8075.035148 EM: Round [4] log likelihood: -8066.873027 EM: Round [5] log likelihood: -8059.824554 EM: Round [6] log likelihood: -8053.615667 EM: Round [7] log likelihood: -8048.080028 EM: Round [8] log likelihood: -8043.110915 EM: Round [9] log likelihood: -8038.634447 EM: Round [10] log likelihood: -8034.595037 EM: Round [11] log likelihood: -8030.947633 EM: Round [12] log likelihood: -8027.653632 EM: Round [13] log likelihood: -8024.678774 EM: Round [14] log likelihood: -8021.992061 EM: Round [15] log likelihood: -8019.565218 EM: Round [16] log likelihood: -8017.372403 EM: Round [17] log likelihood: -8015.390035 EM: Round [18] log likelihood: -8013.596660 EM: Round [19] log likelihood: -8011.972833 EM: Round [20] log likelihood: -8010.500991 EM: Round [21] log likelihood: -8009.165327 EM: Round [22] log likelihood: -8007.951648 EM: Round [23] log likelihood: -8006.847247 EM: Round [24] log likelihood: -8005.840767 EM: Round [25] log likelihood: -8004.922075 EM: Round [26] log likelihood: -8004.082137 EM: Round [27] log likelihood: -8003.312907 EM: Round [28] log likelihood: -8002.607223 EM: Round [29] log likelihood: -8001.958710 EM: Round [30] log likelihood: -8001.361692 EM: Round [31] log likelihood: -8000.811117 EM: Round [32] log likelihood: -8000.302485 EM: Round [33] log likelihood: -7999.831783 EM: Round [34] log likelihood: -7999.395435 EM: Round [35] log likelihood: -7998.990246 EM: Round [36] log likelihood: -7998.613361 EM: Round [37] log likelihood: -7998.262227 EM: Round [38] log likelihood: -7997.934556 EM: Round [39] log likelihood: -7997.628298 EM: Round [40] log likelihood: -7997.341611 EM: Round [41] log likelihood: -7997.072839 EM: Round [42] log likelihood: -7996.820493 EM: Round [43] log likelihood: -7996.583229 EM: Round [44] log likelihood: -7996.359834 EM: Round [45] log likelihood: -7996.149210 EM: Round [46] log likelihood: -7995.950366 EM: Round [47] log likelihood: -7995.762401 EM: Round [48] log likelihood: -7995.584499 EM: Round [49] log likelihood: -7995.415914 EM: Round [50] log likelihood: 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likelihood: -7989.794320 EM: Round [471] log likelihood: -7989.793936 EM: Round [472] log likelihood: -7989.793556 EM: Round [473] log likelihood: -7989.793179 EM: Round [474] log likelihood: -7989.792807 EM: Round [475] log likelihood: -7989.792438 EM: Round [476] log likelihood: -7989.792072 EM: Round [477] log likelihood: -7989.791711 EM: Round [478] log likelihood: -7989.791353 EM: Round [479] log likelihood: -7989.790999 EM: Round [480] log likelihood: -7989.790648 EM: Round [481] log likelihood: -7989.790301 EM: Round [482] log likelihood: -7989.789957 EM: Round [483] log likelihood: -7989.789617 EM: Round [484] log likelihood: -7989.789281 EM: Round [485] log likelihood: -7989.788947 EM: Round [486] log likelihood: -7989.788617 EM: Round [487] log likelihood: -7989.788291 EM: Round [488] log likelihood: -7989.787968 EM: Round [489] log likelihood: -7989.787648 EM: Round [490] log likelihood: -7989.787331 EM: Round [491] log likelihood: -7989.787017 EM: Round [492] log likelihood: -7989.786707 EM: Round [493] log likelihood: -7989.786399 EM: Round [494] log likelihood: -7989.786095 EM: Round [495] log likelihood: -7989.785794 EM: Round [496] log likelihood: -7989.785496 EM: Round [497] log likelihood: -7989.785201 EM: Round [498] log likelihood: -7989.784909 EM: Round [499] log likelihood: -7989.784620 EM: Round [500] log likelihood: -7989.784334 EM: Round [501] log likelihood: -7989.784050 EM: Round [502] log likelihood: -7989.783770 EM: Round [503] log likelihood: -7989.783492 EM: Round [504] log likelihood: -7989.783217 EM: Round [505] log likelihood: -7989.782945 EM: Round [506] log likelihood: -7989.782676 EM: Round [507] log likelihood: -7989.782409 EM: Round [508] log likelihood: -7989.782145 EM: Round [509] log likelihood: -7989.781884 EM: Round [510] log likelihood: -7989.781625 EM: Round [511] log likelihood: -7989.781369 EM: Round [512] log likelihood: -7989.781116 EM: Round [513] log likelihood: -7989.780865 EM: Round [514] log likelihood: -7989.780616 EM: Round [515] log likelihood: -7989.780370 EM: Round [516] log likelihood: -7989.780127 EM: Round [517] log likelihood: -7989.779886 EM: Round [518] log likelihood: -7989.779647 EM: Round [519] log likelihood: -7989.779411 EM: Round [520] log likelihood: -7989.779177 EM: Round [521] log likelihood: -7989.778946 EM: Round [522] log likelihood: -7989.778717 EM: Round [523] log likelihood: -7989.778490 EM: Round [524] log likelihood: -7989.778266 EM: Round [525] log likelihood: -7989.778043 EM: Round [526] log likelihood: -7989.777823 EM: Round [527] log likelihood: -7989.777606 EM: Round [528] log likelihood: -7989.777390 EM: Round [529] log likelihood: -7989.777176 EM: Round [530] log likelihood: -7989.776965 EM: Round [531] log likelihood: -7989.776756 EM: Round [532] log likelihood: -7989.776549 EM: Round [533] log likelihood: -7989.776344 EM: Round [534] log likelihood: -7989.776141 EM: Round [535] log likelihood: -7989.775940 EM: Round [536] log likelihood: -7989.775741 EM: Round [537] log likelihood: -7989.775544 EM: Round [538] log likelihood: -7989.775349 EM: Round [539] log likelihood: -7989.775156 EM: Round [540] log likelihood: -7989.774965 EM: Round [541] log likelihood: -7989.774776 EM: Round [542] log likelihood: -7989.774589 EM: Round [543] log likelihood: -7989.774404 EM: Round [544] log likelihood: -7989.774220 EM: Round [545] log likelihood: -7989.774039 EM: Round [546] log likelihood: -7989.773859 EM: Round [547] log likelihood: -7989.773681 EM: Round [548] log likelihood: -7989.773504 EM: Round [549] log likelihood: -7989.773330 EM: Round [550] log likelihood: -7989.773157 EM: Round [551] log likelihood: -7989.772986 EM: Round [552] log likelihood: -7989.772817 EM: Round [553] log likelihood: -7989.772649 EM: Round [554] log likelihood: -7989.772484 EM: Round [555] log likelihood: -7989.772319 EM: Round [556] log likelihood: -7989.772157 EM: Round [557] log likelihood: -7989.771996 EM: Round [558] log likelihood: -7989.771836 EM: Round [559] log likelihood: -7989.771679 EM: Round [560] log likelihood: -7989.771522 EM: Round [561] log likelihood: -7989.771368 EM: Round [562] log likelihood: -7989.771215 EM: Round [563] log likelihood: -7989.771063 EM: Round [564] log likelihood: -7989.770913 EM: Round [565] log likelihood: -7989.770765 EM: Round [566] log likelihood: -7989.770618 EM: Round [567] log likelihood: -7989.770472 EM: Round [568] log likelihood: -7989.770328 EM: Round [569] log likelihood: -7989.770185 EM: Round [570] log likelihood: -7989.770044 EM: Round [571] log likelihood: -7989.769904 EM: Round [572] log likelihood: -7989.769766 EM: Round [573] log likelihood: -7989.769629 EM: Round [574] log likelihood: -7989.769493 EM: Round [575] log likelihood: -7989.769359 EM: Round [576] log likelihood: -7989.769226 EM: Round [577] log likelihood: -7989.769094 EM: Round [578] log likelihood: -7989.768964 EM: Round [579] log likelihood: -7989.768835 EM: Round [580] log likelihood: -7989.768707 EM: Round [581] log likelihood: -7989.768581 EM: Round [582] log likelihood: -7989.768455 EM: Round [583] log likelihood: -7989.768332 EM: Round [584] log likelihood: -7989.768209 EM: Round [585] log likelihood: -7989.768087 EM: Round [586] log likelihood: -7989.767967 EM: Round [587] log likelihood: -7989.767848 EM: Round [588] log likelihood: -7989.767730 EM: Round [589] log likelihood: -7989.767613 EM: Round [590] log likelihood: -7989.767498 EM: Round [591] log likelihood: -7989.767383 EM: Round [592] log likelihood: -7989.767270 EM: Round [593] log likelihood: -7989.767158 EM: Round [594] log likelihood: -7989.767047 EM: Round [595] log likelihood: -7989.766937 EM: Round [596] log likelihood: -7989.766828 EM: Round [597] log likelihood: -7989.766721 EM: Round [598] log likelihood: -7989.766614 EM: Round [599] log likelihood: -7989.766508 EM: Round [600] log likelihood: -7989.766404 EM: Round [601] log likelihood: -7989.766300 EM: Round [602] log likelihood: -7989.766198 EM: Round [603] log likelihood: -7989.766096 EM: Round [604] log likelihood: -7989.765996 EM: Round [605] log likelihood: -7989.765897 EM: Stopping iterations at round 605 due to insufficient improvement in likelihood. Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam" Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam || : Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/tih_rna_sample_00616_B23MVV7LT4_1.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam Execution Time = 0.02 minutes. CMD: samtools index /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.39 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.FusionJuncSpan Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.FusionJuncSpan Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.Pfam.gff3 Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.Pfam.gff3 > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.Pfam.bed Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.seqsimilar.gff3 Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.seqsimilar.gff3 > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.igv.seqsimilar.bed Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa > /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/tih_rna_sample_00616_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir -done, see /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -3894.504324 EM: Round [1] log likelihood: -3894.387567 EM: Round [2] log likelihood: -3894.387455 EM: Round [3] log likelihood: -3894.387455 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_1.fastp.fastq.gz: 296476201 Execution Time = 5.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa --gtf /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf > /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fa --gtf /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gtf > /tmp/nxf.ILSmsIZhgf/fi_workdir/microH.dat Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.ILSmsIZhgf/fi_workdir/microH.dat /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_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.ILSmsIZhgf/fi_workdir/microH.dat /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.tsv Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.ILSmsIZhgf --json_outfile /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00616_B23MVV7LT4_1 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.ILSmsIZhgf --json_outfile /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fusion_inspector_web.json --file_prefix tih_rna_sample_00616_B23MVV7LT4_1 Running: touch /tmp/nxf.ILSmsIZhgf/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.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00616_B23MVV7LT4_1 --html_output /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fusion_inspector_web.json --input_file_prefix tih_rna_sample_00616_B23MVV7LT4_1 --html_output /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.fusion_inspector_web.html Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000280136.2] 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 [ENSG00000158482.10] WARNING, no entry stored in dbm for [ENSG00000275654.1] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] WARNING, no entry stored in dbm for [ENSG00000286065.2] WARNING, no entry stored in dbm for [ENSG00000286030.2] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.ILSmsIZhgf/ctat_genome_lib_build_dir > /tmp/nxf.ILSmsIZhgf/tih_rna_sample_00616_B23MVV7LT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.ILSmsIZhgf/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory