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/e2/e007397c5e651dca3b1cbee6499b3e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/e007397c5e651dca3b1cbee6499b3e/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/46db04144dd3ab9fbbe91043c05b61/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/46db04144dd3ab9fbbe91043c05b61/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/d6cd878616aaa848bb8f90b152acdd/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv ==> STAGING COMPLETE (6 inputs) Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv --gtf /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000 Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29297095 29297246 . - . gene_id "5_8S_rRNA^ENSG00000283568.1"; transcript_id "ENST00000637374.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.9-201"; exon_number 1; exon_id "ENSE00003799614.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283568.1"; orig_coord_info "chr20,29297095,29297246,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29741510 29741661 . - . gene_id "5_8S_rRNA^ENSG00000283291.1"; transcript_id "ENST00000638132.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.8-201"; exon_number 1; exon_id "ENSE00003794628.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283291.1"; orig_coord_info "chr20,29741510,29741661,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 30484925 30485076 . - . gene_id "5_8S_rRNA^ENSG00000275877.1"; transcript_id "ENST00000614365.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.3-201"; exon_number 1; exon_id "ENSE00003742842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000275877.1"; orig_coord_info "chr20,30484925,30485076,-"; Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 8256781 8256933 . + . gene_id "5_8S_rRNA^ENSG00000277739.1"; transcript_id "ENST00000610460.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.5-201"; exon_number 1; exon_id "ENSE00003746458.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000277739.1"; orig_coord_info "chr21,8256781,8256933,+"; Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 11249809 11249959 . - . gene_id "5_8S_rRNA^ENSG00000276871.1"; transcript_id "ENST00000612732.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.4-201"; exon_number 1; exon_id "ENSE00003735240.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000276871.1"; orig_coord_info "chr22,11249809,11249959,-"; Done. Execution Time = 0.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv --gtf /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --shrink_introns --max_intron_length 1000 Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_contigs.ok Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_contigs_file_workdir Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_gtf_file_workdir.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/cytoBand.txt Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/cytoBand.txt Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cytoband.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed -parsing GTF file: /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/merged_contig_gtf_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.bedsort.ok Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.bgzip.ok Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.sorted.bed.gz Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.bed.tabix.ok Running: samtools faidx /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/merged_contig_fai.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.KXy1ipFxeT/fi_workdir --reads "/tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz" * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' May 28 22:35:49 ..... started STAR run May 28 22:35:49 ..... loading genome May 28 22:37:42 ... generating Suffix Array index May 28 22:41:37 ... completed Suffix Array index May 28 22:41:37 ..... processing annotations GTF May 28 22:41:38 ..... inserting junctions into the genome indices May 28 22:42:39 ..... started mapping May 28 23:43:37 ..... finished mapping May 28 23:43:39 ..... started sorting BAM May 28 23:43:41 ..... finished successfully * Running CMD: mv Aligned.sortedByCoord.out.bam A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam * Running CMD: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam Execution Time = 67.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --max_mate_dist 100000 -G /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --CPU 8 --out_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3.star --out_dir /tmp/nxf.KXy1ipFxeT/fi_workdir --reads "/tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz" Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/run_STAR.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam -o /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --remove_dups 23:44:05 : INFO : Done. Execution Time = 0.34 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam -o /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --remove_dups Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/mark_dup_reads.ok Running: samtools index /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam Execution Time = 0.05 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam -parsing GTF file: /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf -parsing /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] [1300000] [1310000] [1320000] [1330000] [1340000] [1350000] [1360000] [1370000] [1380000] [1390000] [1400000] [1410000] [1420000] [1430000] [1440000] [1450000] [1460000] [1470000] [1480000] [1490000] [1500000] [1510000] [1520000] [1530000] [1540000] [1550000] [1560000] [1570000] [1580000] [1590000] [1600000] [1610000] [1620000] [1630000] [1640000] [1650000] [1660000] [1670000] [1680000] [1690000] [1700000] [1710000] [1720000] [1730000] [1740000] [1750000] [1760000] [1770000] [1780000] [1790000] [1800000] [1810000] [1820000] [1830000] [1840000] [1850000] [1860000] [1870000] [1880000] [1890000] [1900000] [1910000] [1920000] [1930000] [1940000] [1950000] [1960000] [1970000] [1980000] [1990000] [2000000] [2010000] [2020000] [2030000] [2040000] [2050000] [2060000] [2070000] [2080000] [2090000] [2100000] [2110000] [2120000] [2130000] [2140000] [2150000] [2160000] [2170000] [2180000] [2190000] [2200000] [2210000] [2220000] [2230000] [2240000] [2250000] [2260000] [2270000] [2280000] [2290000] [2300000] [2310000] [2320000] [2330000] [2340000] [2350000] [2360000] [2370000] [2380000] [2390000] [2400000] [2410000] [2420000] [2430000] [2440000] [2450000] [2460000] [2470000] [2480000] [2490000] [2500000] [2510000] [2520000] [2530000] [2540000] [2550000] [2560000] [2570000] [2580000] [2590000] [2600000] [2610000] [2620000] [2630000] [2640000] [2650000] [2660000] [2670000] [2680000] [2690000] [2700000] [2710000] [2720000] [2730000] [2740000] [2750000] [2760000] [2770000] [2780000] [2790000] [2800000] [2810000] [2820000] [2830000] [2840000] [2850000] [2860000] [2870000] [2880000] [2890000] [2900000] [2910000] [2920000] [2930000] [2940000] [2950000] [2960000] [2970000] [2980000] [2990000] [3000000] [3010000] [3020000] [3030000] [3040000] [3050000] [3060000] [3070000] [3080000] [3090000] [3100000] [3110000] [3120000] [3130000] [3140000] [3150000] [3160000] [3170000] [3180000] [3190000] [3200000] [3210000] [3220000] [3230000] [3240000] [3250000] [3260000] [3270000] [3280000] [3290000] [3300000] [3310000] [3320000] [3330000] [3340000] [3350000] [3360000] [3370000] [3380000] [3390000] [3400000] [3410000] [3420000] [3430000] [3440000] [3450000] [3460000] [3470000] [3480000] [3490000] [3500000] [3510000] [3520000] [3530000] [3540000] [3550000] [3560000] [3570000] [3580000] [3590000] [3600000] [3610000] [3620000] [3630000] [3640000] [3650000] [3660000] [3670000] -done parsing /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 26, 'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 43, 'seq-similar region overlap' => 1104, 'excessive soft clipping' => 24453, 'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 60, 'per_id < 96' => 20480, 'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 55, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1422, 'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 8, 'num genes matched < 2' => 21, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 885, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 308, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 26, 'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 11, ' ** passed ** ' => 35059, 'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 18, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 15, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 134, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 24, 'small anchor length' => 119, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 39, 'low complexity anchor region' => 21, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 72, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 212, 'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 685, 'exons hit < 2' => 9 }; -writing fusion junction support info. Execution Time = 2.13 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam -outputting the spanning read info: /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [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] -fusion SPANNING read extraction for scaff: AC096555.1--PCSK2 [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] -fusion SPANNING read extraction for scaff: ACKR2--PCSK2 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: AP005597.1--OR4A16 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: CYP7B1--LINC01414 [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] 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[872000] [873000] [874000] [875000] [876000] [877000] -fusion SPANNING read extraction for scaff: EWSR1--FLI1 -fusion SPANNING read extraction for scaff: FRG1DP--MLLT10P1 -fusion SPANNING read extraction for scaff: FRG1DP--5_8S_rRNA [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] -fusion SPANNING read extraction for scaff: IGH-@-ext--SPG7 [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] -fusion SPANNING read extraction for scaff: IGH@-ext--SPG7 [1000] -fusion SPANNING read extraction for scaff: ITGA9--AC108752.1 [1000] -fusion SPANNING read extraction for scaff: ITGA9--MRPS17P3 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: OR4A11P--OR4A16 [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] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [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: PCDHA10--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [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] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [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] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [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] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [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] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [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] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] -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--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [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--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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -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] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] -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--PCDHGA9 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] -fusion SPANNING read extraction for scaff: SMURF2P1--SP2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408 [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] -fusion SPANNING read extraction for scaff: SPG7--PLSCR5 [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] -fusion SPANNING read extraction for scaff: SPG7--AC092957.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: SUCLA2--AL158828.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: SUCLA2--AL353613.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] -fusion SPANNING read extraction for scaff: SUPT20H--CHRDL2 [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] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] -fusion SPANNING read extraction for scaff: TMEM132B--TDG [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: ZNF875--PCSK2 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 213784, 'lacks exon overlap' => 15034 }; Execution Time = 5.59 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/coalesce_junc_n_span.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj EM: Starting log likelihood: -15045.334989 EM: Round [1] log likelihood: -15031.751764 EM: Round [2] log likelihood: -15028.521480 EM: Round [3] log likelihood: -15026.145290 EM: Round [4] log likelihood: -15024.149101 EM: Round [5] log likelihood: -15022.424354 EM: Round [6] log likelihood: -15020.918374 EM: Round [7] log likelihood: -15019.594763 EM: Round [8] log likelihood: -15018.425405 EM: Round [9] log likelihood: -15017.387642 EM: Round [10] log likelihood: -15016.462831 EM: Round [11] log likelihood: -15015.635443 EM: Round [12] log likelihood: -15014.892427 EM: Round [13] log likelihood: -15014.222745 EM: Round [14] log likelihood: -15013.617012 EM: Round [15] log likelihood: -15013.067209 EM: Round [16] log likelihood: -15012.566460 EM: Round [17] log likelihood: -15012.108845 EM: Round [18] log likelihood: -15011.689256 EM: Round [19] log likelihood: -15011.303270 EM: Round [20] log likelihood: -15010.947048 EM: Round [21] log likelihood: -15010.617253 EM: Round [22] log likelihood: -15010.310976 EM: Round [23] log likelihood: -15010.025678 EM: Round [24] log likelihood: -15009.759137 EM: Round [25] log likelihood: -15009.509408 EM: Round [26] log likelihood: -15009.274785 EM: Round [27] log likelihood: -15009.053769 EM: Round [28] log likelihood: -15008.845041 EM: Round [29] log likelihood: -15008.647438 EM: Round [30] log likelihood: -15008.459936 EM: Round [31] log likelihood: -15008.281629 EM: Round [32] log likelihood: -15008.111715 EM: Round [33] log likelihood: -15007.949484 EM: Round [34] log likelihood: -15007.794307 EM: Round [35] log likelihood: -15007.645623 EM: Round [36] log likelihood: -15007.502933 EM: Round [37] log likelihood: -15007.365792 EM: Round [38] log likelihood: -15007.233803 EM: Round [39] log likelihood: -15007.106610 EM: Round [40] log likelihood: -15006.983892 EM: Round [41] log likelihood: -15006.865362 EM: Round [42] log likelihood: -15006.750762 EM: Round [43] log likelihood: -15006.639856 EM: Round [44] log likelihood: -15006.532433 EM: Round [45] log likelihood: -15006.428300 EM: Round [46] log likelihood: -15006.327280 EM: Round [47] log likelihood: -15006.229215 EM: Round [48] log likelihood: -15006.133956 EM: Round [49] log likelihood: -15006.041369 EM: Round [50] log likelihood: -15005.951329 EM: Round [51] log likelihood: -15005.863722 EM: Round [52] log likelihood: -15005.778442 EM: Round [53] log likelihood: -15005.695388 EM: Round [54] log likelihood: -15005.614470 EM: Round [55] log likelihood: -15005.535601 EM: Round [56] log likelihood: -15005.458700 EM: Round [57] log likelihood: -15005.383693 EM: Round [58] log likelihood: -15005.310507 EM: Round [59] log likelihood: -15005.239076 EM: Round [60] log likelihood: -15005.169335 EM: Round [61] log likelihood: -15005.101226 EM: Round [62] log likelihood: -15005.034691 EM: Round [63] log likelihood: -15004.969675 EM: Round [64] log likelihood: -15004.906127 EM: Round [65] log likelihood: -15004.843999 EM: Round [66] log likelihood: -15004.783241 EM: Round [67] log likelihood: -15004.723811 EM: Round [68] log likelihood: -15004.665664 EM: Round [69] log likelihood: -15004.608760 EM: Round [70] log likelihood: -15004.553059 EM: Round [71] log likelihood: -15004.498522 EM: Round [72] log likelihood: -15004.445114 EM: Round [73] log likelihood: -15004.392800 EM: Round [74] log likelihood: -15004.341544 EM: Round [75] log likelihood: -15004.291316 EM: Round [76] log likelihood: -15004.242084 EM: Round [77] log likelihood: -15004.193818 EM: Round [78] log likelihood: -15004.146488 EM: Round [79] log likelihood: -15004.100067 EM: Round [80] log likelihood: -15004.054528 EM: Round [81] log likelihood: -15004.009844 EM: Round [82] log likelihood: -15003.965991 EM: Round [83] log likelihood: -15003.922945 EM: Round [84] log likelihood: -15003.880681 EM: Round [85] log likelihood: -15003.839177 EM: Round [86] log likelihood: -15003.798413 EM: Round [87] log likelihood: -15003.758365 EM: Round [88] log likelihood: -15003.719015 EM: Round [89] log likelihood: -15003.680343 EM: Round [90] log likelihood: -15003.642329 EM: Round [91] log likelihood: -15003.604956 EM: Round [92] log likelihood: -15003.568205 EM: Round [93] log likelihood: -15003.532060 EM: Round [94] log likelihood: -15003.496504 EM: Round [95] log likelihood: -15003.461521 EM: Round [96] log likelihood: -15003.427096 EM: Round [97] log likelihood: -15003.393214 EM: Round [98] log likelihood: -15003.359860 EM: Round [99] log likelihood: -15003.327021 EM: Round [100] log likelihood: -15003.294684 EM: Round [101] log likelihood: -15003.262834 EM: Round [102] log likelihood: -15003.231461 EM: Round [103] log likelihood: -15003.200551 EM: Round [104] log likelihood: -15003.170093 EM: Round [105] log likelihood: -15003.140076 EM: Round [106] log likelihood: -15003.110489 EM: Round [107] log likelihood: -15003.081320 EM: Round [108] log likelihood: -15003.052561 EM: Round [109] log likelihood: -15003.024201 EM: Round [110] log likelihood: -15002.996230 EM: Round [111] log likelihood: -15002.968640 EM: Round [112] log likelihood: -15002.941421 EM: Round [113] log likelihood: -15002.914564 EM: Round [114] log likelihood: -15002.888062 EM: Round [115] log likelihood: -15002.861907 EM: Round [116] log likelihood: -15002.836089 EM: Round [117] log likelihood: -15002.810603 EM: Round [118] log likelihood: -15002.785440 EM: Round [119] log likelihood: -15002.760594 EM: Round [120] log likelihood: -15002.736057 EM: Round [121] log likelihood: -15002.711823 EM: Round [122] log likelihood: -15002.687885 EM: Round [123] log likelihood: -15002.664238 EM: Round [124] log likelihood: -15002.640875 EM: Round [125] log likelihood: -15002.617790 EM: Round [126] log likelihood: -15002.594978 EM: Round [127] log likelihood: -15002.572433 EM: Round [128] log likelihood: -15002.550150 EM: Round [129] log likelihood: -15002.528123 EM: Round [130] log likelihood: -15002.506348 EM: Round [131] log likelihood: -15002.484820 EM: Round [132] log likelihood: -15002.463534 EM: Round [133] log likelihood: -15002.442485 EM: Round [134] log likelihood: -15002.421669 EM: Round [135] log likelihood: -15002.401082 EM: Round [136] log likelihood: -15002.380719 EM: Round [137] log likelihood: -15002.360577 EM: Round [138] log likelihood: -15002.340651 EM: Round [139] log likelihood: -15002.320937 EM: Round [140] log likelihood: -15002.301433 EM: Round [141] log likelihood: -15002.282133 EM: Round [142] log likelihood: -15002.263036 EM: Round [143] log likelihood: -15002.244136 EM: Round [144] log likelihood: -15002.225432 EM: Round [145] log likelihood: -15002.206919 EM: Round [146] log likelihood: -15002.188594 EM: Round [147] log likelihood: -15002.170455 EM: Round [148] log likelihood: -15002.152498 EM: Round [149] log likelihood: -15002.134721 EM: Round [150] log likelihood: -15002.117120 EM: Round [151] log likelihood: -15002.099693 EM: Round [152] log likelihood: -15002.082437 EM: Round [153] log likelihood: -15002.065350 EM: Round [154] log likelihood: -15002.048428 EM: Round [155] log likelihood: -15002.031670 EM: Round [156] log likelihood: -15002.015073 EM: Round [157] log likelihood: -15001.998634 EM: Round [158] log likelihood: -15001.982352 EM: Round [159] log likelihood: -15001.966223 EM: Round [160] log likelihood: -15001.950247 EM: Round [161] log likelihood: -15001.934419 EM: Round [162] log likelihood: -15001.918739 EM: Round [163] log likelihood: -15001.903205 EM: Round [164] log likelihood: -15001.887813 EM: Round [165] log likelihood: -15001.872563 EM: Round [166] log likelihood: -15001.857453 EM: Round [167] log likelihood: -15001.842480 EM: Round [168] log likelihood: -15001.827642 EM: Round [169] log likelihood: -15001.812939 EM: Round [170] log likelihood: -15001.798367 EM: Round [171] log likelihood: -15001.783926 EM: Round [172] log likelihood: -15001.769613 EM: Round [173] log likelihood: -15001.755427 EM: Round [174] log likelihood: -15001.741367 EM: Round [175] log likelihood: -15001.727430 EM: Round [176] log likelihood: -15001.713615 EM: Round [177] log likelihood: -15001.699921 EM: Round [178] log likelihood: -15001.686346 EM: Round [179] log likelihood: -15001.672889 EM: Round [180] log likelihood: -15001.659547 EM: Round [181] log likelihood: -15001.646321 EM: Round [182] log likelihood: -15001.633208 EM: Round [183] log likelihood: -15001.620206 EM: Round [184] log likelihood: -15001.607316 EM: Round [185] log likelihood: -15001.594534 EM: Round [186] log likelihood: -15001.581861 EM: Round [187] log likelihood: -15001.569294 EM: Round [188] log likelihood: -15001.556833 EM: Round [189] log likelihood: -15001.544476 EM: Round [190] log likelihood: -15001.532223 EM: Round [191] log likelihood: -15001.520071 EM: Round [192] log likelihood: -15001.508019 EM: Round [193] log likelihood: -15001.496068 EM: Round [194] log likelihood: -15001.484214 EM: Round [195] log likelihood: -15001.472459 EM: Round [196] log likelihood: -15001.460799 EM: Round [197] log likelihood: -15001.449234 EM: Round [198] log likelihood: -15001.437764 EM: Round [199] log likelihood: -15001.426387 EM: Round [200] log likelihood: -15001.415102 EM: Round [201] log likelihood: -15001.403908 EM: Round [202] log likelihood: -15001.392804 EM: Round [203] log likelihood: -15001.381789 EM: Round [204] log likelihood: -15001.370862 EM: Round [205] log likelihood: -15001.360022 EM: Round [206] log likelihood: -15001.349269 EM: Round [207] log likelihood: -15001.338601 EM: Round [208] log likelihood: -15001.328018 EM: Round [209] log likelihood: -15001.317518 EM: Round [210] log likelihood: -15001.307101 EM: Round [211] log likelihood: -15001.296766 EM: Round [212] log likelihood: -15001.286512 EM: Round [213] log likelihood: -15001.276338 EM: Round [214] log likelihood: -15001.266244 EM: Round [215] log likelihood: -15001.256228 EM: Round [216] log likelihood: -15001.246290 EM: Round [217] log likelihood: -15001.236428 EM: Round [218] log likelihood: -15001.226643 EM: Round [219] log likelihood: -15001.216934 EM: Round [220] log likelihood: -15001.207299 EM: Round [221] log likelihood: -15001.197738 EM: Round [222] log likelihood: -15001.188250 EM: Round [223] log likelihood: -15001.178835 EM: Round [224] log likelihood: -15001.169492 EM: Round [225] log likelihood: -15001.160220 EM: Round [226] log likelihood: -15001.151018 EM: Round [227] log likelihood: -15001.141885 EM: Round [228] log likelihood: -15001.132822 EM: Round [229] log likelihood: -15001.123827 EM: Round [230] log likelihood: -15001.114900 EM: Round [231] log likelihood: -15001.106040 EM: Round [232] log likelihood: -15001.097246 EM: Round [233] log likelihood: -15001.088518 EM: Round [234] log likelihood: -15001.079855 EM: Round [235] log likelihood: -15001.071257 EM: Round [236] log likelihood: -15001.062723 EM: Round [237] log likelihood: -15001.054252 EM: Round [238] log likelihood: -15001.045843 EM: Round [239] log likelihood: -15001.037497 EM: Round [240] log likelihood: -15001.029213 EM: Round [241] log likelihood: -15001.020989 EM: Round [242] log likelihood: -15001.012826 EM: Round [243] log likelihood: -15001.004723 EM: Round [244] log likelihood: -15000.996679 EM: Round [245] log likelihood: -15000.988694 EM: Round [246] log likelihood: -15000.980767 EM: Round [247] log likelihood: -15000.972898 EM: Round [248] log likelihood: -15000.965085 EM: Round [249] log likelihood: -15000.957330 EM: Round [250] log likelihood: -15000.949631 EM: Round [251] log likelihood: -15000.941987 EM: Round [252] log likelihood: -15000.934399 EM: Round [253] log likelihood: -15000.926865 EM: Round [254] log likelihood: -15000.919386 EM: Round [255] log likelihood: -15000.911960 EM: Round [256] log likelihood: -15000.904587 EM: Round [257] log likelihood: -15000.897267 EM: Round [258] log likelihood: -15000.889999 EM: Round [259] log likelihood: -15000.882783 EM: Round [260] log likelihood: -15000.875619 EM: Round [261] log likelihood: -15000.868505 EM: Round [262] log likelihood: -15000.861442 EM: Round [263] log likelihood: -15000.854429 EM: Round [264] log likelihood: -15000.847465 EM: Round [265] log likelihood: -15000.840551 EM: Round [266] log likelihood: -15000.833685 EM: Round [267] log likelihood: -15000.826868 EM: Round [268] log likelihood: -15000.820098 EM: Round [269] log likelihood: -15000.813376 EM: Round [270] log likelihood: -15000.806701 EM: Round [271] log likelihood: -15000.800073 EM: Round [272] log likelihood: -15000.793490 EM: Round [273] log likelihood: -15000.786954 EM: Round [274] log likelihood: -15000.780463 EM: Round [275] log likelihood: -15000.774018 EM: Round [276] log likelihood: -15000.767617 EM: Round [277] log likelihood: -15000.761260 EM: Round [278] log likelihood: -15000.754948 EM: Round [279] log likelihood: -15000.748679 EM: Round [280] log likelihood: -15000.742453 EM: Round [281] log likelihood: -15000.736270 EM: Round [282] log likelihood: -15000.730129 EM: Round [283] log likelihood: -15000.724031 EM: Round [284] log likelihood: -15000.717975 EM: Round [285] log likelihood: -15000.711960 EM: Round [286] log likelihood: -15000.705986 EM: Round [287] log likelihood: -15000.700052 EM: Round [288] log likelihood: -15000.694160 EM: Round [289] log likelihood: -15000.688307 EM: Round [290] log likelihood: -15000.682494 EM: Round [291] log likelihood: -15000.676721 EM: Round [292] log likelihood: -15000.670987 EM: Round [293] log likelihood: -15000.665291 EM: Round [294] log likelihood: -15000.659634 EM: Round [295] log likelihood: -15000.654015 EM: Round [296] log likelihood: -15000.648434 EM: Round [297] log likelihood: -15000.642891 EM: Round [298] log likelihood: -15000.637385 EM: Round [299] log likelihood: -15000.631916 EM: Round [300] log likelihood: -15000.626483 EM: Round [301] log likelihood: -15000.621087 EM: Round [302] log likelihood: -15000.615727 EM: Round [303] log likelihood: -15000.610403 EM: Round [304] log likelihood: -15000.605114 EM: Round [305] log likelihood: -15000.599860 EM: Round [306] log likelihood: -15000.594642 EM: Round [307] log likelihood: -15000.589458 EM: Round [308] log likelihood: -15000.584308 EM: Round [309] log likelihood: -15000.579192 EM: Round [310] log 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-14999.785547 EM: Round [744] log likelihood: -14999.785059 EM: Round [745] log likelihood: -14999.784572 EM: Round [746] log likelihood: -14999.784087 EM: Round [747] log likelihood: -14999.783605 EM: Round [748] log likelihood: -14999.783125 EM: Round [749] log likelihood: -14999.782646 EM: Round [750] log likelihood: -14999.782170 EM: Round [751] log likelihood: -14999.781696 EM: Round [752] log likelihood: -14999.781224 EM: Round [753] log likelihood: -14999.780754 EM: Round [754] log likelihood: -14999.780286 EM: Round [755] log likelihood: -14999.779820 EM: Round [756] log likelihood: -14999.779356 EM: Round [757] log likelihood: -14999.778894 EM: Round [758] log likelihood: -14999.778434 EM: Round [759] log likelihood: -14999.777976 EM: Round [760] log likelihood: -14999.777520 EM: Round [761] log likelihood: -14999.777066 EM: Round [762] log likelihood: -14999.776614 EM: Round [763] log likelihood: -14999.776163 EM: Round [764] log likelihood: -14999.775715 EM: Round [765] log likelihood: -14999.775268 EM: Round [766] log likelihood: -14999.774824 EM: Round [767] log likelihood: -14999.774381 EM: Round [768] log likelihood: -14999.773940 EM: Round [769] log likelihood: -14999.773502 EM: Round [770] log likelihood: -14999.773065 EM: Round [771] log likelihood: -14999.772629 EM: Round [772] log likelihood: -14999.772196 EM: Round [773] log likelihood: -14999.771764 EM: Round [774] log likelihood: -14999.771335 EM: Round [775] log likelihood: -14999.770907 EM: Round [776] log likelihood: -14999.770481 EM: Round [777] log likelihood: -14999.770056 EM: Round [778] log likelihood: -14999.769634 EM: Round [779] log likelihood: -14999.769213 EM: Round [780] log likelihood: -14999.768794 EM: Round [781] log likelihood: -14999.768377 EM: Round [782] log likelihood: -14999.767961 EM: Round [783] log likelihood: -14999.767548 EM: Round [784] log likelihood: -14999.767136 EM: Round [785] log likelihood: -14999.766725 EM: Round [786] log likelihood: -14999.766317 EM: Round [787] log likelihood: -14999.765910 EM: Round [788] log likelihood: -14999.765505 EM: Round [789] log likelihood: -14999.765101 EM: Round [790] log likelihood: -14999.764699 EM: Round [791] log likelihood: -14999.764299 EM: Round [792] log likelihood: -14999.763900 EM: Round [793] log likelihood: -14999.763503 EM: Round [794] log likelihood: -14999.763108 EM: Round [795] log likelihood: -14999.762715 EM: Round [796] log likelihood: -14999.762323 EM: Round [797] log likelihood: -14999.761932 EM: Round [798] log likelihood: -14999.761543 EM: Round [799] log likelihood: -14999.761156 EM: Round [800] log likelihood: -14999.760771 EM: Round [801] log likelihood: -14999.760387 EM: Round [802] log likelihood: -14999.760004 EM: Round [803] log likelihood: -14999.759623 EM: Round [804] log likelihood: -14999.759244 EM: Round [805] log likelihood: -14999.758866 EM: Round [806] log likelihood: -14999.758490 EM: Round [807] log likelihood: -14999.758115 EM: Round [808] log likelihood: -14999.757742 EM: Round [809] log likelihood: -14999.757370 EM: Round [810] log likelihood: -14999.757000 EM: Round [811] log likelihood: -14999.756632 EM: Round [812] log likelihood: -14999.756264 EM: Round [813] log likelihood: -14999.755899 EM: Round [814] log likelihood: -14999.755535 EM: Round [815] log likelihood: -14999.755172 EM: Round [816] log likelihood: -14999.754811 EM: Round [817] log likelihood: -14999.754451 EM: Round [818] log likelihood: -14999.754092 EM: Round [819] log likelihood: -14999.753735 EM: Round [820] log likelihood: -14999.753380 EM: Round [821] log likelihood: -14999.753026 EM: Round [822] log likelihood: -14999.752673 EM: Round [823] log likelihood: -14999.752322 EM: Round [824] log likelihood: -14999.751972 EM: Round [825] log likelihood: -14999.751624 EM: Round [826] log likelihood: -14999.751277 EM: Round [827] log likelihood: -14999.750931 EM: Round [828] log likelihood: -14999.750587 EM: Round [829] log likelihood: -14999.750244 EM: Round [830] log likelihood: -14999.749902 EM: Round [831] log likelihood: -14999.749562 EM: Round [832] log likelihood: -14999.749223 EM: Round [833] log likelihood: -14999.748886 EM: Round [834] log likelihood: -14999.748549 EM: Round [835] log likelihood: -14999.748215 EM: Round [836] log likelihood: -14999.747881 EM: Round [837] log likelihood: -14999.747549 EM: Round [838] log likelihood: -14999.747218 EM: Round [839] log likelihood: -14999.746888 EM: Round [840] log likelihood: -14999.746560 EM: Round [841] log likelihood: -14999.746233 EM: Round [842] log likelihood: -14999.745907 EM: Round [843] log likelihood: -14999.745583 EM: Round [844] log likelihood: -14999.745260 EM: Round [845] log likelihood: -14999.744938 EM: Round [846] log likelihood: -14999.744617 EM: Round [847] log likelihood: -14999.744297 EM: Round [848] log likelihood: -14999.743979 EM: Round [849] log likelihood: -14999.743662 EM: Round [850] log likelihood: -14999.743347 EM: Round [851] log likelihood: -14999.743032 EM: Round [852] log likelihood: -14999.742719 EM: Round [853] log likelihood: -14999.742407 EM: Round [854] log likelihood: -14999.742096 EM: Round [855] log likelihood: -14999.741786 EM: Round [856] log likelihood: -14999.741478 EM: Round [857] log likelihood: -14999.741171 EM: Round [858] log likelihood: -14999.740865 EM: Round [859] log likelihood: -14999.740560 EM: Round [860] log likelihood: -14999.740256 EM: Round [861] log likelihood: -14999.739953 EM: Round [862] log likelihood: -14999.739652 EM: Round [863] log likelihood: -14999.739352 EM: Round [864] log likelihood: -14999.739053 EM: Round [865] log likelihood: -14999.738755 EM: Round [866] log likelihood: -14999.738458 EM: Round [867] log likelihood: -14999.738162 EM: Round [868] log likelihood: -14999.737868 EM: Round [869] log likelihood: -14999.737574 EM: Round [870] log likelihood: -14999.737282 EM: Round [871] log likelihood: -14999.736991 EM: Round [872] log likelihood: -14999.736700 EM: Round [873] log likelihood: -14999.736411 EM: Round [874] log likelihood: -14999.736124 EM: Round [875] log likelihood: -14999.735837 EM: Round [876] log likelihood: -14999.735551 EM: Round [877] log likelihood: -14999.735266 EM: Round [878] log likelihood: -14999.734983 EM: Round [879] log likelihood: -14999.734700 EM: Round [880] log likelihood: -14999.734419 EM: Round [881] log likelihood: -14999.734138 EM: Round [882] log likelihood: -14999.733859 EM: Round [883] log likelihood: -14999.733581 EM: Round [884] log likelihood: -14999.733303 EM: Round [885] log likelihood: -14999.733027 EM: Round [886] log likelihood: -14999.732752 EM: Round [887] log likelihood: -14999.732478 EM: Round [888] log likelihood: -14999.732205 EM: Round [889] log likelihood: -14999.731933 EM: Round [890] log likelihood: -14999.731661 EM: Round [891] log likelihood: -14999.731391 EM: Round [892] log likelihood: -14999.731122 EM: Round [893] log likelihood: -14999.730854 EM: Round [894] log likelihood: -14999.730587 EM: Round [895] log likelihood: -14999.730321 EM: Round [896] log likelihood: -14999.730056 EM: Round [897] log likelihood: -14999.729792 EM: Round [898] log likelihood: -14999.729528 EM: Round [899] log likelihood: -14999.729266 EM: Round [900] log likelihood: -14999.729005 EM: Round [901] log likelihood: -14999.728745 EM: Round [902] log likelihood: -14999.728485 EM: Round [903] log likelihood: -14999.728227 EM: Round [904] log likelihood: -14999.727969 EM: Round [905] log likelihood: -14999.727713 EM: Round [906] log likelihood: -14999.727457 EM: Round [907] log likelihood: -14999.727203 EM: Round [908] log likelihood: -14999.726949 EM: Round [909] log likelihood: -14999.726696 EM: Round [910] log likelihood: -14999.726444 EM: Round [911] log likelihood: -14999.726193 EM: Round [912] log likelihood: -14999.725943 EM: Round [913] log likelihood: -14999.725694 EM: Round [914] log likelihood: -14999.725446 EM: Round [915] log likelihood: -14999.725199 EM: Round [916] log likelihood: -14999.724952 EM: Round [917] log likelihood: -14999.724707 EM: Round [918] log likelihood: -14999.724462 EM: Round [919] log likelihood: -14999.724218 EM: Round [920] log likelihood: -14999.723975 EM: Round [921] log likelihood: -14999.723733 EM: Round [922] log likelihood: -14999.723492 EM: Round [923] log likelihood: -14999.723252 EM: Round [924] log likelihood: -14999.723012 EM: Round [925] log likelihood: -14999.722774 EM: Round [926] log likelihood: -14999.722536 EM: Round [927] log likelihood: -14999.722299 EM: Round [928] log likelihood: -14999.722063 EM: Round [929] log likelihood: -14999.721828 EM: Round [930] log likelihood: -14999.721594 EM: Round [931] log likelihood: -14999.721360 EM: Round [932] log likelihood: -14999.721128 EM: Round [933] log likelihood: -14999.720896 EM: Round [934] log likelihood: -14999.720665 EM: Round [935] log likelihood: -14999.720434 EM: Round [936] log likelihood: -14999.720205 EM: Round [937] log likelihood: -14999.719977 EM: Round [938] log likelihood: -14999.719749 EM: Round [939] log likelihood: -14999.719522 EM: Round [940] log likelihood: -14999.719296 EM: Round [941] log likelihood: -14999.719070 EM: Round [942] log likelihood: -14999.718846 EM: Round [943] log likelihood: -14999.718622 EM: Round [944] log likelihood: -14999.718399 EM: Round [945] log likelihood: -14999.718177 EM: Round [946] log likelihood: -14999.717955 EM: Round [947] log likelihood: -14999.717734 EM: Round [948] log likelihood: -14999.717514 EM: Round [949] log likelihood: -14999.717295 EM: Round [950] log likelihood: -14999.717077 EM: Round [951] log likelihood: -14999.716859 EM: Round [952] log likelihood: -14999.716642 EM: Round [953] log likelihood: -14999.716426 EM: Round [954] log likelihood: -14999.716211 EM: Round [955] log likelihood: -14999.715996 EM: Round [956] log likelihood: -14999.715783 EM: Round [957] log likelihood: -14999.715569 EM: Round [958] log likelihood: -14999.715357 EM: Round [959] log likelihood: -14999.715145 EM: Round [960] log likelihood: -14999.714934 EM: Round [961] log likelihood: -14999.714724 EM: Round [962] log likelihood: -14999.714515 EM: Round [963] log likelihood: -14999.714306 EM: Round [964] log likelihood: -14999.714098 EM: Round [965] log likelihood: -14999.713891 EM: Round [966] log likelihood: -14999.713684 EM: Round [967] log likelihood: -14999.713478 EM: Round [968] log likelihood: -14999.713273 EM: Round [969] log likelihood: -14999.713068 EM: Round [970] log likelihood: -14999.712864 EM: Round [971] log likelihood: -14999.712661 EM: Round [972] log likelihood: -14999.712459 EM: Round [973] log likelihood: -14999.712257 EM: Round [974] log likelihood: -14999.712056 EM: Round [975] log likelihood: -14999.711856 EM: Round [976] log likelihood: -14999.711656 EM: Round [977] log likelihood: -14999.711457 EM: Round [978] log likelihood: -14999.711259 EM: Round [979] log likelihood: -14999.711061 EM: Round [980] log likelihood: -14999.710864 EM: Round [981] log likelihood: -14999.710668 EM: Round [982] log likelihood: -14999.710472 EM: Round [983] log likelihood: -14999.710277 EM: Round [984] log likelihood: -14999.710083 EM: Round [985] log likelihood: -14999.709889 EM: Round [986] log likelihood: -14999.709696 EM: Round [987] log likelihood: -14999.709503 EM: Round [988] log likelihood: -14999.709312 EM: Round [989] log likelihood: -14999.709121 EM: Round [990] log likelihood: -14999.708930 EM: Round [991] log likelihood: -14999.708740 EM: Round [992] log likelihood: -14999.708551 EM: Round [993] log likelihood: -14999.708362 EM: Round [994] log likelihood: -14999.708174 EM: Round [995] log likelihood: -14999.707987 EM: Round [996] log likelihood: -14999.707800 EM: Round [997] log likelihood: -14999.707614 EM: Round [998] log likelihood: -14999.707429 EM: Round [999] log likelihood: -14999.707244 EM: Round [1000] log likelihood: -14999.707060 EM: Round [1001] log likelihood: -14999.706876 Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/filter_by_frag_threshs.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam" Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_junc_reads_bam.ok Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/samtools_idx_junc_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.junction_reads.bam.tabix.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/span_reads_acc.ok Running: samtools view -H /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/init_spanning_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa - | samtools sort -@ 8 - -o /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam || : Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_spanning_reads.ok Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/samtools_index_span_reads_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bam_to_bed.ok Running: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bedsort.ok Running: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bgzip.ok Running: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.bed.sorted.bed.gz Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/A673_FFPE_RNA_0001_B23LG7FLT4_3.spanning_reads.bam.tabix.ok Running: cp /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_consol_bam.ok Running: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam Execution Time = 0.04 minutes. CMD: samtools index /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/index_consol_bam.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000 -extracting read coordinates from /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam into /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords CMD: touch /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords.coord_sorted Execution Time = 0.93 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam --max_insert_size 10000000 Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.FusionJuncSpan Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_juncspan_fmt.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_pfam_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.Pfam.bed Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/prep_igv_seqsim_gff3.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.gff3 > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.igv.seqsimilar.bed Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa > /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/add_splice_info.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/blast_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir -done, see /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/annot_filter.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj EM: Starting log likelihood: -7093.933202 EM: Round [1] log likelihood: -7092.052756 EM: Round [2] log likelihood: -7092.052745 EM: Stopping iterations at round 2 due to insufficient improvement in likelihood. Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/EM_adj_counts.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM -total frags in /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz: 295197448 Execution Time = 5.77 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/add_FFPM.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat Execution Time = 0.04 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --gtf /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf > /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/microH.dat.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.KXy1ipFxeT/fi_workdir/microH.dat /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/append_microH_info.ok Running: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/cp_final.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/final.abridged.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.KXy1ipFxeT --json_outfile /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.KXy1ipFxeT --json_outfile /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 Running: touch /tmp/nxf.KXy1ipFxeT/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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html Warning - not locating file: /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.gmap_trinity_GG.fusions.gff3.bed Execution Time = 0.04 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.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.json --input_file_prefix A673_FFPE_RNA_0001_B23LG7FLT4_3 --html_output /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_inspector_web.html Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_reports_html.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_annotator.ok Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000253554.7] WARNING, no entry stored in dbm for [ENSG00000253554.7] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000286152.1] WARNING, no entry stored in dbm for [IGH-.g@-ext] Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.KXy1ipFxeT/ctat_genome_lib_build_dir > /tmp/nxf.KXy1ipFxeT/A673_FFPE_RNA_0001_B23LG7FLT4_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect Running: touch /tmp/nxf.KXy1ipFxeT/chckpts_dir/fusion_coding_region_effect.ok ls: cannot access 'IGV_inputs': No such file or directory