Error, strand conflict in gtf info for chr1 ENSEMBL exon 43716467 43716556 . + . gene_id "U6^ENSG00000283414.1"; transcript_id "ENST00000637979.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.104-201"; exon_number 1; exon_id "ENSE00003791911.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283414.1"; orig_coord_info "chr1,43716467,43716556,+"; Error, strand conflict in gtf info for chr1 ENSEMBL exon 180758722 180758817 . + . gene_id "U6^ENSG00000283575.1"; transcript_id "ENST00000636407.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.114-201"; exon_number 1; exon_id "ENSE00003794679.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283575.1"; orig_coord_info "chr1,180758722,180758817,+"; Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 47781379 47781465 . + . gene_id "U6^ENSG00000283502.1"; transcript_id "ENST00000636749.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.109-201"; exon_number 1; exon_id "ENSE00003797274.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283502.1"; orig_coord_info "chr2,47781379,47781465,+"; Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 88367793 88367862 . - . gene_id "U6^ENSG00000283262.1"; transcript_id "ENST00000636931.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.95-201"; exon_number 1; exon_id "ENSE00003794432.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283262.1"; orig_coord_info "chr2,88367793,88367862,-"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 129819777 129819876 . + . gene_id "U6^ENSG00000283509.1"; transcript_id "ENST00000637725.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.110-201"; exon_number 1; exon_id "ENSE00003800884.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283509.1"; orig_coord_info "chr3,129819777,129819876,+"; Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 139388277 139388364 . + . gene_id "U6^ENSG00000283418.1"; transcript_id "ENST00000637379.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.105-201"; exon_number 1; exon_id "ENSE00003796411.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283418.1"; orig_coord_info "chr3,139388277,139388364,+"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 13051342 13051411 . + . gene_id "U6^ENSG00000283271.1"; transcript_id "ENST00000636425.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.96-201"; exon_number 1; exon_id "ENSE00003794917.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283271.1"; orig_coord_info "chr4,13051342,13051411,+"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 29510635 29510737 . + . gene_id "U6^ENSG00000283666.1"; transcript_id "ENST00000636045.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.115-201"; exon_number 1; exon_id "ENSE00003798657.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283666.1"; orig_coord_info "chr4,29510635,29510737,+"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 48109353 48109410 . - . gene_id "U6^ENSG00000283499.1"; transcript_id "ENST00000637764.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.108-201"; exon_number 1; exon_id "ENSE00003792913.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283499.1"; orig_coord_info "chr4,48109353,48109410,-"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 70848136 70848218 . - . gene_id "U6^ENSG00000283313.1"; transcript_id "ENST00000637524.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.99-201"; exon_number 1; exon_id "ENSE00003794269.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283313.1"; orig_coord_info "chr4,70848136,70848218,-"; Error, chr discrepancy in gtf info for chr4 ENSEMBL exon 135315418 135315522 . - . gene_id "U6^ENSG00000283432.1"; transcript_id "ENST00000636360.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.106-201"; exon_number 1; exon_id "ENSE00003800825.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283432.1"; orig_coord_info "chr4,135315418,135315522,-"; Error, chr discrepancy in gtf info for chr9 ENSEMBL exon 64082429 64082534 . + . gene_id "U6^ENSG00000275068.1"; transcript_id "ENST00000618523.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.48-201"; exon_number 1; exon_id "ENSE00003712247.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000275068.1"; orig_coord_info "chr9,64082429,64082534,+"; Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 102868421 102868519 . + . gene_id "U6^ENSG00000283337.1"; transcript_id "ENST00000636230.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.100-201"; exon_number 1; exon_id "ENSE00003800313.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283337.1"; orig_coord_info "chr10,102868421,102868519,+"; Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 87648489 87648549 . - . gene_id "U6^ENSG00000283412.1"; transcript_id "ENST00000637085.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.103-201"; exon_number 1; exon_id "ENSE00003793834.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283412.1"; orig_coord_info "chr11,87648489,87648549,-"; Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 132525809 132525887 . + . gene_id "U6^ENSG00000283489.1"; transcript_id "ENST00000637108.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.107-201"; exon_number 1; exon_id "ENSE00003795495.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283489.1"; orig_coord_info "chr11,132525809,132525887,+"; Error, chr discrepancy in gtf info for chr12 ENSEMBL exon 31366288 31366366 . + . gene_id "U6^ENSG00000283256.1"; transcript_id "ENST00000635778.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.94-201"; exon_number 1; exon_id "ENSE00003799600.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283256.1"; orig_coord_info "chr12,31366288,31366366,+"; Error, chr discrepancy in gtf info for chr12 ENSEMBL exon 45554590 45554659 . - . gene_id "U6^ENSG00000283545.1"; transcript_id "ENST00000384129.2"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.112-201"; exon_number 1; exon_id "ENSE00001808939.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283545.1"; orig_coord_info "chr12,45554590,45554659,-"; Error, chr discrepancy in gtf info for chr13 ENSEMBL exon 18418526 18418632 . + . gene_id "U6^ENSG00000276183.1"; transcript_id "ENST00000615686.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.59-201"; exon_number 1; exon_id "ENSE00003719890.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000276183.1"; orig_coord_info "chr13,18418526,18418632,+"; Error, chr discrepancy in gtf info for chr14 ENSEMBL exon 24352057 24352157 . - . gene_id "U6^ENSG00000283290.1"; transcript_id "ENST00000636904.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.97-201"; exon_number 1; exon_id "ENSE00003800280.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283290.1"; orig_coord_info "chr14,24352057,24352157,-"; Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 21428879 21428985 . - . gene_id "U6^ENSG00000275174.1"; transcript_id "ENST00000612037.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.50-201"; exon_number 1; exon_id "ENSE00003750231.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000275174.1"; orig_coord_info "chr15,21428879,21428985,-"; Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 65843484 65843558 . + . gene_id "U6^ENSG00000283249.1"; transcript_id "ENST00000636829.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.93-201"; exon_number 1; exon_id "ENSE00003798324.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283249.1"; orig_coord_info "chr15,65843484,65843558,+"; Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 98026042 98026139 . + . gene_id "U6^ENSG00000283372.1"; transcript_id "ENST00000637737.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.102-201"; exon_number 1; exon_id "ENSE00003800921.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283372.1"; orig_coord_info "chr15,98026042,98026139,+"; Error, chr discrepancy in gtf info for chr16 ENSEMBL exon 72376704 72376760 . + . gene_id "U6^ENSG00000283564.1"; transcript_id "ENST00000637761.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.113-201"; exon_number 1; exon_id "ENSE00003793842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283564.1"; orig_coord_info "chr16,72376704,72376760,+"; Error, chr discrepancy in gtf info for chr17 ENSEMBL exon 90796 90899 . - . gene_id "U6^ENSG00000277613.1"; transcript_id "ENST00000620287.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.70-201"; exon_number 1; exon_id "ENSE00003744841.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000277613.1"; orig_coord_info "chr17,90796,90899,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 30713240 30713346 . - . gene_id "U6^ENSG00000274385.1"; transcript_id "ENST00000618440.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.42-201"; exon_number 1; exon_id "ENSE00003712066.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000274385.1"; orig_coord_info "chr20,30713240,30713346,-"; Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 35769785 35769867 . - . gene_id "U6^ENSG00000283527.1"; transcript_id "ENST00000636093.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.111-201"; exon_number 1; exon_id "ENSE00003795784.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283527.1"; orig_coord_info "chr20,35769785,35769867,-"; Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 28743208 28743291 . + . gene_id "U6^ENSG00000283300.1"; transcript_id "ENST00000637157.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.98-201"; exon_number 1; exon_id "ENSE00003800948.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000283300.1"; orig_coord_info "chr21,28743208,28743291,+"; Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 15273855 15273961 . + . gene_id "U6^ENSG00000276138.1"; transcript_id "ENST00000613107.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.58-201"; exon_number 1; exon_id "ENSE00003736970.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000276138.1"; orig_coord_info "chr22,15273855,15273961,+"; Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 16141767 16141872 . + . gene_id "U6^ENSG00000278188.1"; transcript_id "ENST00000612550.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.81-201"; exon_number 1; exon_id "ENSE00003714392.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000278188.1"; orig_coord_info "chr22,16141767,16141872,+"; Error, chr discrepancy in gtf info for chrX ENSEMBL exon 86481028 86481130 . + . gene_id "U6^ENSG00000277717.1"; transcript_id "ENST00000619194.1"; gene_type "snRNA"; gene_name "U6"; transcript_type "snRNA"; transcript_name "U6.73-201"; exon_number 1; exon_id "ENSE00003738865.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U6^ENSG00000277717.1"; orig_coord_info "chrX,86481028,86481130,+"; Error - no gene spans 100M bases in length.... likely problem at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 589. main::get_gene_span_info("chr1\x{9}ENSEMBL\x{9}exon\x{9}516376\x{9}516479\x{9}.\x{9}-\x{9}.\x{9}gene_id \"U6^ENSG0000027"...) called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 417 main::get_gene_contig_gtf("chr1\x{9}ENSEMBL\x{9}exon\x{9}516376\x{9}516479\x{9}.\x{9}-\x{9}.\x{9}gene_id \"U6^ENSG0000027"..., "/tmp/nxf.ip1B8zh3GJ/ctat_genome_lib_build_dir/ref_genome.fa") called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 214 eval {...} called at /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl line 210 Done. -parsing GTF file: /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.ip1B8zh3GJ/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.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam 11:15:46 : INFO : Done. -parsing GTF file: /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] [200000] [210000] [220000] [230000] [240000] [250000] [260000] [270000] [280000] [290000] [300000] [310000] [320000] [330000] [340000] [350000] [360000] [370000] [380000] [390000] [400000] [410000] [420000] [430000] [440000] [450000] [460000] [470000] [480000] [490000] [500000] [510000] [520000] [530000] [540000] [550000] [560000] [570000] [580000] [590000] [600000] [610000] [620000] [630000] [640000] [650000] [660000] [670000] [680000] [690000] [700000] [710000] [720000] [730000] [740000] [750000] [760000] [770000] [780000] [790000] [800000] [810000] [820000] [830000] [840000] [850000] [860000] [870000] [880000] [890000] [900000] [910000] [920000] [930000] [940000] [950000] [960000] [970000] [980000] [990000] [1000000] [1010000] [1020000] [1030000] [1040000] [1050000] [1060000] [1070000] [1080000] [1090000] [1100000] [1110000] [1120000] [1130000] [1140000] [1150000] [1160000] [1170000] [1180000] [1190000] [1200000] [1210000] [1220000] [1230000] [1240000] [1250000] [1260000] [1270000] [1280000] [1290000] [1300000] [1310000] [1320000] [1330000] [1340000] [1350000] [1360000] [1370000] [1380000] [1390000] [1400000] [1410000] [1420000] [1430000] [1440000] [1450000] [1460000] [1470000] [1480000] [1490000] [1500000] [1510000] [1520000] [1530000] [1540000] [1550000] [1560000] [1570000] [1580000] [1590000] [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] -done parsing /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { ' ** passed ** ' => 7010, 'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 80, 'seq-similar region overlap' => 1540, 'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 8, 'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 4, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 525, 'low complexity anchor region' => 5, 'num genes matched < 2' => 291, 'excessive soft clipping' => 28003, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 99, 'exons hit < 2' => 8, 'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12, 'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 6, 'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 64, 'per_id < 96' => 13895, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 55, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 81, 'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 5, 'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 2, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 15, 'small anchor length' => 88, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 130 }; -writing fusion junction support info. -outputting the spanning read info: /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [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] -fusion SPANNING read extraction for scaff: AC008443.2--BAGE2 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: AC092470.1--GRIN2B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] [5000] [6000] -fusion SPANNING read extraction for scaff: AC135001.1--GRIN2B [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: AKT1S1--AF279873.3 [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] -fusion SPANNING read extraction for scaff: ANKRD27--TDRD12 [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] -fusion SPANNING read extraction for scaff: BACH1--GRIK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: BCL7A--LRRC43 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: BTBD10--POTEB3 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] -fusion SPANNING read extraction for scaff: CD2AP--AL451166.1 [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] -fusion SPANNING read extraction for scaff: CHIC2--HDAC9 [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: COL9A3--TRHDE [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] [261000] [262000] [263000] [264000] [265000] [266000] [267000] [268000] [269000] [270000] [271000] [272000] [273000] [274000] [275000] [276000] [277000] [278000] [279000] [280000] [281000] [282000] [283000] [284000] [285000] [286000] [287000] [288000] [289000] [290000] [291000] [292000] [293000] [294000] [295000] [296000] [297000] [298000] [299000] [300000] [301000] [302000] [303000] [304000] [305000] [306000] [307000] [308000] [309000] [310000] [311000] -fusion SPANNING read extraction for scaff: CU104787.1--KMT2C [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] -fusion SPANNING read extraction for scaff: ELOVL5--CLIC5 [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: GNE--MROH2B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: GPR149--ARHGEF26-AS1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] -fusion SPANNING read extraction for scaff: GRK2--SSH3 [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] -fusion SPANNING read extraction for scaff: HELZ--CCR10 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] -fusion SPANNING read extraction for scaff: IQGAP1--BLM [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] -fusion SPANNING read extraction for scaff: KDM4C--RCL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] -fusion SPANNING read extraction for scaff: KIAA1549--ZC3HAV1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] -fusion SPANNING read extraction for scaff: KIF13A--NFYA [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: LCORL--LINC02438 [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: LRRC1--HCRTR2 [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: MED20--AL031767.2 [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: MED20--LINC00581 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] -fusion SPANNING read extraction for scaff: N6AMT1--HUNK [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: NDFIP1--SPRY4-AS1 [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] -fusion SPANNING read extraction for scaff: NOCT--NAA15 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: PCDHA2--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] -fusion SPANNING read extraction for scaff: PCDHA4--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] -fusion SPANNING read extraction for scaff: PCDHA4--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] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] -fusion SPANNING read extraction for scaff: PICK1--HORMAD2-AS1 [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: PIP5K1A--AL031599.1 [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] -fusion SPANNING read extraction for scaff: PIP5K1A--GOT2P2 [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: PMS2P7--CCDC146 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] -fusion SPANNING read extraction for scaff: SBNO1--AC117503.5 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] -fusion SPANNING read extraction for scaff: SFI1--BPIFC [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] -fusion SPANNING read extraction for scaff: SH2D4A--AC087269.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] [70000] [71000] [72000] [73000] [74000] [75000] [76000] [77000] [78000] [79000] [80000] [81000] [82000] [83000] [84000] [85000] [86000] [87000] [88000] [89000] [90000] [91000] [92000] [93000] [94000] [95000] [96000] [97000] [98000] [99000] [100000] [101000] [102000] [103000] [104000] [105000] [106000] [107000] [108000] [109000] [110000] [111000] [112000] [113000] [114000] [115000] [116000] [117000] [118000] [119000] [120000] [121000] [122000] [123000] [124000] [125000] [126000] [127000] [128000] [129000] [130000] [131000] [132000] [133000] [134000] [135000] [136000] [137000] [138000] [139000] [140000] [141000] [142000] [143000] [144000] [145000] [146000] [147000] [148000] [149000] [150000] [151000] [152000] [153000] [154000] [155000] [156000] [157000] [158000] [159000] [160000] [161000] [162000] [163000] [164000] [165000] [166000] [167000] [168000] [169000] [170000] [171000] [172000] [173000] [174000] [175000] [176000] [177000] [178000] [179000] [180000] [181000] [182000] [183000] [184000] [185000] [186000] [187000] [188000] [189000] [190000] [191000] [192000] [193000] [194000] [195000] [196000] [197000] [198000] [199000] [200000] [201000] [202000] [203000] [204000] [205000] [206000] [207000] [208000] [209000] [210000] [211000] [212000] [213000] [214000] [215000] [216000] [217000] [218000] [219000] [220000] [221000] [222000] [223000] [224000] [225000] [226000] [227000] [228000] [229000] [230000] [231000] [232000] [233000] [234000] [235000] [236000] [237000] [238000] [239000] [240000] [241000] [242000] [243000] [244000] [245000] [246000] [247000] [248000] [249000] [250000] [251000] [252000] [253000] [254000] [255000] [256000] [257000] [258000] [259000] [260000] -fusion SPANNING read extraction for scaff: SKAP2--HNRNPA2B1 [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] -fusion SPANNING read extraction for scaff: SNHG14--HTR4 [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] -fusion SPANNING read extraction for scaff: STX16--NPEPL1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] [32000] [33000] [34000] [35000] [36000] [37000] [38000] [39000] [40000] [41000] [42000] [43000] [44000] [45000] [46000] [47000] [48000] [49000] [50000] [51000] [52000] [53000] [54000] [55000] [56000] [57000] [58000] [59000] [60000] [61000] [62000] [63000] [64000] [65000] [66000] [67000] [68000] [69000] -fusion SPANNING read extraction for scaff: TMEM165--TBL1X [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] -fusion SPANNING read extraction for scaff: TPCN2--ARID5B [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] -fusion SPANNING read extraction for scaff: TPTE--AL356585.3 [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] -fusion SPANNING read extraction for scaff: TSEN2--PPARG [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] [22000] [23000] [24000] [25000] [26000] [27000] [28000] [29000] [30000] [31000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 [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: UBAP1--PTPRD [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] -fusion SPANNING read extraction for scaff: URB1--N6AMT1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: ZCCHC7--AL354977.2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] [18000] [19000] [20000] [21000] -fusion SPANNING read extraction for scaff: ZCCHC7--RFX3-AS1 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: ZNF257--AC074135.1 [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] -fusion SPANNING read extraction for scaff: ZNF528--ZNF610 [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] -fusion SPANNING read extraction for scaff: ZNF528--ZNF880 -filtered reads reasons: $VAR1 = { 'seq similar region alignment' => 99021, 'lacks exon overlap' => 76178 }; EM: Starting log likelihood: -12025.002784 EM: Round [1] log likelihood: -12021.409928 EM: Round [2] log likelihood: -12021.267832 EM: Round [3] log likelihood: -12021.262865 EM: Round [4] log likelihood: -12021.262698 EM: Round [5] log likelihood: -12021.262693 EM: Stopping iterations at round 5 due to insufficient improvement in likelihood. [bam_sort_core] merging from 0 files and 8 in-memory blocks... -extracting read coordinates from /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.ip1B8zh3GJ/fi_workdir/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter -done, see /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass EM: Starting log likelihood: -9923.169679 EM: Round [1] log likelihood: -9923.048128 EM: Round [2] log likelihood: -9923.048065 EM: Stopping iterations at round 2 due to insufficient improvement in likelihood. -total frags in /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296790345 Warning - not locating file: /tmp/nxf.ip1B8zh3GJ/aih-tih-sc-fa55c3-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed WARNING, no entry stored in dbm for [ENSG00000229018.5] WARNING, no entry stored in dbm for [ENSG00000229018.5] WARNING, no entry stored in dbm for [ENSG00000229018.5] WARNING, no entry stored in dbm for [ENSG00000229018.5] WARNING, no entry stored in dbm for [ENSG00000286092.1] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000231185.7] WARNING, no entry stored in dbm for [ENSG00000231185.7] WARNING, no entry stored in dbm for [ENSG00000279973.2] WARNING, no entry stored in dbm for [ENSG00000279973.2] WARNING, no entry stored in dbm for [ENSG00000279973.2] WARNING, no entry stored in dbm for [ENSG00000254367.5] WARNING, no entry stored in dbm for [ENSG00000254367.5] WARNING, no entry stored in dbm for [ENSG00000248238.2] WARNING, no entry stored in dbm for [ENSG00000279231.1] WARNING, no entry stored in dbm for [ENSG00000279231.1] WARNING, no entry stored in dbm for [ENSG00000279231.1] WARNING, no entry stored in dbm for [ENSG00000279231.1] WARNING, no entry stored in dbm for [ENSG00000279231.1] WARNING, no entry stored in dbm for [ENSG00000267886.1] WARNING, no entry stored in dbm for [ENSG00000267886.1] WARNING, no entry stored in dbm for [ENSG00000267886.1] WARNING, no entry stored in dbm for [ENSG00000267886.1] WARNING, no entry stored in dbm for [ENSG00000267886.1] WARNING, no entry stored in dbm for [ENSG00000248103.1] WARNING, no entry stored in dbm for [ENSG00000187172.15] WARNING, no entry stored in dbm for [ENSG00000243069.8] WARNING, no entry stored in dbm for [ENSG00000243069.8] WARNING, no entry stored in dbm for [ENSG00000243069.8] WARNING, no entry stored in dbm for [ENSG00000243069.8] WARNING, no entry stored in dbm for [ENSG00000237359.2] WARNING, no entry stored in dbm for [ENSG00000232104.3] WARNING, no entry stored in dbm for [ENSG00000232104.3] ls: cannot access 'IGV_inputs': No such file or directory