Done. -parsing GTF file: /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.2hP2eAdsNm/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.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' * Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam 22:27:16 : INFO : Done. -parsing GTF file: /tmp/nxf.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gtf -parsing /tmp/nxf.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-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] -done parsing /tmp/nxf.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { ' ** passed ** ' => 1793, 'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 6, 'excessive soft clipping' => 4696, 'per_id < 96' => 2855, 'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 24, 'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 6, 'low complexity anchor region' => 30, 'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3, 'small anchor length' => 3, 'seq-similar region overlap' => 232, 'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 33, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 34, 'num genes matched < 2' => 12 }; -writing fusion junction support info. -outputting the spanning read info: /tmp/nxf.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info. - counting read alignments among fusion contigs. [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: ASAH2B--PRKG1 [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] -fusion SPANNING read extraction for scaff: CSMD3--RNU4-37P [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] -fusion SPANNING read extraction for scaff: CSMD3--LINC02237 [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] -fusion SPANNING read extraction for scaff: GDPD1--SETD2 [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: GUSBP13--NAIP [1000] [2000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [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] -fusion SPANNING read extraction for scaff: PARD6B--RASSF2 [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: 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] -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] -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] -fusion SPANNING read extraction for scaff: SETD2--CA4 [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: SFMBT1--RFT1 [1000] [2000] -fusion SPANNING read extraction for scaff: SORCS1--AL353740.1 [1000] [2000] -fusion SPANNING read extraction for scaff: SORCS1--LINC02661 [1000] [2000] [3000] [4000] -fusion SPANNING read extraction for scaff: SREK1IP1--RGS7BP [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: SREK1IP1--MRPL49P1 [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: TLK2--AC240565.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] -fusion SPANNING read extraction for scaff: TTC39C--ISM1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: TTC39C--AL121782.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] [15000] [16000] [17000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 3247, 'seq similar region alignment' => 25791 }; EM: Starting log likelihood: -1964.421602 EM: Round [1] log likelihood: -1963.669062 EM: Round [2] log likelihood: -1963.031438 EM: Round [3] log likelihood: -1962.487651 EM: Round [4] log likelihood: -1962.021404 EM: Round [5] log likelihood: -1961.619859 EM: Round [6] log likelihood: -1961.272750 EM: Round [7] log likelihood: -1960.971752 EM: Round [8] log likelihood: -1960.710044 EM: Round [9] log likelihood: -1960.481977 EM: Round [10] log likelihood: -1960.282838 EM: Round [11] log likelihood: -1960.108666 EM: Round [12] log likelihood: -1959.956107 EM: Round [13] log likelihood: -1959.822312 EM: Round [14] log likelihood: -1959.704843 EM: Round [15] log likelihood: -1959.601611 EM: Round [16] log likelihood: -1959.510813 EM: Round [17] log likelihood: -1959.430895 EM: Round [18] log likelihood: -1959.360507 EM: Round [19] log likelihood: -1959.298479 EM: Round [20] log likelihood: -1959.243790 EM: Round [21] log likelihood: -1959.195552 EM: Round [22] log likelihood: -1959.152987 EM: Round [23] log likelihood: -1959.115416 EM: Round [24] log likelihood: -1959.082243 EM: Round [25] log likelihood: -1959.052946 EM: Round [26] log likelihood: -1959.027066 EM: Round [27] log likelihood: -1959.004200 EM: Round [28] log likelihood: -1958.983993 EM: Round [29] log likelihood: -1958.966133 EM: Round [30] log likelihood: -1958.950346 EM: Round [31] log likelihood: -1958.936389 EM: Round [32] log likelihood: -1958.924049 EM: Round [33] log likelihood: -1958.913137 EM: Round [34] log likelihood: -1958.903487 EM: Round [35] log likelihood: -1958.894953 EM: Round [36] log likelihood: -1958.887405 EM: Round [37] log likelihood: -1958.880729 EM: Round [38] log likelihood: -1958.874823 EM: Round [39] log likelihood: -1958.869600 EM: Round [40] log likelihood: -1958.864979 EM: Round [41] log likelihood: -1958.860891 EM: Round [42] log likelihood: -1958.857274 EM: Round [43] log likelihood: -1958.854074 EM: Round [44] log likelihood: -1958.851244 EM: Round [45] log likelihood: -1958.848739 EM: Round [46] log likelihood: -1958.846523 EM: Round [47] log likelihood: -1958.844563 EM: Round [48] log likelihood: -1958.842828 EM: Round [49] log likelihood: -1958.841293 EM: Round [50] log likelihood: -1958.839935 EM: Round [51] log likelihood: -1958.838733 EM: Round [52] log likelihood: -1958.837670 EM: Round [53] log likelihood: -1958.836729 EM: Round [54] log likelihood: -1958.835897 EM: Round [55] log likelihood: -1958.835160 EM: Round [56] log likelihood: -1958.834508 EM: Round [57] log likelihood: -1958.833932 EM: Round [58] log likelihood: -1958.833421 EM: Round [59] log likelihood: -1958.832970 EM: Round [60] log likelihood: -1958.832570 EM: Round [61] log likelihood: -1958.832217 EM: Round [62] log likelihood: -1958.831904 EM: Round [63] log likelihood: -1958.831627 EM: Round [64] log likelihood: -1958.831382 EM: Round [65] log likelihood: -1958.831165 EM: Round [66] log likelihood: -1958.830973 EM: Round [67] log likelihood: -1958.830804 EM: Round [68] log likelihood: -1958.830653 EM: Round [69] log likelihood: -1958.830520 EM: Round [70] log likelihood: -1958.830403 EM: Round [71] log likelihood: -1958.830299 EM: Round [72] log likelihood: -1958.830207 EM: Stopping iterations at round 72 due to insufficient improvement in likelihood. [bam_sort_core] merging from 0 files and 8 in-memory blocks... -extracting read coordinates from /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-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.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-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.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-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.2hP2eAdsNm/fi_workdir/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter -done, see /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass EM: Starting log likelihood: -1899.700396 EM: Round [1] log likelihood: -1899.700396 EM: Stopping iterations at round 1 due to insufficient improvement in likelihood. -total frags in /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296382314 Warning - not locating file: /tmp/nxf.2hP2eAdsNm/aih-tih-sc-f0dbdf-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed WARNING, no entry stored in dbm for [ENSG00000198237.8] 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] ls: cannot access 'IGV_inputs': No such file or directory