Done. -parsing GTF file: /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.gtf * Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.0PtJTg7ijV/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.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c' * Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00686_B23MVV7LT4_1.star.sortedByCoord.out.bam * Running CMD: samtools index tih_rna_sample_00686_B23MVV7LT4_1.star.sortedByCoord.out.bam 12:06:35 : INFO : Done. -parsing GTF file: /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_1.gtf -parsing /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_1.star.cSorted.dupsMarked.bam [10000] [20000] [30000] [40000] [50000] [60000] [70000] [80000] [90000] [100000] [110000] [120000] [130000] [140000] [150000] [160000] [170000] [180000] [190000] -done parsing /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info. junction read elimination tally: $VAR1 = { 'excessive soft clipping' => 1124, 'seq-similar region overlap' => 75, 'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 92, 'small anchor length' => 17, 'low complexity anchor region' => 1, 'per_id < 96' => 511, 'exons hit < 2' => 1, 'num genes matched < 2' => 16, ' ** passed ** ' => 1223 }; -writing fusion junction support info. -outputting the spanning read info: /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_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] -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B [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] -fusion SPANNING read extraction for scaff: OPA3--ERCC2 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] -fusion SPANNING read extraction for scaff: PMS2P8--CCDC146 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] [14000] -fusion SPANNING read extraction for scaff: SLCO1B3--SLCO1B7 [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: STX16--NPEPL1 [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: TLK2--AC240565.1 [1000] [2000] [3000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1 [1000] [2000] [3000] [4000] [5000] [6000] [7000] [8000] [9000] [10000] [11000] [12000] [13000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4 -filtered reads reasons: $VAR1 = { 'lacks exon overlap' => 2658, 'seq similar region alignment' => 13965 }; EM: Starting log likelihood: -1971.307981 EM: Round [1] log likelihood: -1969.612312 EM: Round [2] log likelihood: -1969.609455 EM: Round [3] log likelihood: -1969.609450 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. [bam_sort_core] merging from 0 files and 8 in-memory blocks... -extracting read coordinates from /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.consolidated.bam.read_coords CMD: touch /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.consolidated.bam.read_coords.ok CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50 CMD: cp /tmp/nxf.0PtJTg7ijV/fi_workdir/tih_rna_sample_00686_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.post_blast_and_promiscuity_filter -done, see /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass EM: Starting log likelihood: -1888.566857 EM: Round [1] log likelihood: -1888.321621 EM: Round [2] log likelihood: -1888.321024 EM: Round [3] log likelihood: -1888.321022 EM: Stopping iterations at round 3 due to insufficient improvement in likelihood. -total frags in /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1_1.fastp.fastq.gz: 295611244 Warning - not locating file: /tmp/nxf.0PtJTg7ijV/tih_rna_sample_00686_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000273897.1] WARNING, no entry stored in dbm for [ENSG00000242193.11] WARNING, no entry stored in dbm for [ENSG00000242193.11] WARNING, no entry stored in dbm for [ENSG00000242193.11] WARNING, no entry stored in dbm for [ENSG00000242193.11] WARNING, no entry stored in dbm for [ENSG00000242193.11] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] ls: cannot access 'IGV_inputs': No such file or directory