[2026-06-08T08:31:07] Launching Arriba 2.4.0
[2026-06-08T08:31:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:27] Reading chimeric alignments from 'tih_rna_sample_00164_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=11735457)
[2026-06-08T08:38:53] Marking multi-mapping alignments (marked=8151039)
[2026-06-08T08:38:58] Detecting strandedness (reverse)
[2026-06-08T08:38:58] Assigning strands to alignments 
[2026-06-08T08:39:00] Annotating alignments 
[2026-06-08T08:39:38] Filtering duplicates (remaining=2901760)
[2026-06-08T08:39:43] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=2613126)
[2026-06-08T08:39:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2613126)
[2026-06-08T08:39:48] Filtering viral contigs with expression lower than the top 5 (remaining=2613126)
[2026-06-08T08:39:52] Filtering viral contigs with less than 5% coverage (remaining=2613126)
[2026-06-08T08:39:55] Estimating fragment length (mate gap mean=-88.9198, mate gap stddev=27.3747, read length mean=127.046)
[2026-06-08T08:39:55] Filtering read-through fragments with a distance <=10000bp (remaining=2519488)
[2026-06-08T08:39:57] Filtering inconsistently clipped mates (remaining=2476730)
[2026-06-08T08:39:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2403688)
[2026-06-08T08:40:03] Filtering fragments with small insert size (remaining=2403072)
[2026-06-08T08:40:05] Filtering alignments with long gaps (remaining=2403072)
[2026-06-08T08:40:07] Filtering fragments with both mates in the same gene (remaining=2402583)
[2026-06-08T08:40:09] Filtering fusions arising from hairpin structures (remaining=2307879)
[2026-06-08T08:40:12] Filtering reads with a mismatch p-value <=0.01 (remaining=731661)
[2026-06-08T08:40:19] Filtering reads with low entropy (k-mer content >=60%) (remaining=271979)
[2026-06-08T08:40:26] Finding fusions and counting supporting reads (total=231526)
[2026-06-08T08:40:40] Merging adjacent fusion breakpoints (remaining=229426)
[2026-06-08T08:40:41] Filtering multi-mapping fusions by alignment score and read support (remaining=130445)
[2026-06-08T08:41:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=129723)
[2026-06-08T08:41:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=78813)
[2026-06-08T08:41:24] Filtering fusions with <2 supporting reads (remaining=7624)
[2026-06-08T08:41:25] Filtering fusions with an e-value >=0.3 (remaining=1664)
[2026-06-08T08:41:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1679)
[2026-06-08T08:41:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1642)
[2026-06-08T08:41:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1642)
[2026-06-08T08:41:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1506)
[2026-06-08T08:41:33] Searching for fusions with spliced split reads (remaining=1604)
[2026-06-08T08:41:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=1253)
[2026-06-08T08:41:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1239)
[2026-06-08T08:41:38] Searching for fusions with >=4 spliced events (remaining=1301)
[2026-06-08T08:41:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=450)
[2026-06-08T08:41:52] Filtering fusions with anchors <=23nt (remaining=306)
[2026-06-08T08:41:53] Filtering end-to-end fusions with low support (remaining=262)
[2026-06-08T08:41:53] Filtering fusions with no coverage around the breakpoints (remaining=242)
[2026-06-08T08:41:53] Indexing gene sequences 
[2026-06-08T08:41:55] Filtering genes with >=30% identity (remaining=78)
[2026-06-08T08:41:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=32)
[2026-06-08T08:41:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=29)
[2026-06-08T08:41:57] Searching for additional isoforms (remaining=34)
[2026-06-08T08:41:58] Assigning confidence scores to events 
[2026-06-08T08:42:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:00] Writing fusions to file 'tih_rna_sample_00164_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:00] Writing discarded fusions to file 'tih_rna_sample_00164_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:16] Freeing resources
[2026-06-08T08:42:34] Done (elapsed time=00:11:27, CPU time=00:11:25, peak memory=16.3gb)