[2026-06-03T20:10:48] Launching Arriba 2.4.0
[2026-06-03T20:10:48] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:10:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:11:03] Reading chimeric alignments from 'aih-tih-sc-64cd51-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11111465)
[2026-06-03T20:18:37] Marking multi-mapping alignments (marked=7458587)
[2026-06-03T20:18:42] Detecting strandedness (reverse)
[2026-06-03T20:18:42] Assigning strands to alignments 
[2026-06-03T20:18:45] Annotating alignments 
[2026-06-03T20:19:28] Filtering duplicates (remaining=7309810)
[2026-06-03T20:19:37] 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=6787908)
[2026-06-03T20:19:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6787908)
[2026-06-03T20:19:43] Filtering viral contigs with expression lower than the top 5 (remaining=6787908)
[2026-06-03T20:19:49] Filtering viral contigs with less than 5% coverage (remaining=6787908)
[2026-06-03T20:19:52] Estimating fragment length (mate gap mean=-84.3951, mate gap stddev=28.9756, read length mean=125.697)
[2026-06-03T20:19:52] Filtering read-through fragments with a distance <=10000bp (remaining=6374302)
[2026-06-03T20:19:55] Filtering inconsistently clipped mates (remaining=6242678)
[2026-06-03T20:19:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6069465)
[2026-06-03T20:20:03] Filtering fragments with small insert size (remaining=6068454)
[2026-06-03T20:20:06] Filtering alignments with long gaps (remaining=6068454)
[2026-06-03T20:20:09] Filtering fragments with both mates in the same gene (remaining=6067351)
[2026-06-03T20:20:12] Filtering fusions arising from hairpin structures (remaining=5678360)
[2026-06-03T20:20:15] Filtering reads with a mismatch p-value <=0.01 (remaining=2349927)
[2026-06-03T20:20:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=1166554)
[2026-06-03T20:20:44] Finding fusions and counting supporting reads (total=918335)
[2026-06-03T20:21:05] Merging adjacent fusion breakpoints (remaining=909627)
[2026-06-03T20:21:07] Filtering multi-mapping fusions by alignment score and read support (remaining=555453)
[2026-06-03T20:21:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:21:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=553149)
[2026-06-03T20:21:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=330166)
[2026-06-03T20:21:59] Filtering fusions with <2 supporting reads (remaining=36629)
[2026-06-03T20:22:00] Filtering fusions with an e-value >=0.3 (remaining=8582)
[2026-06-03T20:22:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8639)
[2026-06-03T20:22:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8535)
[2026-06-03T20:22:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8535)
[2026-06-03T20:22:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7737)
[2026-06-03T20:22:14] Searching for fusions with spliced split reads (remaining=7766)
[2026-06-03T20:22:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=5037)
[2026-06-03T20:22:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4989)
[2026-06-03T20:22:23] Searching for fusions with >=4 spliced events (remaining=6058)
[2026-06-03T20:22:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2534)
[2026-06-03T20:22:43] Filtering fusions with anchors <=23nt (remaining=2005)
[2026-06-03T20:22:44] Filtering end-to-end fusions with low support (remaining=1928)
[2026-06-03T20:22:45] Filtering fusions with no coverage around the breakpoints (remaining=1874)
[2026-06-03T20:22:46] Indexing gene sequences 
[2026-06-03T20:22:53] Filtering genes with >=30% identity (remaining=572)
[2026-06-03T20:22:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=257)
[2026-06-03T20:23:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=223)
[2026-06-03T20:23:02] Searching for additional isoforms (remaining=278)
[2026-06-03T20:23:04] Assigning confidence scores to events 
[2026-06-03T20:23:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:23:08] Writing fusions to file 'aih-tih-sc-64cd51-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:23:11] Writing discarded fusions to file 'aih-tih-sc-64cd51-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:23:52] Freeing resources
[2026-06-03T20:24:11] Done (elapsed time=00:13:23, CPU time=00:13:22, peak memory=16gb)