[2026-06-03T19:05:23] Launching Arriba 2.4.0
[2026-06-03T19:05:23] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:05:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:05:50] Reading chimeric alignments from 'aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=2083711)
[2026-06-03T19:07:18] Marking multi-mapping alignments (marked=1622423)
[2026-06-03T19:07:19] Detecting strandedness (reverse)
[2026-06-03T19:07:19] Assigning strands to alignments 
[2026-06-03T19:07:19] Annotating alignments 
[2026-06-03T19:07:29] Filtering duplicates (remaining=715905)
[2026-06-03T19:07:31] 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=534726)
[2026-06-03T19:07:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=534726)
[2026-06-03T19:07:32] Filtering viral contigs with expression lower than the top 5 (remaining=534726)
[2026-06-03T19:07:33] Filtering viral contigs with less than 5% coverage (remaining=534726)
[2026-06-03T19:07:33] Estimating fragment length (mate gap mean=-72.6883, mate gap stddev=28.4788, read length mean=107.111)
[2026-06-03T19:07:34] Filtering read-through fragments with a distance <=10000bp (remaining=514276)
[2026-06-03T19:07:34] Filtering inconsistently clipped mates (remaining=496591)
[2026-06-03T19:07:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=484002)
[2026-06-03T19:07:35] Filtering fragments with small insert size (remaining=483468)
[2026-06-03T19:07:36] Filtering alignments with long gaps (remaining=483468)
[2026-06-03T19:07:36] Filtering fragments with both mates in the same gene (remaining=483160)
[2026-06-03T19:07:37] Filtering fusions arising from hairpin structures (remaining=451869)
[2026-06-03T19:07:37] Filtering reads with a mismatch p-value <=0.01 (remaining=153240)
[2026-06-03T19:07:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=57552)
[2026-06-03T19:07:40] Finding fusions and counting supporting reads (total=52120)
[2026-06-03T19:07:44] Merging adjacent fusion breakpoints (remaining=51701)
[2026-06-03T19:07:44] Filtering multi-mapping fusions by alignment score and read support (remaining=27447)
[2026-06-03T19:07:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:07:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=27129)
[2026-06-03T19:07:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17589)
[2026-06-03T19:07:54] Filtering fusions with <2 supporting reads (remaining=1155)
[2026-06-03T19:07:54] Filtering fusions with an e-value >=0.3 (remaining=312)
[2026-06-03T19:07:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=319)
[2026-06-03T19:07:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=301)
[2026-06-03T19:07:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=301)
[2026-06-03T19:07:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=237)
[2026-06-03T19:07:57] Searching for fusions with spliced split reads (remaining=242)
[2026-06-03T19:07:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=201)
[2026-06-03T19:07:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=198)
[2026-06-03T19:07:58] Searching for fusions with >=4 spliced events (remaining=207)
[2026-06-03T19:07:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=68)
[2026-06-03T19:08:26] Filtering fusions with anchors <=23nt (remaining=59)
[2026-06-03T19:08:26] Filtering end-to-end fusions with low support (remaining=58)
[2026-06-03T19:08:26] Filtering fusions with no coverage around the breakpoints (remaining=57)
[2026-06-03T19:08:26] Indexing gene sequences 
[2026-06-03T19:08:27] Filtering genes with >=30% identity (remaining=28)
[2026-06-03T19:08:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=19)
[2026-06-03T19:08:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=16)
[2026-06-03T19:08:28] Searching for additional isoforms (remaining=16)
[2026-06-03T19:08:28] Assigning confidence scores to events 
[2026-06-03T19:08:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:08:29] Writing fusions to file 'aih-tih-sc-0754d2-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:08:29] Writing discarded fusions to file 'aih-tih-sc-0754d2-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:08:35] Freeing resources
[2026-06-03T19:08:41] Done (elapsed time=00:03:18, CPU time=00:03:17, peak memory=6.22gb)