[2026-06-03T20:12:00] Launching Arriba 2.4.0
[2026-06-03T20:12:00] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:12:14] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:12:18] Reading chimeric alignments from 'aih-tih-sc-573e21-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=12339329)
[2026-06-03T20:20:57] Marking multi-mapping alignments (marked=8515309)
[2026-06-03T20:21:04] Detecting strandedness (reverse)
[2026-06-03T20:21:04] Assigning strands to alignments 
[2026-06-03T20:21:07] Annotating alignments 
[2026-06-03T20:22:02] Filtering duplicates (remaining=6511385)
[2026-06-03T20:22:14] 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=5905934)
[2026-06-03T20:22:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5905934)
[2026-06-03T20:22:20] Filtering viral contigs with expression lower than the top 5 (remaining=5905934)
[2026-06-03T20:22:27] Filtering viral contigs with less than 5% coverage (remaining=5905934)
[2026-06-03T20:22:31] Estimating fragment length (mate gap mean=-82.8891, mate gap stddev=29.8351, read length mean=126.252)
[2026-06-03T20:22:31] Filtering read-through fragments with a distance <=10000bp (remaining=5608239)
[2026-06-03T20:22:34] Filtering inconsistently clipped mates (remaining=5485869)
[2026-06-03T20:22:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5346244)
[2026-06-03T20:22:43] Filtering fragments with small insert size (remaining=5344599)
[2026-06-03T20:22:46] Filtering alignments with long gaps (remaining=5344598)
[2026-06-03T20:22:49] Filtering fragments with both mates in the same gene (remaining=5343506)
[2026-06-03T20:22:53] Filtering fusions arising from hairpin structures (remaining=5005161)
[2026-06-03T20:22:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2029857)
[2026-06-03T20:23:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=827680)
[2026-06-03T20:23:24] Finding fusions and counting supporting reads (total=638495)
[2026-06-03T20:23:51] Merging adjacent fusion breakpoints (remaining=631864)
[2026-06-03T20:23:53] Filtering multi-mapping fusions by alignment score and read support (remaining=393431)
[2026-06-03T20:24:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:24:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=391461)
[2026-06-03T20:24:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=214278)
[2026-06-03T20:24:59] Filtering fusions with <2 supporting reads (remaining=25821)
[2026-06-03T20:25:00] Filtering fusions with an e-value >=0.3 (remaining=7637)
[2026-06-03T20:25:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7698)
[2026-06-03T20:25:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7625)
[2026-06-03T20:25:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7625)
[2026-06-03T20:25:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5125)
[2026-06-03T20:25:17] Searching for fusions with spliced split reads (remaining=5261)
[2026-06-03T20:25:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=3410)
[2026-06-03T20:25:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3369)
[2026-06-03T20:25:28] Searching for fusions with >=4 spliced events (remaining=3979)
[2026-06-03T20:25:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1596)
[2026-06-03T20:25:54] Filtering fusions with anchors <=23nt (remaining=1281)
[2026-06-03T20:25:55] Filtering end-to-end fusions with low support (remaining=1242)
[2026-06-03T20:25:56] Filtering fusions with no coverage around the breakpoints (remaining=1222)
[2026-06-03T20:25:57] Indexing gene sequences 
[2026-06-03T20:26:05] Filtering genes with >=30% identity (remaining=441)
[2026-06-03T20:26:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=235)
[2026-06-03T20:26:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=198)
[2026-06-03T20:26:16] Searching for additional isoforms (remaining=301)
[2026-06-03T20:26:18] Assigning confidence scores to events 
[2026-06-03T20:26:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:26:23] Writing fusions to file 'aih-tih-sc-573e21-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:26:27] Writing discarded fusions to file 'aih-tih-sc-573e21-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:27:10] Freeing resources
[2026-06-03T20:27:41] Done (elapsed time=00:15:41, CPU time=00:15:40, peak memory=17gb)