[2026-06-03T19:52:33] Launching Arriba 2.4.0
[2026-06-03T19:52:33] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:52:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:52:49] Reading chimeric alignments from 'aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11493074)
[2026-06-03T19:59:09] Marking multi-mapping alignments (marked=8545255)
[2026-06-03T19:59:15] Detecting strandedness (no)
[2026-06-03T19:59:15] Annotating alignments 
[2026-06-03T20:00:08] Filtering duplicates (remaining=4999000)
[2026-06-03T20:00:15] 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=4454779)
[2026-06-03T20:00:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4454779)
[2026-06-03T20:00:21] Filtering viral contigs with expression lower than the top 5 (remaining=4454779)
[2026-06-03T20:00:27] Filtering viral contigs with less than 5% coverage (remaining=4454779)
[2026-06-03T20:00:30] Estimating fragment length (mate gap mean=-82.1999, mate gap stddev=28.6188, read length mean=119.592)
[2026-06-03T20:00:30] Filtering read-through fragments with a distance <=10000bp (remaining=4273704)
[2026-06-03T20:00:33] Filtering inconsistently clipped mates (remaining=4156816)
[2026-06-03T20:00:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3987774)
[2026-06-03T20:00:41] Filtering fragments with small insert size (remaining=3986337)
[2026-06-03T20:00:43] Filtering alignments with long gaps (remaining=3986337)
[2026-06-03T20:00:46] Filtering fragments with both mates in the same gene (remaining=3985340)
[2026-06-03T20:00:49] Filtering fusions arising from hairpin structures (remaining=3675912)
[2026-06-03T20:00:52] Filtering reads with a mismatch p-value <=0.01 (remaining=1426544)
[2026-06-03T20:01:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=587681)
[2026-06-03T20:01:15] Finding fusions and counting supporting reads (total=476530)
[2026-06-03T20:01:32] Merging adjacent fusion breakpoints (remaining=472229)
[2026-06-03T20:01:33] Filtering multi-mapping fusions by alignment score and read support (remaining=260443)
[2026-06-03T20:02:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:02:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=258876)
[2026-06-03T20:02:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=156601)
[2026-06-03T20:02:22] Filtering fusions with <2 supporting reads (remaining=15157)
[2026-06-03T20:02:22] Filtering fusions with an e-value >=0.3 (remaining=4085)
[2026-06-03T20:02:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4152)
[2026-06-03T20:02:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4032)
[2026-06-03T20:02:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4034)
[2026-06-03T20:02:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3852)
[2026-06-03T20:02:34] Searching for fusions with spliced split reads (remaining=3922)
[2026-06-03T20:02:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=2830)
[2026-06-03T20:02:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2801)
[2026-06-03T20:02:41] Searching for fusions with >=4 spliced events (remaining=3195)
[2026-06-03T20:02:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1235)
[2026-06-03T20:03:01] Filtering fusions with anchors <=23nt (remaining=1027)
[2026-06-03T20:03:02] Filtering end-to-end fusions with low support (remaining=990)
[2026-06-03T20:03:03] Filtering fusions with no coverage around the breakpoints (remaining=961)
[2026-06-03T20:03:03] Indexing gene sequences 
[2026-06-03T20:03:09] Filtering genes with >=30% identity (remaining=360)
[2026-06-03T20:03:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=211)
[2026-06-03T20:03:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=160)
[2026-06-03T20:03:17] Searching for additional isoforms (remaining=196)
[2026-06-03T20:03:19] Assigning confidence scores to events 
[2026-06-03T20:03:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:03:22] Writing fusions to file 'aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:03:23] Writing discarded fusions to file 'aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:03:49] Freeing resources
[2026-06-03T20:04:13] Done (elapsed time=00:11:40, CPU time=00:11:39, peak memory=16.2gb)