[2026-06-08T08:33:14] Launching Arriba 2.4.0
[2026-06-08T08:33:14] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:34] Reading chimeric alignments from 'aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11493074)
[2026-06-08T08:40:47] Marking multi-mapping alignments (marked=8545255)
[2026-06-08T08:40:52] Detecting strandedness (no)
[2026-06-08T08:40:52] Annotating alignments 
[2026-06-08T08:41:39] Filtering duplicates (remaining=4999000)
[2026-06-08T08:41:45] 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)
[2026-06-08T08:41:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4454779)
[2026-06-08T08:41:49] Filtering viral contigs with expression lower than the top 5 (remaining=4454779)
[2026-06-08T08:41:53] Filtering viral contigs with less than 5% coverage (remaining=4454779)
[2026-06-08T08:41:55] Estimating fragment length (mate gap mean=-82.1999, mate gap stddev=28.6188, read length mean=119.592)
[2026-06-08T08:41:56] Filtering read-through fragments with a distance <=10000bp (remaining=4273704)
[2026-06-08T08:41:58] Filtering inconsistently clipped mates (remaining=4156816)
[2026-06-08T08:42:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3987774)
[2026-06-08T08:42:04] Filtering fragments with small insert size (remaining=3986337)
[2026-06-08T08:42:06] Filtering alignments with long gaps (remaining=3986337)
[2026-06-08T08:42:08] Filtering fragments with both mates in the same gene (remaining=3985340)
[2026-06-08T08:42:11] Filtering fusions arising from hairpin structures (remaining=3675912)
[2026-06-08T08:42:13] Filtering reads with a mismatch p-value <=0.01 (remaining=1426544)
[2026-06-08T08:42:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=587681)
[2026-06-08T08:42:33] Finding fusions and counting supporting reads (total=476530)
[2026-06-08T08:42:46] Merging adjacent fusion breakpoints (remaining=472229)
[2026-06-08T08:42:47] Filtering multi-mapping fusions by alignment score and read support (remaining=260443)
[2026-06-08T08:43:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=258876)
[2026-06-08T08:43:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=156601)
[2026-06-08T08:43:24] Filtering fusions with <2 supporting reads (remaining=15157)
[2026-06-08T08:43:24] Filtering fusions with an e-value >=0.3 (remaining=4085)
[2026-06-08T08:43:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4152)
[2026-06-08T08:43:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4032)
[2026-06-08T08:43:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4034)
[2026-06-08T08:43:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3852)
[2026-06-08T08:43:34] Searching for fusions with spliced split reads (remaining=3922)
[2026-06-08T08:43:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=2830)
[2026-06-08T08:43:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2801)
[2026-06-08T08:43:40] Searching for fusions with >=4 spliced events (remaining=3195)
[2026-06-08T08:43:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1235)
[2026-06-08T08:43:58] Filtering fusions with anchors <=23nt (remaining=1027)
[2026-06-08T08:43:59] Filtering end-to-end fusions with low support (remaining=990)
[2026-06-08T08:43:59] Filtering fusions with no coverage around the breakpoints (remaining=961)
[2026-06-08T08:44:00] Indexing gene sequences 
[2026-06-08T08:44:06] Filtering genes with >=30% identity (remaining=360)
[2026-06-08T08:44:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=211)
[2026-06-08T08:44:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=160)
[2026-06-08T08:44:16] Searching for additional isoforms (remaining=196)
[2026-06-08T08:44:17] Assigning confidence scores to events 
[2026-06-08T08:44:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:21] Writing fusions to file 'aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:44:22] Writing discarded fusions to file 'aih-tih-sc-3abdf4-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:45] Freeing resources
[2026-06-08T08:45:06] Done (elapsed time=00:11:52, CPU time=00:11:50, peak memory=16.2gb)