[2026-06-03T19:53:50] Launching Arriba 2.4.0
[2026-06-03T19:53:50] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:54:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:54:13] Reading chimeric alignments from 'aih-tih-sc-318819-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11715535)
[2026-06-03T20:04:11] Marking multi-mapping alignments (marked=8366930)
[2026-06-03T20:04:17] Detecting strandedness (reverse)
[2026-06-03T20:04:17] Assigning strands to alignments 
[2026-06-03T20:04:20] Annotating alignments 
[2026-06-03T20:05:24] Filtering duplicates (remaining=4957164)
[2026-06-03T20:05:35] 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=4541246)
[2026-06-03T20:05:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4541246)
[2026-06-03T20:05:41] Filtering viral contigs with expression lower than the top 5 (remaining=4541246)
[2026-06-03T20:05:48] Filtering viral contigs with less than 5% coverage (remaining=4541246)
[2026-06-03T20:05:51] Estimating fragment length (mate gap mean=-79.5614, mate gap stddev=26.7767, read length mean=113.84)
[2026-06-03T20:05:51] Filtering read-through fragments with a distance <=10000bp (remaining=4254796)
[2026-06-03T20:05:54] Filtering inconsistently clipped mates (remaining=4149476)
[2026-06-03T20:05:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3966785)
[2026-06-03T20:06:02] Filtering fragments with small insert size (remaining=3965393)
[2026-06-03T20:06:05] Filtering alignments with long gaps (remaining=3965392)
[2026-06-03T20:06:08] Filtering fragments with both mates in the same gene (remaining=3964165)
[2026-06-03T20:06:11] Filtering fusions arising from hairpin structures (remaining=3703161)
[2026-06-03T20:06:14] Filtering reads with a mismatch p-value <=0.01 (remaining=1312730)
[2026-06-03T20:06:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=632149)
[2026-06-03T20:06:40] Finding fusions and counting supporting reads (total=542632)
[2026-06-03T20:07:06] Merging adjacent fusion breakpoints (remaining=535108)
[2026-06-03T20:07:08] Filtering multi-mapping fusions by alignment score and read support (remaining=281233)
[2026-06-03T20:08:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:08:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=280169)
[2026-06-03T20:08:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=166749)
[2026-06-03T20:08:22] Filtering fusions with <2 supporting reads (remaining=14521)
[2026-06-03T20:08:22] Filtering fusions with an e-value >=0.3 (remaining=3256)
[2026-06-03T20:08:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3311)
[2026-06-03T20:08:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3213)
[2026-06-03T20:08:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3213)
[2026-06-03T20:08:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3200)
[2026-06-03T20:08:39] Searching for fusions with spliced split reads (remaining=3263)
[2026-06-03T20:08:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=2389)
[2026-06-03T20:08:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2371)
[2026-06-03T20:08:50] Searching for fusions with >=4 spliced events (remaining=2703)
[2026-06-03T20:08:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1149)
[2026-06-03T20:09:24] Filtering fusions with anchors <=23nt (remaining=969)
[2026-06-03T20:09:25] Filtering end-to-end fusions with low support (remaining=951)
[2026-06-03T20:09:26] Filtering fusions with no coverage around the breakpoints (remaining=936)
[2026-06-03T20:09:26] Indexing gene sequences 
[2026-06-03T20:09:36] Filtering genes with >=30% identity (remaining=321)
[2026-06-03T20:09:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=146)
[2026-06-03T20:09:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=108)
[2026-06-03T20:09:41] Searching for additional isoforms (remaining=132)
[2026-06-03T20:09:43] Assigning confidence scores to events 
[2026-06-03T20:09:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:09:47] Writing fusions to file 'aih-tih-sc-318819-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:09:49] Writing discarded fusions to file 'aih-tih-sc-318819-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:10:30] Freeing resources
[2026-06-03T20:10:57] Done (elapsed time=00:17:07, CPU time=00:17:06, peak memory=16.4gb)