[2026-06-08T08:52:22] Launching Arriba 2.4.0
[2026-06-08T08:52:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:35] Reading chimeric alignments from 'aih-tih-sc-674b78-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11960308)
[2026-06-08T09:00:32] Marking multi-mapping alignments (marked=8098928)
[2026-06-08T09:00:38] Detecting strandedness (reverse)
[2026-06-08T09:00:38] Assigning strands to alignments 
[2026-06-08T09:00:41] Annotating alignments 
[2026-06-08T09:01:28] Filtering duplicates (remaining=6386834)
[2026-06-08T09:01:37] 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=5945229)
[2026-06-08T09:01:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5945229)
[2026-06-08T09:01:43] Filtering viral contigs with expression lower than the top 5 (remaining=5945229)
[2026-06-08T09:01:50] Filtering viral contigs with less than 5% coverage (remaining=5945229)
[2026-06-08T09:01:53] Estimating fragment length (mate gap mean=-85.9336, mate gap stddev=28.87, read length mean=128.995)
[2026-06-08T09:01:54] Filtering read-through fragments with a distance <=10000bp (remaining=5447289)
[2026-06-08T09:01:57] Filtering inconsistently clipped mates (remaining=5353629)
[2026-06-08T09:01:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5242593)
[2026-06-08T09:02:05] Filtering fragments with small insert size (remaining=5241690)
[2026-06-08T09:02:08] Filtering alignments with long gaps (remaining=5241690)
[2026-06-08T09:02:11] Filtering fragments with both mates in the same gene (remaining=5240718)
[2026-06-08T09:02:14] Filtering fusions arising from hairpin structures (remaining=4926227)
[2026-06-08T09:02:17] Filtering reads with a mismatch p-value <=0.01 (remaining=2219563)
[2026-06-08T09:02:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=932559)
[2026-06-08T09:02:44] Finding fusions and counting supporting reads (total=737406)
[2026-06-08T09:03:06] Merging adjacent fusion breakpoints (remaining=725760)
[2026-06-08T09:03:08] Filtering multi-mapping fusions by alignment score and read support (remaining=426904)
[2026-06-08T09:03:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=424229)
[2026-06-08T09:04:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=228808)
[2026-06-08T09:04:04] Filtering fusions with <2 supporting reads (remaining=28066)
[2026-06-08T09:04:05] Filtering fusions with an e-value >=0.3 (remaining=8173)
[2026-06-08T09:04:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8224)
[2026-06-08T09:04:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8134)
[2026-06-08T09:04:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8134)
[2026-06-08T09:04:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6077)
[2026-06-08T09:04:19] Searching for fusions with spliced split reads (remaining=6169)
[2026-06-08T09:04:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=3920)
[2026-06-08T09:04:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3880)
[2026-06-08T09:04:28] Searching for fusions with >=4 spliced events (remaining=4585)
[2026-06-08T09:04:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1834)
[2026-06-08T09:04:46] Filtering fusions with anchors <=23nt (remaining=1450)
[2026-06-08T09:04:47] Filtering end-to-end fusions with low support (remaining=1393)
[2026-06-08T09:04:48] Filtering fusions with no coverage around the breakpoints (remaining=1363)
[2026-06-08T09:04:49] Indexing gene sequences 
[2026-06-08T09:04:54] Filtering genes with >=30% identity (remaining=371)
[2026-06-08T09:04:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=134)
[2026-06-08T09:04:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=125)
[2026-06-08T09:05:00] Searching for additional isoforms (remaining=164)
[2026-06-08T09:05:02] Assigning confidence scores to events 
[2026-06-08T09:05:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:06] Writing fusions to file 'aih-tih-sc-674b78-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:07] Writing discarded fusions to file 'aih-tih-sc-674b78-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:42] Freeing resources
[2026-06-08T09:06:01] Done (elapsed time=00:13:39, CPU time=00:13:37, peak memory=16.7gb)