[2026-06-08T08:58:20] Launching Arriba 2.4.0
[2026-06-08T08:58:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:38] Reading chimeric alignments from 'aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9682478)
[2026-06-08T09:06:39] Marking multi-mapping alignments (marked=6121397)
[2026-06-08T09:06:44] Detecting strandedness (reverse)
[2026-06-08T09:06:44] Assigning strands to alignments 
[2026-06-08T09:06:45] Annotating alignments 
[2026-06-08T09:07:17] Filtering duplicates (remaining=5937593)
[2026-06-08T09:07:23] 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=5668860)
[2026-06-08T09:07:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5668860)
[2026-06-08T09:07:27] Filtering viral contigs with expression lower than the top 5 (remaining=5668860)
[2026-06-08T09:07:31] Filtering viral contigs with less than 5% coverage (remaining=5668860)
[2026-06-08T09:07:33] Estimating fragment length (mate gap mean=-87.4671, mate gap stddev=29.023, read length mean=133.274)
[2026-06-08T09:07:33] Filtering read-through fragments with a distance <=10000bp (remaining=5311019)
[2026-06-08T09:07:35] Filtering inconsistently clipped mates (remaining=5211160)
[2026-06-08T09:07:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5059450)
[2026-06-08T09:07:41] Filtering fragments with small insert size (remaining=5058722)
[2026-06-08T09:07:43] Filtering alignments with long gaps (remaining=5058722)
[2026-06-08T09:07:45] Filtering fragments with both mates in the same gene (remaining=5057619)
[2026-06-08T09:07:47] Filtering fusions arising from hairpin structures (remaining=4711949)
[2026-06-08T09:07:49] Filtering reads with a mismatch p-value <=0.01 (remaining=2232632)
[2026-06-08T09:08:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=980796)
[2026-06-08T09:08:13] Finding fusions and counting supporting reads (total=761950)
[2026-06-08T09:08:28] Merging adjacent fusion breakpoints (remaining=755091)
[2026-06-08T09:08:30] Filtering multi-mapping fusions by alignment score and read support (remaining=461859)
[2026-06-08T09:09:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:09:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=458997)
[2026-06-08T09:09:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=259457)
[2026-06-08T09:09:08] Filtering fusions with <2 supporting reads (remaining=32744)
[2026-06-08T09:09:08] Filtering fusions with an e-value >=0.3 (remaining=10618)
[2026-06-08T09:09:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10670)
[2026-06-08T09:09:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10557)
[2026-06-08T09:09:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10557)
[2026-06-08T09:09:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7219)
[2026-06-08T09:09:19] Searching for fusions with spliced split reads (remaining=7243)
[2026-06-08T09:09:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=4352)
[2026-06-08T09:09:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4295)
[2026-06-08T09:09:25] Searching for fusions with >=4 spliced events (remaining=5313)
[2026-06-08T09:09:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2415)
[2026-06-08T09:09:44] Filtering fusions with anchors <=23nt (remaining=1999)
[2026-06-08T09:09:45] Filtering end-to-end fusions with low support (remaining=1927)
[2026-06-08T09:09:45] Filtering fusions with no coverage around the breakpoints (remaining=1881)
[2026-06-08T09:09:46] Indexing gene sequences 
[2026-06-08T09:09:54] Filtering genes with >=30% identity (remaining=711)
[2026-06-08T09:09:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=411)
[2026-06-08T09:10:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=301)
[2026-06-08T09:10:10] Searching for additional isoforms (remaining=400)
[2026-06-08T09:10:11] Assigning confidence scores to events 
[2026-06-08T09:10:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:10:14] Writing fusions to file 'aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:17] Writing discarded fusions to file 'aih-tih-sc-7d33b9-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:46] Freeing resources
[2026-06-08T09:11:02] Done (elapsed time=00:12:42, CPU time=00:12:41, peak memory=14.4gb)