[2026-06-08T08:10:12] Launching Arriba 2.4.0
[2026-06-08T08:10:12] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:10:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:10:24] Reading chimeric alignments from 'aih-tih-sc-31d31f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9948983)
[2026-06-08T08:15:05] Marking multi-mapping alignments (marked=7604403)
[2026-06-08T08:15:09] Detecting strandedness (reverse)
[2026-06-08T08:15:09] Assigning strands to alignments 
[2026-06-08T08:15:11] Annotating alignments 
[2026-06-08T08:15:42] Filtering duplicates (remaining=3263985)
[2026-06-08T08:15:47] 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=2817812)
[2026-06-08T08:15:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2817812)
[2026-06-08T08:15:50] Filtering viral contigs with expression lower than the top 5 (remaining=2817812)
[2026-06-08T08:15:54] Filtering viral contigs with less than 5% coverage (remaining=2817812)
[2026-06-08T08:15:56] Estimating fragment length (mate gap mean=-80.2352, mate gap stddev=29.2848, read length mean=115.033)
[2026-06-08T08:15:57] Filtering read-through fragments with a distance <=10000bp (remaining=2693397)
[2026-06-08T08:15:58] Filtering inconsistently clipped mates (remaining=2620149)
[2026-06-08T08:16:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2479693)
[2026-06-08T08:16:03] Filtering fragments with small insert size (remaining=2478362)
[2026-06-08T08:16:05] Filtering alignments with long gaps (remaining=2478362)
[2026-06-08T08:16:07] Filtering fragments with both mates in the same gene (remaining=2477519)
[2026-06-08T08:16:09] Filtering fusions arising from hairpin structures (remaining=2311191)
[2026-06-08T08:16:11] Filtering reads with a mismatch p-value <=0.01 (remaining=790055)
[2026-06-08T08:16:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=296392)
[2026-06-08T08:16:24] Finding fusions and counting supporting reads (total=253481)
[2026-06-08T08:16:36] Merging adjacent fusion breakpoints (remaining=250769)
[2026-06-08T08:16:37] Filtering multi-mapping fusions by alignment score and read support (remaining=117618)
[2026-06-08T08:17:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:17:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=116619)
[2026-06-08T08:17:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=73678)
[2026-06-08T08:17:12] Filtering fusions with <2 supporting reads (remaining=5562)
[2026-06-08T08:17:12] Filtering fusions with an e-value >=0.3 (remaining=1437)
[2026-06-08T08:17:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1468)
[2026-06-08T08:17:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1413)
[2026-06-08T08:17:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1413)
[2026-06-08T08:17:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1408)
[2026-06-08T08:17:20] Searching for fusions with spliced split reads (remaining=1496)
[2026-06-08T08:17:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=1116)
[2026-06-08T08:17:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1106)
[2026-06-08T08:17:25] Searching for fusions with >=4 spliced events (remaining=1175)
[2026-06-08T08:17:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=397)
[2026-06-08T08:17:39] Filtering fusions with anchors <=23nt (remaining=315)
[2026-06-08T08:17:39] Filtering end-to-end fusions with low support (remaining=294)
[2026-06-08T08:17:39] Filtering fusions with no coverage around the breakpoints (remaining=284)
[2026-06-08T08:17:40] Indexing gene sequences 
[2026-06-08T08:17:42] Filtering genes with >=30% identity (remaining=94)
[2026-06-08T08:17:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=38)
[2026-06-08T08:17:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=38)
[2026-06-08T08:17:45] Searching for additional isoforms (remaining=44)
[2026-06-08T08:17:45] Assigning confidence scores to events 
[2026-06-08T08:17:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:17:47] Writing fusions to file 'aih-tih-sc-31d31f-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:17:48] Writing discarded fusions to file 'aih-tih-sc-31d31f-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:03] Freeing resources
[2026-06-08T08:18:18] Done (elapsed time=00:08:06, CPU time=00:08:05, peak memory=14.3gb)