[2026-06-08T08:08:47] Launching Arriba 2.4.0
[2026-06-08T08:08:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:09:02] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:09:06] Reading chimeric alignments from 'aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=8395296)
[2026-06-08T08:13:39] Marking multi-mapping alignments (marked=5869753)
[2026-06-08T08:13:42] Detecting strandedness (reverse)
[2026-06-08T08:13:42] Assigning strands to alignments 
[2026-06-08T08:13:43] Annotating alignments 
[2026-06-08T08:14:05] Filtering duplicates (remaining=3110765)
[2026-06-08T08:14:08] 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=2901205)
[2026-06-08T08:14:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2901205)
[2026-06-08T08:14:11] Filtering viral contigs with expression lower than the top 5 (remaining=2901205)
[2026-06-08T08:14:14] Filtering viral contigs with less than 5% coverage (remaining=2901205)
[2026-06-08T08:14:15] Estimating fragment length (mate gap mean=-83.1479, mate gap stddev=27.7769, read length mean=121.18)
[2026-06-08T08:14:15] Filtering read-through fragments with a distance <=10000bp (remaining=2797930)
[2026-06-08T08:14:17] Filtering inconsistently clipped mates (remaining=2734555)
[2026-06-08T08:14:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2600638)
[2026-06-08T08:14:20] Filtering fragments with small insert size (remaining=2599958)
[2026-06-08T08:14:21] Filtering alignments with long gaps (remaining=2599958)
[2026-06-08T08:14:23] Filtering fragments with both mates in the same gene (remaining=2599175)
[2026-06-08T08:14:24] Filtering fusions arising from hairpin structures (remaining=2454662)
[2026-06-08T08:14:25] Filtering reads with a mismatch p-value <=0.01 (remaining=1009755)
[2026-06-08T08:14:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=294929)
[2026-06-08T08:14:37] Finding fusions and counting supporting reads (total=260092)
[2026-06-08T08:14:46] Merging adjacent fusion breakpoints (remaining=258143)
[2026-06-08T08:14:46] Filtering multi-mapping fusions by alignment score and read support (remaining=129879)
[2026-06-08T08:15:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:15:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=129066)
[2026-06-08T08:15:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=79129)
[2026-06-08T08:15:12] Filtering fusions with <2 supporting reads (remaining=6340)
[2026-06-08T08:15:12] Filtering fusions with an e-value >=0.3 (remaining=1602)
[2026-06-08T08:15:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1642)
[2026-06-08T08:15:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1579)
[2026-06-08T08:15:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1579)
[2026-06-08T08:15:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1577)
[2026-06-08T08:15:18] Searching for fusions with spliced split reads (remaining=1727)
[2026-06-08T08:15:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=1274)
[2026-06-08T08:15:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1255)
[2026-06-08T08:15:22] Searching for fusions with >=4 spliced events (remaining=1445)
[2026-06-08T08:15:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=592)
[2026-06-08T08:15:36] Filtering fusions with anchors <=23nt (remaining=473)
[2026-06-08T08:15:37] Filtering end-to-end fusions with low support (remaining=461)
[2026-06-08T08:15:37] Filtering fusions with no coverage around the breakpoints (remaining=451)
[2026-06-08T08:15:37] Indexing gene sequences 
[2026-06-08T08:15:40] Filtering genes with >=30% identity (remaining=130)
[2026-06-08T08:15:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=75)
[2026-06-08T08:15:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=60)
[2026-06-08T08:15:42] Searching for additional isoforms (remaining=77)
[2026-06-08T08:15:43] Assigning confidence scores to events 
[2026-06-08T08:15:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:15:45] Writing fusions to file 'aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:15:46] Writing discarded fusions to file 'aih-tih-sc-f4e5c4-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:16:00] Freeing resources
[2026-06-08T08:16:11] Done (elapsed time=00:07:24, CPU time=00:07:24, peak memory=12.6gb)