[2026-06-08T08:27:05] Launching Arriba 2.4.0
[2026-06-08T08:27:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:22] Reading chimeric alignments from 'aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9801995)
[2026-06-08T08:32:42] Marking multi-mapping alignments (marked=6727784)
[2026-06-08T08:32:45] Detecting strandedness (reverse)
[2026-06-08T08:32:45] Assigning strands to alignments 
[2026-06-08T08:32:47] Annotating alignments 
[2026-06-08T08:33:15] Filtering duplicates (remaining=3164589)
[2026-06-08T08:33:20] 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=2945012)
[2026-06-08T08:33:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2945012)
[2026-06-08T08:33:23] Filtering viral contigs with expression lower than the top 5 (remaining=2945012)
[2026-06-08T08:33:27] Filtering viral contigs with less than 5% coverage (remaining=2945012)
[2026-06-08T08:33:28] Estimating fragment length (mate gap mean=-81.3471, mate gap stddev=27.6146, read length mean=117.573)
[2026-06-08T08:33:29] Filtering read-through fragments with a distance <=10000bp (remaining=2811953)
[2026-06-08T08:33:30] Filtering inconsistently clipped mates (remaining=2757609)
[2026-06-08T08:33:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2658120)
[2026-06-08T08:33:35] Filtering fragments with small insert size (remaining=2657401)
[2026-06-08T08:33:36] Filtering alignments with long gaps (remaining=2657401)
[2026-06-08T08:33:38] Filtering fragments with both mates in the same gene (remaining=2656477)
[2026-06-08T08:33:40] Filtering fusions arising from hairpin structures (remaining=2535072)
[2026-06-08T08:33:41] Filtering reads with a mismatch p-value <=0.01 (remaining=971945)
[2026-06-08T08:33:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=334854)
[2026-06-08T08:33:53] Finding fusions and counting supporting reads (total=299665)
[2026-06-08T08:34:05] Merging adjacent fusion breakpoints (remaining=296943)
[2026-06-08T08:34:05] Filtering multi-mapping fusions by alignment score and read support (remaining=161937)
[2026-06-08T08:34:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=161096)
[2026-06-08T08:34:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=98663)
[2026-06-08T08:34:36] Filtering fusions with <2 supporting reads (remaining=9187)
[2026-06-08T08:34:36] Filtering fusions with an e-value >=0.3 (remaining=2111)
[2026-06-08T08:34:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2134)
[2026-06-08T08:34:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2090)
[2026-06-08T08:34:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2090)
[2026-06-08T08:34:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2042)
[2026-06-08T08:34:43] Searching for fusions with spliced split reads (remaining=2083)
[2026-06-08T08:34:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=1493)
[2026-06-08T08:34:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1479)
[2026-06-08T08:34:48] Searching for fusions with >=4 spliced events (remaining=1665)
[2026-06-08T08:34:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=639)
[2026-06-08T08:35:01] Filtering fusions with anchors <=23nt (remaining=556)
[2026-06-08T08:35:02] Filtering end-to-end fusions with low support (remaining=540)
[2026-06-08T08:35:02] Filtering fusions with no coverage around the breakpoints (remaining=526)
[2026-06-08T08:35:02] Indexing gene sequences 
[2026-06-08T08:35:06] Filtering genes with >=30% identity (remaining=189)
[2026-06-08T08:35:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=90)
[2026-06-08T08:35:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=75)
[2026-06-08T08:35:13] Searching for additional isoforms (remaining=108)
[2026-06-08T08:35:13] Assigning confidence scores to events 
[2026-06-08T08:35:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:15] Writing fusions to file 'aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:35:17] Writing discarded fusions to file 'aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:33] Freeing resources
[2026-06-08T08:35:47] Done (elapsed time=00:08:42, CPU time=00:08:42, peak memory=14.1gb)