[2026-06-08T08:24:01] Launching Arriba 2.4.0
[2026-06-08T08:24:01] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:15] Reading chimeric alignments from 'aih-tih-sc-0419d4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=7621398)
[2026-06-08T08:28:34] Marking multi-mapping alignments (marked=4940515)
[2026-06-08T08:28:38] Detecting strandedness (reverse)
[2026-06-08T08:28:38] Assigning strands to alignments 
[2026-06-08T08:28:39] Annotating alignments 
[2026-06-08T08:29:11] Filtering duplicates (remaining=3068767)
[2026-06-08T08:29:15] 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=2890724)
[2026-06-08T08:29:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2890724)
[2026-06-08T08:29:19] Filtering viral contigs with expression lower than the top 5 (remaining=2890724)
[2026-06-08T08:29:23] Filtering viral contigs with less than 5% coverage (remaining=2890724)
[2026-06-08T08:29:25] Estimating fragment length (mate gap mean=-85.3783, mate gap stddev=27.5558, read length mean=123.227)
[2026-06-08T08:29:25] Filtering read-through fragments with a distance <=10000bp (remaining=2712412)
[2026-06-08T08:29:27] Filtering inconsistently clipped mates (remaining=2666364)
[2026-06-08T08:29:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2597738)
[2026-06-08T08:29:32] Filtering fragments with small insert size (remaining=2597073)
[2026-06-08T08:29:33] Filtering alignments with long gaps (remaining=2597073)
[2026-06-08T08:29:35] Filtering fragments with both mates in the same gene (remaining=2596413)
[2026-06-08T08:29:37] Filtering fusions arising from hairpin structures (remaining=2485364)
[2026-06-08T08:29:39] Filtering reads with a mismatch p-value <=0.01 (remaining=1016003)
[2026-06-08T08:29:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=392790)
[2026-06-08T08:29:53] Finding fusions and counting supporting reads (total=363705)
[2026-06-08T08:30:06] Merging adjacent fusion breakpoints (remaining=361043)
[2026-06-08T08:30:07] Filtering multi-mapping fusions by alignment score and read support (remaining=212509)
[2026-06-08T08:30:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=211607)
[2026-06-08T08:30:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=117171)
[2026-06-08T08:30:42] Filtering fusions with <2 supporting reads (remaining=10563)
[2026-06-08T08:30:42] Filtering fusions with an e-value >=0.3 (remaining=2662)
[2026-06-08T08:30:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2693)
[2026-06-08T08:30:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2664)
[2026-06-08T08:30:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2664)
[2026-06-08T08:30:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2498)
[2026-06-08T08:30:50] Searching for fusions with spliced split reads (remaining=2542)
[2026-06-08T08:30:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=1887)
[2026-06-08T08:30:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1854)
[2026-06-08T08:30:55] Searching for fusions with >=4 spliced events (remaining=2005)
[2026-06-08T08:30:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=767)
[2026-06-08T08:31:11] Filtering fusions with anchors <=23nt (remaining=649)
[2026-06-08T08:31:11] Filtering end-to-end fusions with low support (remaining=630)
[2026-06-08T08:31:12] Filtering fusions with no coverage around the breakpoints (remaining=618)
[2026-06-08T08:31:12] Indexing gene sequences 
[2026-06-08T08:31:17] Filtering genes with >=30% identity (remaining=263)
[2026-06-08T08:31:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=156)
[2026-06-08T08:31:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=147)
[2026-06-08T08:31:21] Searching for additional isoforms (remaining=163)
[2026-06-08T08:31:22] Assigning confidence scores to events 
[2026-06-08T08:31:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:31:24] Writing fusions to file 'aih-tih-sc-0419d4-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:31:26] Writing discarded fusions to file 'aih-tih-sc-0419d4-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:31:49] Freeing resources
[2026-06-08T08:32:04] Done (elapsed time=00:08:03, CPU time=00:08:02, peak memory=11.9gb)