[2026-06-03T19:31:15] Launching Arriba 2.4.0
[2026-06-03T19:31:15] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:31:25] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:31:29] Reading chimeric alignments from 'aih-tih-sc-a558c6-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7149121)
[2026-06-03T19:35:59] Marking multi-mapping alignments (marked=5230993)
[2026-06-03T19:36:03] Detecting strandedness (reverse)
[2026-06-03T19:36:03] Assigning strands to alignments 
[2026-06-03T19:36:04] Annotating alignments 
[2026-06-03T19:36:33] Filtering duplicates (remaining=2959530)
[2026-06-03T19:36:40] 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=2654936)
[2026-06-03T19:36:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2654936)
[2026-06-03T19:36:43] Filtering viral contigs with expression lower than the top 5 (remaining=2654936)
[2026-06-03T19:36:46] Filtering viral contigs with less than 5% coverage (remaining=2654936)
[2026-06-03T19:36:48] Estimating fragment length (mate gap mean=-79.9726, mate gap stddev=27.8061, read length mean=114.254)
[2026-06-03T19:36:48] Filtering read-through fragments with a distance <=10000bp (remaining=2544397)
[2026-06-03T19:36:50] Filtering inconsistently clipped mates (remaining=2476915)
[2026-06-03T19:36:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2370080)
[2026-06-03T19:36:54] Filtering fragments with small insert size (remaining=2369217)
[2026-06-03T19:36:56] Filtering alignments with long gaps (remaining=2369217)
[2026-06-03T19:36:58] Filtering fragments with both mates in the same gene (remaining=2368422)
[2026-06-03T19:36:59] Filtering fusions arising from hairpin structures (remaining=2210454)
[2026-06-03T19:37:01] Filtering reads with a mismatch p-value <=0.01 (remaining=762852)
[2026-06-03T19:37:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=326472)
[2026-06-03T19:37:14] Finding fusions and counting supporting reads (total=285972)
[2026-06-03T19:37:27] Merging adjacent fusion breakpoints (remaining=283515)
[2026-06-03T19:37:28] Filtering multi-mapping fusions by alignment score and read support (remaining=146976)
[2026-06-03T19:37:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:38:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=146194)
[2026-06-03T19:38:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90759)
[2026-06-03T19:38:03] Filtering fusions with <2 supporting reads (remaining=7473)
[2026-06-03T19:38:04] Filtering fusions with an e-value >=0.3 (remaining=1901)
[2026-06-03T19:38:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1952)
[2026-06-03T19:38:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1904)
[2026-06-03T19:38:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1904)
[2026-06-03T19:38:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1893)
[2026-06-03T19:38:11] Searching for fusions with spliced split reads (remaining=2038)
[2026-06-03T19:38:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=1484)
[2026-06-03T19:38:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1464)
[2026-06-03T19:38:16] Searching for fusions with >=4 spliced events (remaining=1635)
[2026-06-03T19:38:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=573)
[2026-06-03T19:38:30] Filtering fusions with anchors <=23nt (remaining=487)
[2026-06-03T19:38:31] Filtering end-to-end fusions with low support (remaining=477)
[2026-06-03T19:38:31] Filtering fusions with no coverage around the breakpoints (remaining=465)
[2026-06-03T19:38:31] Indexing gene sequences 
[2026-06-03T19:38:34] Filtering genes with >=30% identity (remaining=170)
[2026-06-03T19:38:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=103)
[2026-06-03T19:38:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=89)
[2026-06-03T19:38:37] Searching for additional isoforms (remaining=110)
[2026-06-03T19:38:38] Assigning confidence scores to events 
[2026-06-03T19:38:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:38:40] Writing fusions to file 'aih-tih-sc-a558c6-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:38:41] Writing discarded fusions to file 'aih-tih-sc-a558c6-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:39:00] Freeing resources
[2026-06-03T19:39:12] Done (elapsed time=00:07:57, CPU time=00:07:56, peak memory=11.6gb)