[2026-06-03T19:56:52] Launching Arriba 2.4.0
[2026-06-03T19:56:52] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:57:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:57:16] Reading chimeric alignments from 'aih-tih-sc-242a7d-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11218056)
[2026-06-03T20:08:36] Marking multi-mapping alignments (marked=7876662)
[2026-06-03T20:08:43] Detecting strandedness (reverse)
[2026-06-03T20:08:43] Assigning strands to alignments 
[2026-06-03T20:08:46] Annotating alignments 
[2026-06-03T20:09:37] Filtering duplicates (remaining=3196498)
[2026-06-03T20:09:44] 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=2845244)
[2026-06-03T20:09:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2845244)
[2026-06-03T20:09:49] Filtering viral contigs with expression lower than the top 5 (remaining=2845244)
[2026-06-03T20:09:54] Filtering viral contigs with less than 5% coverage (remaining=2845244)
[2026-06-03T20:09:57] Estimating fragment length (mate gap mean=-81.4657, mate gap stddev=27.9561, read length mean=117.139)
[2026-06-03T20:09:57] Filtering read-through fragments with a distance <=10000bp (remaining=2730089)
[2026-06-03T20:09:59] Filtering inconsistently clipped mates (remaining=2650263)
[2026-06-03T20:10:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2502575)
[2026-06-03T20:10:05] Filtering fragments with small insert size (remaining=2501172)
[2026-06-03T20:10:08] Filtering alignments with long gaps (remaining=2501172)
[2026-06-03T20:10:10] Filtering fragments with both mates in the same gene (remaining=2500194)
[2026-06-03T20:10:12] Filtering fusions arising from hairpin structures (remaining=2324392)
[2026-06-03T20:10:15] Filtering reads with a mismatch p-value <=0.01 (remaining=810615)
[2026-06-03T20:10:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=327432)
[2026-06-03T20:10:29] Finding fusions and counting supporting reads (total=289021)
[2026-06-03T20:10:45] Merging adjacent fusion breakpoints (remaining=285977)
[2026-06-03T20:10:46] Filtering multi-mapping fusions by alignment score and read support (remaining=149205)
[2026-06-03T20:11:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:11:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=148207)
[2026-06-03T20:11:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90390)
[2026-06-03T20:11:32] Filtering fusions with <2 supporting reads (remaining=8170)
[2026-06-03T20:11:32] Filtering fusions with an e-value >=0.3 (remaining=1875)
[2026-06-03T20:11:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1902)
[2026-06-03T20:11:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1831)
[2026-06-03T20:11:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1831)
[2026-06-03T20:11:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1815)
[2026-06-03T20:11:41] Searching for fusions with spliced split reads (remaining=1945)
[2026-06-03T20:11:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=1481)
[2026-06-03T20:11:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1451)
[2026-06-03T20:11:47] Searching for fusions with >=4 spliced events (remaining=1600)
[2026-06-03T20:11:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=507)
[2026-06-03T20:12:05] Filtering fusions with anchors <=23nt (remaining=384)
[2026-06-03T20:12:06] Filtering end-to-end fusions with low support (remaining=372)
[2026-06-03T20:12:06] Filtering fusions with no coverage around the breakpoints (remaining=363)
[2026-06-03T20:12:06] Indexing gene sequences 
[2026-06-03T20:12:09] Filtering genes with >=30% identity (remaining=137)
[2026-06-03T20:12:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=88)
[2026-06-03T20:12:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=81)
[2026-06-03T20:12:12] Searching for additional isoforms (remaining=92)
[2026-06-03T20:12:13] Assigning confidence scores to events 
[2026-06-03T20:12:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:12:15] Writing fusions to file 'aih-tih-sc-242a7d-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:12:16] Writing discarded fusions to file 'aih-tih-sc-242a7d-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:12:40] Freeing resources
[2026-06-03T20:13:00] Done (elapsed time=00:16:08, CPU time=00:16:08, peak memory=15.7gb)