[2026-06-08T08:13:52] Launching Arriba 2.4.0
[2026-06-08T08:13:52] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:14:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:14:11] Reading chimeric alignments from 'aih-tih-sc-0183f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10629656)
[2026-06-08T08:19:16] Marking multi-mapping alignments (marked=7610649)
[2026-06-08T08:19:20] Detecting strandedness (reverse)
[2026-06-08T08:19:20] Assigning strands to alignments 
[2026-06-08T08:19:22] Annotating alignments 
[2026-06-08T08:19:49] Filtering duplicates (remaining=3920346)
[2026-06-08T08:19:54] 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=3711475)
[2026-06-08T08:19:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3711475)
[2026-06-08T08:19:58] Filtering viral contigs with expression lower than the top 5 (remaining=3711475)
[2026-06-08T08:20:02] Filtering viral contigs with less than 5% coverage (remaining=3711475)
[2026-06-08T08:20:04] Estimating fragment length (mate gap mean=-80.924, mate gap stddev=26.2938, read length mean=118.214)
[2026-06-08T08:20:04] Filtering read-through fragments with a distance <=10000bp (remaining=3516118)
[2026-06-08T08:20:06] Filtering inconsistently clipped mates (remaining=3451811)
[2026-06-08T08:20:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3305572)
[2026-06-08T08:20:11] Filtering fragments with small insert size (remaining=3304698)
[2026-06-08T08:20:13] Filtering alignments with long gaps (remaining=3304698)
[2026-06-08T08:20:15] Filtering fragments with both mates in the same gene (remaining=3303701)
[2026-06-08T08:20:17] Filtering fusions arising from hairpin structures (remaining=3168714)
[2026-06-08T08:20:18] Filtering reads with a mismatch p-value <=0.01 (remaining=1294563)
[2026-06-08T08:20:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=406476)
[2026-06-08T08:20:33] Finding fusions and counting supporting reads (total=344375)
[2026-06-08T08:20:45] Merging adjacent fusion breakpoints (remaining=340622)
[2026-06-08T08:20:46] Filtering multi-mapping fusions by alignment score and read support (remaining=166846)
[2026-06-08T08:21:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:21:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=166171)
[2026-06-08T08:21:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=103709)
[2026-06-08T08:21:18] Filtering fusions with <2 supporting reads (remaining=9072)
[2026-06-08T08:21:18] Filtering fusions with an e-value >=0.3 (remaining=2348)
[2026-06-08T08:21:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2388)
[2026-06-08T08:21:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2318)
[2026-06-08T08:21:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2318)
[2026-06-08T08:21:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2313)
[2026-06-08T08:21:26] Searching for fusions with spliced split reads (remaining=2440)
[2026-06-08T08:21:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=1746)
[2026-06-08T08:21:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1733)
[2026-06-08T08:21:31] Searching for fusions with >=4 spliced events (remaining=1908)
[2026-06-08T08:21:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=770)
[2026-06-08T08:21:47] Filtering fusions with anchors <=23nt (remaining=649)
[2026-06-08T08:21:47] Filtering end-to-end fusions with low support (remaining=632)
[2026-06-08T08:21:48] Filtering fusions with no coverage around the breakpoints (remaining=619)
[2026-06-08T08:21:48] Indexing gene sequences 
[2026-06-08T08:21:51] Filtering genes with >=30% identity (remaining=178)
[2026-06-08T08:21:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=52)
[2026-06-08T08:21:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=52)
[2026-06-08T08:21:55] Searching for additional isoforms (remaining=65)
[2026-06-08T08:21:55] Assigning confidence scores to events 
[2026-06-08T08:21:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:21:58] Writing fusions to file 'aih-tih-sc-0183f6-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:21:58] Writing discarded fusions to file 'aih-tih-sc-0183f6-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:22:14] Freeing resources
[2026-06-08T08:22:28] Done (elapsed time=00:08:36, CPU time=00:08:36, peak memory=14.8gb)