[2026-06-08T08:26:55] Launching Arriba 2.4.0
[2026-06-08T08:26:55] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:07] Reading chimeric alignments from 'aih-tih-sc-97ecde-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11188273)
[2026-06-08T08:32:33] Marking multi-mapping alignments (marked=7735406)
[2026-06-08T08:32:38] Detecting strandedness (reverse)
[2026-06-08T08:32:38] Assigning strands to alignments 
[2026-06-08T08:32:40] Annotating alignments 
[2026-06-08T08:33:16] Filtering duplicates (remaining=3906689)
[2026-06-08T08:33:22] 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=3632155)
[2026-06-08T08:33:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3632155)
[2026-06-08T08:33:26] Filtering viral contigs with expression lower than the top 5 (remaining=3632155)
[2026-06-08T08:33:31] Filtering viral contigs with less than 5% coverage (remaining=3632155)
[2026-06-08T08:33:34] Estimating fragment length (mate gap mean=-82.7639, mate gap stddev=27.6888, read length mean=123.215)
[2026-06-08T08:33:34] Filtering read-through fragments with a distance <=10000bp (remaining=3495540)
[2026-06-08T08:33:36] Filtering inconsistently clipped mates (remaining=3432285)
[2026-06-08T08:33:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3285014)
[2026-06-08T08:33:41] Filtering fragments with small insert size (remaining=3284320)
[2026-06-08T08:33:43] Filtering alignments with long gaps (remaining=3284320)
[2026-06-08T08:33:46] Filtering fragments with both mates in the same gene (remaining=3283267)
[2026-06-08T08:33:48] Filtering fusions arising from hairpin structures (remaining=3158180)
[2026-06-08T08:33:50] Filtering reads with a mismatch p-value <=0.01 (remaining=1293924)
[2026-06-08T08:33:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=356970)
[2026-06-08T08:34:05] Finding fusions and counting supporting reads (total=305478)
[2026-06-08T08:34:20] Merging adjacent fusion breakpoints (remaining=302809)
[2026-06-08T08:34:21] Filtering multi-mapping fusions by alignment score and read support (remaining=155151)
[2026-06-08T08:34:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=154095)
[2026-06-08T08:35:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=95605)
[2026-06-08T08:35:02] Filtering fusions with <2 supporting reads (remaining=8492)
[2026-06-08T08:35:02] Filtering fusions with an e-value >=0.3 (remaining=2399)
[2026-06-08T08:35:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2433)
[2026-06-08T08:35:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2333)
[2026-06-08T08:35:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2333)
[2026-06-08T08:35:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2239)
[2026-06-08T08:35:12] Searching for fusions with spliced split reads (remaining=2282)
[2026-06-08T08:35:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=1681)
[2026-06-08T08:35:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1656)
[2026-06-08T08:35:18] Searching for fusions with >=4 spliced events (remaining=1873)
[2026-06-08T08:35:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=771)
[2026-06-08T08:35:31] Filtering fusions with anchors <=23nt (remaining=665)
[2026-06-08T08:35:31] Filtering end-to-end fusions with low support (remaining=646)
[2026-06-08T08:35:32] Filtering fusions with no coverage around the breakpoints (remaining=632)
[2026-06-08T08:35:32] Indexing gene sequences 
[2026-06-08T08:35:36] Filtering genes with >=30% identity (remaining=254)
[2026-06-08T08:35:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=152)
[2026-06-08T08:35:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=143)
[2026-06-08T08:35:40] Searching for additional isoforms (remaining=165)
[2026-06-08T08:35:41] Assigning confidence scores to events 
[2026-06-08T08:35:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:44] Writing fusions to file 'aih-tih-sc-97ecde-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:35:45] Writing discarded fusions to file 'aih-tih-sc-97ecde-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:04] Freeing resources
[2026-06-08T08:36:20] Done (elapsed time=00:09:25, CPU time=00:09:25, peak memory=15.3gb)