[2026-06-03T19:52:42] Launching Arriba 2.4.0
[2026-06-03T19:52:42] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:52:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:52:57] Reading chimeric alignments from 'aih-tih-sc-1274d4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=8880504)
[2026-06-03T20:00:25] Marking multi-mapping alignments (marked=5780628)
[2026-06-03T20:00:31] Detecting strandedness (reverse)
[2026-06-03T20:00:31] Assigning strands to alignments 
[2026-06-03T20:00:34] Annotating alignments 
[2026-06-03T20:01:25] Filtering duplicates (remaining=5632924)
[2026-06-03T20:01:36] 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=5373146)
[2026-06-03T20:01:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5373146)
[2026-06-03T20:01:41] Filtering viral contigs with expression lower than the top 5 (remaining=5373146)
[2026-06-03T20:01:48] Filtering viral contigs with less than 5% coverage (remaining=5373146)
[2026-06-03T20:01:52] Estimating fragment length (mate gap mean=-82.4248, mate gap stddev=29.1417, read length mean=123.578)
[2026-06-03T20:01:52] Filtering read-through fragments with a distance <=10000bp (remaining=5048869)
[2026-06-03T20:01:55] Filtering inconsistently clipped mates (remaining=4935322)
[2026-06-03T20:01:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4790729)
[2026-06-03T20:02:03] Filtering fragments with small insert size (remaining=4789745)
[2026-06-03T20:02:06] Filtering alignments with long gaps (remaining=4789745)
[2026-06-03T20:02:09] Filtering fragments with both mates in the same gene (remaining=4788291)
[2026-06-03T20:02:13] Filtering fusions arising from hairpin structures (remaining=4451905)
[2026-06-03T20:02:17] Filtering reads with a mismatch p-value <=0.01 (remaining=1962876)
[2026-06-03T20:02:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=934137)
[2026-06-03T20:02:45] Finding fusions and counting supporting reads (total=735237)
[2026-06-03T20:03:13] Merging adjacent fusion breakpoints (remaining=729140)
[2026-06-03T20:03:15] Filtering multi-mapping fusions by alignment score and read support (remaining=448900)
[2026-06-03T20:04:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:04:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=447277)
[2026-06-03T20:04:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=260226)
[2026-06-03T20:04:19] Filtering fusions with <2 supporting reads (remaining=28212)
[2026-06-03T20:04:20] Filtering fusions with an e-value >=0.3 (remaining=6666)
[2026-06-03T20:04:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6725)
[2026-06-03T20:04:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6656)
[2026-06-03T20:04:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6656)
[2026-06-03T20:04:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6218)
[2026-06-03T20:04:36] Searching for fusions with spliced split reads (remaining=6321)
[2026-06-03T20:04:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=4186)
[2026-06-03T20:04:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4094)
[2026-06-03T20:04:47] Searching for fusions with >=4 spliced events (remaining=4866)
[2026-06-03T20:04:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1869)
[2026-06-03T20:05:17] Filtering fusions with anchors <=23nt (remaining=1527)
[2026-06-03T20:05:18] Filtering end-to-end fusions with low support (remaining=1483)
[2026-06-03T20:05:19] Filtering fusions with no coverage around the breakpoints (remaining=1448)
[2026-06-03T20:05:20] Indexing gene sequences 
[2026-06-03T20:05:32] Filtering genes with >=30% identity (remaining=511)
[2026-06-03T20:05:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=294)
[2026-06-03T20:05:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=237)
[2026-06-03T20:05:45] Searching for additional isoforms (remaining=292)
[2026-06-03T20:05:47] Assigning confidence scores to events 
[2026-06-03T20:05:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:05:53] Writing fusions to file 'aih-tih-sc-1274d4-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:05:57] Writing discarded fusions to file 'aih-tih-sc-1274d4-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:06:46] Freeing resources
[2026-06-03T20:07:20] Done (elapsed time=00:14:38, CPU time=00:14:36, peak memory=13.5gb)