[2026-06-03T20:28:58] Launching Arriba 2.4.0
[2026-06-03T20:28:58] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:29:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:29:10] Reading chimeric alignments from 'aih-tih-sc-816ec7-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10637307)
[2026-06-03T20:35:46] Marking multi-mapping alignments (marked=7062138)
[2026-06-03T20:35:50] Detecting strandedness (reverse)
[2026-06-03T20:35:50] Assigning strands to alignments 
[2026-06-03T20:35:52] Annotating alignments 
[2026-06-03T20:36:26] Filtering duplicates (remaining=6960548)
[2026-06-03T20:36:33] 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=6518811)
[2026-06-03T20:36:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6518811)
[2026-06-03T20:36:37] Filtering viral contigs with expression lower than the top 5 (remaining=6518811)
[2026-06-03T20:36:42] Filtering viral contigs with less than 5% coverage (remaining=6518811)
[2026-06-03T20:36:44] Estimating fragment length (mate gap mean=-86.0118, mate gap stddev=29.0746, read length mean=128.808)
[2026-06-03T20:36:44] Filtering read-through fragments with a distance <=10000bp (remaining=6132371)
[2026-06-03T20:36:46] Filtering inconsistently clipped mates (remaining=5994902)
[2026-06-03T20:36:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5827514)
[2026-06-03T20:36:53] Filtering fragments with small insert size (remaining=5826518)
[2026-06-03T20:36:55] Filtering alignments with long gaps (remaining=5826518)
[2026-06-03T20:36:57] Filtering fragments with both mates in the same gene (remaining=5825404)
[2026-06-03T20:36:59] Filtering fusions arising from hairpin structures (remaining=5398624)
[2026-06-03T20:37:02] Filtering reads with a mismatch p-value <=0.01 (remaining=2335804)
[2026-06-03T20:37:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=1080138)
[2026-06-03T20:37:25] Finding fusions and counting supporting reads (total=838631)
[2026-06-03T20:37:42] Merging adjacent fusion breakpoints (remaining=829353)
[2026-06-03T20:37:44] Filtering multi-mapping fusions by alignment score and read support (remaining=508633)
[2026-06-03T20:38:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:38:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=506546)
[2026-06-03T20:38:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=297441)
[2026-06-03T20:38:28] Filtering fusions with <2 supporting reads (remaining=32997)
[2026-06-03T20:38:28] Filtering fusions with an e-value >=0.3 (remaining=8451)
[2026-06-03T20:38:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8500)
[2026-06-03T20:38:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8395)
[2026-06-03T20:38:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8395)
[2026-06-03T20:38:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6955)
[2026-06-03T20:38:41] Searching for fusions with spliced split reads (remaining=7067)
[2026-06-03T20:38:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=4640)
[2026-06-03T20:38:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4585)
[2026-06-03T20:38:48] Searching for fusions with >=4 spliced events (remaining=5442)
[2026-06-03T20:38:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2261)
[2026-06-03T20:39:05] Filtering fusions with anchors <=23nt (remaining=1769)
[2026-06-03T20:39:06] Filtering end-to-end fusions with low support (remaining=1712)
[2026-06-03T20:39:06] Filtering fusions with no coverage around the breakpoints (remaining=1677)
[2026-06-03T20:39:07] Indexing gene sequences 
[2026-06-03T20:39:14] Filtering genes with >=30% identity (remaining=585)
[2026-06-03T20:39:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=257)
[2026-06-03T20:39:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-06-03T20:39:21] Searching for additional isoforms (remaining=270)
[2026-06-03T20:39:23] Assigning confidence scores to events 
[2026-06-03T20:39:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:39:27] Writing fusions to file 'aih-tih-sc-816ec7-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:39:29] Writing discarded fusions to file 'aih-tih-sc-816ec7-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:40:00] Freeing resources
[2026-06-03T20:40:17] Done (elapsed time=00:11:19, CPU time=00:11:17, peak memory=15.4gb)