[2026-06-08T08:28:08] Launching Arriba 2.4.0
[2026-06-08T08:28:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:21] Reading chimeric alignments from 'aih-tih-sc-be4b28-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=8665843)
[2026-06-08T08:33:13] Marking multi-mapping alignments (marked=5502468)
[2026-06-08T08:33:16] Detecting strandedness (reverse)
[2026-06-08T08:33:16] Assigning strands to alignments 
[2026-06-08T08:33:17] Annotating alignments 
[2026-06-08T08:33:44] Filtering duplicates (remaining=4949124)
[2026-06-08T08:33:49] 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=4742527)
[2026-06-08T08:33:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4742527)
[2026-06-08T08:33:52] Filtering viral contigs with expression lower than the top 5 (remaining=4742527)
[2026-06-08T08:33:56] Filtering viral contigs with less than 5% coverage (remaining=4742527)
[2026-06-08T08:33:58] Estimating fragment length (mate gap mean=-85.776, mate gap stddev=26.4635, read length mean=125.401)
[2026-06-08T08:33:58] Filtering read-through fragments with a distance <=10000bp (remaining=4457413)
[2026-06-08T08:33:59] Filtering inconsistently clipped mates (remaining=4399981)
[2026-06-08T08:34:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4304096)
[2026-06-08T08:34:04] Filtering fragments with small insert size (remaining=4303547)
[2026-06-08T08:34:06] Filtering alignments with long gaps (remaining=4303547)
[2026-06-08T08:34:07] Filtering fragments with both mates in the same gene (remaining=4302748)
[2026-06-08T08:34:09] Filtering fusions arising from hairpin structures (remaining=4160597)
[2026-06-08T08:34:11] Filtering reads with a mismatch p-value <=0.01 (remaining=1940201)
[2026-06-08T08:34:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=664131)
[2026-06-08T08:34:28] Finding fusions and counting supporting reads (total=509830)
[2026-06-08T08:34:41] Merging adjacent fusion breakpoints (remaining=504601)
[2026-06-08T08:34:42] Filtering multi-mapping fusions by alignment score and read support (remaining=304445)
[2026-06-08T08:35:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=303665)
[2026-06-08T08:35:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=180928)
[2026-06-08T08:35:15] Filtering fusions with <2 supporting reads (remaining=22245)
[2026-06-08T08:35:16] Filtering fusions with an e-value >=0.3 (remaining=5277)
[2026-06-08T08:35:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5311)
[2026-06-08T08:35:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5269)
[2026-06-08T08:35:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5269)
[2026-06-08T08:35:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5096)
[2026-06-08T08:35:25] Searching for fusions with spliced split reads (remaining=5156)
[2026-06-08T08:35:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=3446)
[2026-06-08T08:35:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3402)
[2026-06-08T08:35:30] Searching for fusions with >=4 spliced events (remaining=3886)
[2026-06-08T08:35:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1518)
[2026-06-08T08:35:45] Filtering fusions with anchors <=23nt (remaining=1272)
[2026-06-08T08:35:46] Filtering end-to-end fusions with low support (remaining=1246)
[2026-06-08T08:35:46] Filtering fusions with no coverage around the breakpoints (remaining=1213)
[2026-06-08T08:35:47] Indexing gene sequences 
[2026-06-08T08:35:52] Filtering genes with >=30% identity (remaining=346)
[2026-06-08T08:35:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=123)
[2026-06-08T08:35:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=114)
[2026-06-08T08:35:59] Searching for additional isoforms (remaining=149)
[2026-06-08T08:36:01] Assigning confidence scores to events 
[2026-06-08T08:36:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:03] Writing fusions to file 'aih-tih-sc-be4b28-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:04] Writing discarded fusions to file 'aih-tih-sc-be4b28-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:26] Freeing resources
[2026-06-08T08:36:39] Done (elapsed time=00:08:31, CPU time=00:08:29, peak memory=12.9gb)