[2026-06-08T08:48:07] Launching Arriba 2.4.0
[2026-06-08T08:48:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:21] Reading chimeric alignments from 'aih-tih-sc-8a623b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11341212)
[2026-06-08T08:55:08] Marking multi-mapping alignments (marked=7258589)
[2026-06-08T08:55:13] Detecting strandedness (reverse)
[2026-06-08T08:55:13] Assigning strands to alignments 
[2026-06-08T08:55:16] Annotating alignments 
[2026-06-08T08:55:53] Filtering duplicates (remaining=6160194)
[2026-06-08T08:56:01] 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=5890258)
[2026-06-08T08:56:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5890258)
[2026-06-08T08:56:05] Filtering viral contigs with expression lower than the top 5 (remaining=5890258)
[2026-06-08T08:56:10] Filtering viral contigs with less than 5% coverage (remaining=5890258)
[2026-06-08T08:56:13] Estimating fragment length (mate gap mean=-86.0739, mate gap stddev=27.2968, read length mean=127.393)
[2026-06-08T08:56:13] Filtering read-through fragments with a distance <=10000bp (remaining=5584860)
[2026-06-08T08:56:15] Filtering inconsistently clipped mates (remaining=5503946)
[2026-06-08T08:56:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5354425)
[2026-06-08T08:56:22] Filtering fragments with small insert size (remaining=5353653)
[2026-06-08T08:56:24] Filtering alignments with long gaps (remaining=5353653)
[2026-06-08T08:56:27] Filtering fragments with both mates in the same gene (remaining=5352545)
[2026-06-08T08:56:29] Filtering fusions arising from hairpin structures (remaining=5139105)
[2026-06-08T08:56:32] Filtering reads with a mismatch p-value <=0.01 (remaining=2344328)
[2026-06-08T08:56:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=811923)
[2026-06-08T08:56:56] Finding fusions and counting supporting reads (total=605522)
[2026-06-08T08:57:14] Merging adjacent fusion breakpoints (remaining=598686)
[2026-06-08T08:57:16] Filtering multi-mapping fusions by alignment score and read support (remaining=362855)
[2026-06-08T08:57:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=361535)
[2026-06-08T08:58:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=222970)
[2026-06-08T08:58:03] Filtering fusions with <2 supporting reads (remaining=26993)
[2026-06-08T08:58:04] Filtering fusions with an e-value >=0.3 (remaining=6258)
[2026-06-08T08:58:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6301)
[2026-06-08T08:58:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6234)
[2026-06-08T08:58:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6238)
[2026-06-08T08:58:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6128)
[2026-06-08T08:58:17] Searching for fusions with spliced split reads (remaining=6258)
[2026-06-08T08:58:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=4325)
[2026-06-08T08:58:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4258)
[2026-06-08T08:58:25] Searching for fusions with >=4 spliced events (remaining=5013)
[2026-06-08T08:58:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2069)
[2026-06-08T08:58:42] Filtering fusions with anchors <=23nt (remaining=1713)
[2026-06-08T08:58:43] Filtering end-to-end fusions with low support (remaining=1671)
[2026-06-08T08:58:43] Filtering fusions with no coverage around the breakpoints (remaining=1637)
[2026-06-08T08:58:44] Indexing gene sequences 
[2026-06-08T08:58:51] Filtering genes with >=30% identity (remaining=625)
[2026-06-08T08:58:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=375)
[2026-06-08T08:59:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=294)
[2026-06-08T08:59:03] Searching for additional isoforms (remaining=387)
[2026-06-08T08:59:04] Assigning confidence scores to events 
[2026-06-08T08:59:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:08] Writing fusions to file 'aih-tih-sc-8a623b-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:10] Writing discarded fusions to file 'aih-tih-sc-8a623b-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:39] Freeing resources
[2026-06-08T08:59:56] Done (elapsed time=00:11:49, CPU time=00:11:47, peak memory=15.5gb)