[2026-06-08T08:41:55] Launching Arriba 2.4.0
[2026-06-08T08:41:55] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:12] Reading chimeric alignments from 'aih-tih-sc-446670-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=8909252)
[2026-06-08T08:48:15] Marking multi-mapping alignments (marked=5873130)
[2026-06-08T08:48:19] Detecting strandedness (reverse)
[2026-06-08T08:48:19] Assigning strands to alignments 
[2026-06-08T08:48:20] Annotating alignments 
[2026-06-08T08:48:48] Filtering duplicates (remaining=5154890)
[2026-06-08T08:48:55] 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=4904900)
[2026-06-08T08:48:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4904900)
[2026-06-08T08:48:59] Filtering viral contigs with expression lower than the top 5 (remaining=4904900)
[2026-06-08T08:49:03] Filtering viral contigs with less than 5% coverage (remaining=4904900)
[2026-06-08T08:49:05] Estimating fragment length (mate gap mean=-89.0822, mate gap stddev=28.4063, read length mean=134.466)
[2026-06-08T08:49:05] Filtering read-through fragments with a distance <=10000bp (remaining=4657380)
[2026-06-08T08:49:07] Filtering inconsistently clipped mates (remaining=4583026)
[2026-06-08T08:49:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4481156)
[2026-06-08T08:49:12] Filtering fragments with small insert size (remaining=4480749)
[2026-06-08T08:49:14] Filtering alignments with long gaps (remaining=4480749)
[2026-06-08T08:49:16] Filtering fragments with both mates in the same gene (remaining=4480040)
[2026-06-08T08:49:18] Filtering fusions arising from hairpin structures (remaining=4224000)
[2026-06-08T08:49:21] Filtering reads with a mismatch p-value <=0.01 (remaining=1977796)
[2026-06-08T08:49:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=627229)
[2026-06-08T08:49:41] Finding fusions and counting supporting reads (total=449802)
[2026-06-08T08:49:55] Merging adjacent fusion breakpoints (remaining=443262)
[2026-06-08T08:49:56] Filtering multi-mapping fusions by alignment score and read support (remaining=273795)
[2026-06-08T08:50:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=272625)
[2026-06-08T08:50:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=157660)
[2026-06-08T08:50:34] Filtering fusions with <2 supporting reads (remaining=20101)
[2026-06-08T08:50:34] Filtering fusions with an e-value >=0.3 (remaining=6394)
[2026-06-08T08:50:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6456)
[2026-06-08T08:50:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6391)
[2026-06-08T08:50:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6391)
[2026-06-08T08:50:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4513)
[2026-06-08T08:50:44] Searching for fusions with spliced split reads (remaining=4575)
[2026-06-08T08:50:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=3029)
[2026-06-08T08:50:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3003)
[2026-06-08T08:50:51] Searching for fusions with >=4 spliced events (remaining=3422)
[2026-06-08T08:50:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1153)
[2026-06-08T08:51:12] Filtering fusions with anchors <=23nt (remaining=893)
[2026-06-08T08:51:12] Filtering end-to-end fusions with low support (remaining=867)
[2026-06-08T08:51:13] Filtering fusions with no coverage around the breakpoints (remaining=846)
[2026-06-08T08:51:13] Indexing gene sequences 
[2026-06-08T08:51:19] Filtering genes with >=30% identity (remaining=274)
[2026-06-08T08:51:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=127)
[2026-06-08T08:51:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=114)
[2026-06-08T08:51:24] Searching for additional isoforms (remaining=141)
[2026-06-08T08:51:25] Assigning confidence scores to events 
[2026-06-08T08:51:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:29] Writing fusions to file 'aih-tih-sc-446670-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:30] Writing discarded fusions to file 'aih-tih-sc-446670-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:58] Freeing resources
[2026-06-08T08:52:15] Done (elapsed time=00:10:20, CPU time=00:10:19, peak memory=13.2gb)