[2026-06-08T08:40:13] Launching Arriba 2.4.0
[2026-06-08T08:40:13] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:24] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:28] Reading chimeric alignments from 'aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8105218)
[2026-06-08T08:45:52] Marking multi-mapping alignments (marked=5182885)
[2026-06-08T08:45:54] Detecting strandedness (reverse)
[2026-06-08T08:45:54] Assigning strands to alignments 
[2026-06-08T08:45:56] Annotating alignments 
[2026-06-08T08:46:17] Filtering duplicates (remaining=5294580)
[2026-06-08T08:46:21] 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=5029549)
[2026-06-08T08:46:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5029549)
[2026-06-08T08:46:24] Filtering viral contigs with expression lower than the top 5 (remaining=5029549)
[2026-06-08T08:46:27] Filtering viral contigs with less than 5% coverage (remaining=5029549)
[2026-06-08T08:46:28] Estimating fragment length (mate gap mean=-85.3156, mate gap stddev=30.1572, read length mean=134.41)
[2026-06-08T08:46:29] Filtering read-through fragments with a distance <=10000bp (remaining=4736311)
[2026-06-08T08:46:30] Filtering inconsistently clipped mates (remaining=4644754)
[2026-06-08T08:46:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4523851)
[2026-06-08T08:46:34] Filtering fragments with small insert size (remaining=4523233)
[2026-06-08T08:46:35] Filtering alignments with long gaps (remaining=4523233)
[2026-06-08T08:46:37] Filtering fragments with both mates in the same gene (remaining=4522383)
[2026-06-08T08:46:38] Filtering fusions arising from hairpin structures (remaining=4191907)
[2026-06-08T08:46:40] Filtering reads with a mismatch p-value <=0.01 (remaining=2097088)
[2026-06-08T08:46:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=907198)
[2026-06-08T08:46:59] Finding fusions and counting supporting reads (total=666952)
[2026-06-08T08:47:10] Merging adjacent fusion breakpoints (remaining=660146)
[2026-06-08T08:47:11] Filtering multi-mapping fusions by alignment score and read support (remaining=408967)
[2026-06-08T08:47:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=406304)
[2026-06-08T08:47:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=223758)
[2026-06-08T08:47:38] Filtering fusions with <2 supporting reads (remaining=34841)
[2026-06-08T08:47:39] Filtering fusions with an e-value >=0.3 (remaining=12306)
[2026-06-08T08:47:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12358)
[2026-06-08T08:47:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12246)
[2026-06-08T08:47:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12246)
[2026-06-08T08:47:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8298)
[2026-06-08T08:47:47] Searching for fusions with spliced split reads (remaining=8323)
[2026-06-08T08:47:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=4636)
[2026-06-08T08:47:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4576)
[2026-06-08T08:47:52] Searching for fusions with >=4 spliced events (remaining=5498)
[2026-06-08T08:47:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2102)
[2026-06-08T08:48:07] Filtering fusions with anchors <=23nt (remaining=1671)
[2026-06-08T08:48:08] Filtering end-to-end fusions with low support (remaining=1628)
[2026-06-08T08:48:08] Filtering fusions with no coverage around the breakpoints (remaining=1582)
[2026-06-08T08:48:09] Indexing gene sequences 
[2026-06-08T08:48:15] Filtering genes with >=30% identity (remaining=530)
[2026-06-08T08:48:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=310)
[2026-06-08T08:48:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=249)
[2026-06-08T08:48:29] Searching for additional isoforms (remaining=381)
[2026-06-08T08:48:30] Assigning confidence scores to events 
[2026-06-08T08:48:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:32] Writing fusions to file 'aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:36] Writing discarded fusions to file 'aih-tih-sc-3e4d53-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:55] Freeing resources
[2026-06-08T08:49:08] Done (elapsed time=00:08:55, CPU time=00:08:54, peak memory=12.8gb)