[2026-06-08T08:52:23] Launching Arriba 2.4.0
[2026-06-08T08:52:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:35] Reading chimeric alignments from 'aih-tih-sc-3cac57-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=12085525)
[2026-06-08T09:00:18] Marking multi-mapping alignments (marked=7784359)
[2026-06-08T09:00:24] Detecting strandedness (reverse)
[2026-06-08T09:00:24] Assigning strands to alignments 
[2026-06-08T09:00:27] Annotating alignments 
[2026-06-08T09:01:15] Filtering duplicates (remaining=6920828)
[2026-06-08T09:01:25] 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=6488542)
[2026-06-08T09:01:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6488542)
[2026-06-08T09:01:30] Filtering viral contigs with expression lower than the top 5 (remaining=6488542)
[2026-06-08T09:01:37] Filtering viral contigs with less than 5% coverage (remaining=6488542)
[2026-06-08T09:01:40] Estimating fragment length (mate gap mean=-88.3149, mate gap stddev=30.4789, read length mean=134.894)
[2026-06-08T09:01:40] Filtering read-through fragments with a distance <=10000bp (remaining=6074642)
[2026-06-08T09:01:43] Filtering inconsistently clipped mates (remaining=5982347)
[2026-06-08T09:01:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5851002)
[2026-06-08T09:01:52] Filtering fragments with small insert size (remaining=5850268)
[2026-06-08T09:01:54] Filtering alignments with long gaps (remaining=5850268)
[2026-06-08T09:01:57] Filtering fragments with both mates in the same gene (remaining=5849375)
[2026-06-08T09:02:00] Filtering fusions arising from hairpin structures (remaining=5517099)
[2026-06-08T09:02:03] Filtering reads with a mismatch p-value <=0.01 (remaining=2363914)
[2026-06-08T09:02:19] Filtering reads with low entropy (k-mer content >=60%) (remaining=972674)
[2026-06-08T09:02:32] Finding fusions and counting supporting reads (total=767501)
[2026-06-08T09:02:53] Merging adjacent fusion breakpoints (remaining=756769)
[2026-06-08T09:02:55] Filtering multi-mapping fusions by alignment score and read support (remaining=496378)
[2026-06-08T09:03:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=492595)
[2026-06-08T09:03:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=265702)
[2026-06-08T09:03:49] Filtering fusions with <2 supporting reads (remaining=39091)
[2026-06-08T09:03:50] Filtering fusions with an e-value >=0.3 (remaining=14874)
[2026-06-08T09:03:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14919)
[2026-06-08T09:03:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14737)
[2026-06-08T09:03:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14739)
[2026-06-08T09:03:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8669)
[2026-06-08T09:04:04] Searching for fusions with spliced split reads (remaining=8696)
[2026-06-08T09:04:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=4532)
[2026-06-08T09:04:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4458)
[2026-06-08T09:04:13] Searching for fusions with >=4 spliced events (remaining=5140)
[2026-06-08T09:04:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1983)
[2026-06-08T09:04:35] Filtering fusions with anchors <=23nt (remaining=1233)
[2026-06-08T09:04:36] Filtering end-to-end fusions with low support (remaining=1173)
[2026-06-08T09:04:37] Filtering fusions with no coverage around the breakpoints (remaining=1140)
[2026-06-08T09:04:38] Indexing gene sequences 
[2026-06-08T09:04:42] Filtering genes with >=30% identity (remaining=332)
[2026-06-08T09:04:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=187)
[2026-06-08T09:04:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-06-08T09:04:49] Searching for additional isoforms (remaining=228)
[2026-06-08T09:04:51] Assigning confidence scores to events 
[2026-06-08T09:04:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:54] Writing fusions to file 'aih-tih-sc-3cac57-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:56] Writing discarded fusions to file 'aih-tih-sc-3cac57-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:33] Freeing resources
[2026-06-08T09:05:52] Done (elapsed time=00:13:29, CPU time=00:13:28, peak memory=17.1gb)