[2026-06-08T08:49:21] Launching Arriba 2.4.0
[2026-06-08T08:49:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:33] Reading chimeric alignments from 'aih-tih-sc-da460d-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9999452)
[2026-06-08T08:56:29] Marking multi-mapping alignments (marked=5991630)
[2026-06-08T08:56:33] Detecting strandedness (no)
[2026-06-08T08:56:33] Annotating alignments 
[2026-06-08T08:57:14] Filtering duplicates (remaining=5775072)
[2026-06-08T08:57:20] 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=5557510)
[2026-06-08T08:57:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5557510)
[2026-06-08T08:57:24] Filtering viral contigs with expression lower than the top 5 (remaining=5557510)
[2026-06-08T08:57:29] Filtering viral contigs with less than 5% coverage (remaining=5557510)
[2026-06-08T08:57:31] Estimating fragment length (mate gap mean=-86.2009, mate gap stddev=28.1127, read length mean=130.507)
[2026-06-08T08:57:31] Filtering read-through fragments with a distance <=10000bp (remaining=5159381)
[2026-06-08T08:57:33] Filtering inconsistently clipped mates (remaining=5060115)
[2026-06-08T08:57:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4945384)
[2026-06-08T08:57:40] Filtering fragments with small insert size (remaining=4944042)
[2026-06-08T08:57:42] Filtering alignments with long gaps (remaining=4944042)
[2026-06-08T08:57:44] Filtering fragments with both mates in the same gene (remaining=4943057)
[2026-06-08T08:57:46] Filtering fusions arising from hairpin structures (remaining=4640737)
[2026-06-08T08:57:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2187260)
[2026-06-08T08:58:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=972212)
[2026-06-08T08:58:12] Finding fusions and counting supporting reads (total=752019)
[2026-06-08T08:58:28] Merging adjacent fusion breakpoints (remaining=742812)
[2026-06-08T08:58:29] Filtering multi-mapping fusions by alignment score and read support (remaining=485689)
[2026-06-08T08:59:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=483991)
[2026-06-08T08:59:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=247845)
[2026-06-08T08:59:12] Filtering fusions with <2 supporting reads (remaining=34688)
[2026-06-08T08:59:12] Filtering fusions with an e-value >=0.3 (remaining=9284)
[2026-06-08T08:59:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9346)
[2026-06-08T08:59:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9260)
[2026-06-08T08:59:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9260)
[2026-06-08T08:59:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6284)
[2026-06-08T08:59:24] Searching for fusions with spliced split reads (remaining=6394)
[2026-06-08T08:59:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=4178)
[2026-06-08T08:59:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4134)
[2026-06-08T08:59:30] Searching for fusions with >=4 spliced events (remaining=4930)
[2026-06-08T08:59:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1811)
[2026-06-08T08:59:47] Filtering fusions with anchors <=23nt (remaining=1496)
[2026-06-08T08:59:47] Filtering end-to-end fusions with low support (remaining=1460)
[2026-06-08T08:59:48] Filtering fusions with no coverage around the breakpoints (remaining=1424)
[2026-06-08T08:59:49] Indexing gene sequences 
[2026-06-08T08:59:53] Filtering genes with >=30% identity (remaining=417)
[2026-06-08T08:59:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=126)
[2026-06-08T08:59:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=126)
[2026-06-08T08:59:59] Searching for additional isoforms (remaining=150)
[2026-06-08T09:00:00] Assigning confidence scores to events 
[2026-06-08T09:00:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:03] Writing fusions to file 'aih-tih-sc-da460d-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:05] Writing discarded fusions to file 'aih-tih-sc-da460d-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:32] Freeing resources
[2026-06-08T09:00:50] Done (elapsed time=00:11:29, CPU time=00:11:28, peak memory=14.6gb)