[2026-06-08T08:47:24] Launching Arriba 2.4.0
[2026-06-08T08:47:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:41] Reading chimeric alignments from 'aih-tih-sc-bec563-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9639675)
[2026-06-08T08:54:40] Marking multi-mapping alignments (marked=5893937)
[2026-06-08T08:54:44] Detecting strandedness (reverse)
[2026-06-08T08:54:44] Assigning strands to alignments 
[2026-06-08T08:54:46] Annotating alignments 
[2026-06-08T08:55:14] Filtering duplicates (remaining=6063283)
[2026-06-08T08:55:21] 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=5813470)
[2026-06-08T08:55:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5813470)
[2026-06-08T08:55:24] Filtering viral contigs with expression lower than the top 5 (remaining=5813470)
[2026-06-08T08:55:28] Filtering viral contigs with less than 5% coverage (remaining=5813470)
[2026-06-08T08:55:30] Estimating fragment length (mate gap mean=-87.0064, mate gap stddev=30.1078, read length mean=136.005)
[2026-06-08T08:55:30] Filtering read-through fragments with a distance <=10000bp (remaining=5401555)
[2026-06-08T08:55:32] Filtering inconsistently clipped mates (remaining=5310101)
[2026-06-08T08:55:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5176145)
[2026-06-08T08:55:38] Filtering fragments with small insert size (remaining=5175548)
[2026-06-08T08:55:40] Filtering alignments with long gaps (remaining=5175548)
[2026-06-08T08:55:42] Filtering fragments with both mates in the same gene (remaining=5174553)
[2026-06-08T08:55:43] Filtering fusions arising from hairpin structures (remaining=4851152)
[2026-06-08T08:55:46] Filtering reads with a mismatch p-value <=0.01 (remaining=2393599)
[2026-06-08T08:55:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=1048238)
[2026-06-08T08:56:09] Finding fusions and counting supporting reads (total=773103)
[2026-06-08T08:56:24] Merging adjacent fusion breakpoints (remaining=765649)
[2026-06-08T08:56:25] Filtering multi-mapping fusions by alignment score and read support (remaining=501896)
[2026-06-08T08:56:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=498611)
[2026-06-08T08:56:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=259817)
[2026-06-08T08:56:59] Filtering fusions with <2 supporting reads (remaining=40843)
[2026-06-08T08:57:00] Filtering fusions with an e-value >=0.3 (remaining=13629)
[2026-06-08T08:57:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13689)
[2026-06-08T08:57:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13568)
[2026-06-08T08:57:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13568)
[2026-06-08T08:57:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8570)
[2026-06-08T08:57:10] Searching for fusions with spliced split reads (remaining=8590)
[2026-06-08T08:57:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=5136)
[2026-06-08T08:57:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5068)
[2026-06-08T08:57:16] Searching for fusions with >=4 spliced events (remaining=6303)
[2026-06-08T08:57:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2504)
[2026-06-08T08:57:32] Filtering fusions with anchors <=23nt (remaining=2053)
[2026-06-08T08:57:33] Filtering end-to-end fusions with low support (remaining=1989)
[2026-06-08T08:57:33] Filtering fusions with no coverage around the breakpoints (remaining=1958)
[2026-06-08T08:57:34] Indexing gene sequences 
[2026-06-08T08:57:41] Filtering genes with >=30% identity (remaining=745)
[2026-06-08T08:57:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=480)
[2026-06-08T08:57:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=312)
[2026-06-08T08:57:56] Searching for additional isoforms (remaining=425)
[2026-06-08T08:57:58] Assigning confidence scores to events 
[2026-06-08T08:58:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:01] Writing fusions to file 'aih-tih-sc-bec563-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:04] Writing discarded fusions to file 'aih-tih-sc-bec563-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:30] Freeing resources
[2026-06-08T08:58:45] Done (elapsed time=00:11:21, CPU time=00:11:19, peak memory=14.4gb)