[2026-06-08T08:08:09] Launching Arriba 2.4.0
[2026-06-08T08:08:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:08:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:08:28] Reading chimeric alignments from 'aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9843702)
[2026-06-08T08:13:41] Marking multi-mapping alignments (marked=6746183)
[2026-06-08T08:13:46] Detecting strandedness (reverse)
[2026-06-08T08:13:46] Assigning strands to alignments 
[2026-06-08T08:13:47] Annotating alignments 
[2026-06-08T08:14:19] Filtering duplicates (remaining=4788265)
[2026-06-08T08:14:25] 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=4456058)
[2026-06-08T08:14:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4456058)
[2026-06-08T08:14:29] Filtering viral contigs with expression lower than the top 5 (remaining=4456058)
[2026-06-08T08:14:33] Filtering viral contigs with less than 5% coverage (remaining=4456058)
[2026-06-08T08:14:35] Estimating fragment length (mate gap mean=-79.7379, mate gap stddev=27.3582, read length mean=113.707)
[2026-06-08T08:14:35] Filtering read-through fragments with a distance <=10000bp (remaining=4138589)
[2026-06-08T08:14:37] Filtering inconsistently clipped mates (remaining=4040237)
[2026-06-08T08:14:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3893720)
[2026-06-08T08:14:43] Filtering fragments with small insert size (remaining=3892188)
[2026-06-08T08:14:46] Filtering alignments with long gaps (remaining=3892187)
[2026-06-08T08:14:48] Filtering fragments with both mates in the same gene (remaining=3891148)
[2026-06-08T08:14:50] Filtering fusions arising from hairpin structures (remaining=3675125)
[2026-06-08T08:14:52] Filtering reads with a mismatch p-value <=0.01 (remaining=1267465)
[2026-06-08T08:15:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=648712)
[2026-06-08T08:15:12] Finding fusions and counting supporting reads (total=576658)
[2026-06-08T08:15:28] Merging adjacent fusion breakpoints (remaining=569429)
[2026-06-08T08:15:30] Filtering multi-mapping fusions by alignment score and read support (remaining=316599)
[2026-06-08T08:16:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:16:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=315564)
[2026-06-08T08:16:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=186657)
[2026-06-08T08:16:08] Filtering fusions with <2 supporting reads (remaining=17848)
[2026-06-08T08:16:09] Filtering fusions with an e-value >=0.3 (remaining=4235)
[2026-06-08T08:16:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4283)
[2026-06-08T08:16:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4206)
[2026-06-08T08:16:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4206)
[2026-06-08T08:16:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4198)
[2026-06-08T08:16:19] Searching for fusions with spliced split reads (remaining=4237)
[2026-06-08T08:16:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=3089)
[2026-06-08T08:16:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3058)
[2026-06-08T08:16:25] Searching for fusions with >=4 spliced events (remaining=3431)
[2026-06-08T08:16:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1500)
[2026-06-08T08:16:48] Filtering fusions with anchors <=23nt (remaining=1084)
[2026-06-08T08:16:48] Filtering end-to-end fusions with low support (remaining=1049)
[2026-06-08T08:16:49] Filtering fusions with no coverage around the breakpoints (remaining=1022)
[2026-06-08T08:16:49] Indexing gene sequences 
[2026-06-08T08:16:55] Filtering genes with >=30% identity (remaining=374)
[2026-06-08T08:16:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=176)
[2026-06-08T08:16:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-08T08:17:00] Searching for additional isoforms (remaining=203)
[2026-06-08T08:17:01] Assigning confidence scores to events 
[2026-06-08T08:17:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:17:04] Writing fusions to file 'aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:17:05] Writing discarded fusions to file 'aih-tih-sc-bbc28d-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:17:32] Freeing resources
[2026-06-08T08:17:48] Done (elapsed time=00:09:39, CPU time=00:09:37, peak memory=14.5gb)