[2026-06-08T08:30:21] Launching Arriba 2.4.0
[2026-06-08T08:30:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:33] Reading chimeric alignments from 'aih-tih-sc-49909d-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=13829312)
[2026-06-08T08:37:09] Marking multi-mapping alignments (marked=10228206)
[2026-06-08T08:37:14] Detecting strandedness (reverse)
[2026-06-08T08:37:14] Assigning strands to alignments 
[2026-06-08T08:37:17] Annotating alignments 
[2026-06-08T08:38:05] Filtering duplicates (remaining=7239487)
[2026-06-08T08:38:14] 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=6198421)
[2026-06-08T08:38:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6198421)
[2026-06-08T08:38:20] Filtering viral contigs with expression lower than the top 5 (remaining=6198421)
[2026-06-08T08:38:26] Filtering viral contigs with less than 5% coverage (remaining=6198421)
[2026-06-08T08:38:30] Estimating fragment length (mate gap mean=-83.2977, mate gap stddev=28.9351, read length mean=118.331)
[2026-06-08T08:38:30] Filtering read-through fragments with a distance <=10000bp (remaining=5945252)
[2026-06-08T08:38:33] Filtering inconsistently clipped mates (remaining=5800028)
[2026-06-08T08:38:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5624807)
[2026-06-08T08:38:41] Filtering fragments with small insert size (remaining=5623208)
[2026-06-08T08:38:44] Filtering alignments with long gaps (remaining=5623207)
[2026-06-08T08:38:47] Filtering fragments with both mates in the same gene (remaining=5622105)
[2026-06-08T08:38:50] Filtering fusions arising from hairpin structures (remaining=5226163)
[2026-06-08T08:38:54] Filtering reads with a mismatch p-value <=0.01 (remaining=1896867)
[2026-06-08T08:39:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=937338)
[2026-06-08T08:39:19] Finding fusions and counting supporting reads (total=722490)
[2026-06-08T08:39:41] Merging adjacent fusion breakpoints (remaining=713729)
[2026-06-08T08:39:43] Filtering multi-mapping fusions by alignment score and read support (remaining=415848)
[2026-06-08T08:40:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=414122)
[2026-06-08T08:40:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=262759)
[2026-06-08T08:40:38] Filtering fusions with <2 supporting reads (remaining=24450)
[2026-06-08T08:40:38] Filtering fusions with an e-value >=0.3 (remaining=5445)
[2026-06-08T08:40:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5501)
[2026-06-08T08:40:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5402)
[2026-06-08T08:40:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5402)
[2026-06-08T08:40:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5249)
[2026-06-08T08:40:53] Searching for fusions with spliced split reads (remaining=5325)
[2026-06-08T08:41:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=3728)
[2026-06-08T08:41:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3664)
[2026-06-08T08:41:02] Searching for fusions with >=4 spliced events (remaining=4158)
[2026-06-08T08:41:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1607)
[2026-06-08T08:41:19] Filtering fusions with anchors <=23nt (remaining=1154)
[2026-06-08T08:41:20] Filtering end-to-end fusions with low support (remaining=1090)
[2026-06-08T08:41:21] Filtering fusions with no coverage around the breakpoints (remaining=1066)
[2026-06-08T08:41:22] Indexing gene sequences 
[2026-06-08T08:41:27] Filtering genes with >=30% identity (remaining=323)
[2026-06-08T08:41:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=150)
[2026-06-08T08:41:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T08:41:33] Searching for additional isoforms (remaining=173)
[2026-06-08T08:41:35] Assigning confidence scores to events 
[2026-06-08T08:41:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:39] Writing fusions to file 'aih-tih-sc-49909d-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:40] Writing discarded fusions to file 'aih-tih-sc-49909d-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:16] Freeing resources
[2026-06-08T08:42:37] Done (elapsed time=00:12:16, CPU time=00:12:15, peak memory=18.9gb)