[2026-06-08T08:51:51] Launching Arriba 2.4.0
[2026-06-08T08:51:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:05] Reading chimeric alignments from 'aih-tih-sc-d963a2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11750201)
[2026-06-08T08:59:48] Marking multi-mapping alignments (marked=8131391)
[2026-06-08T08:59:54] Detecting strandedness (reverse)
[2026-06-08T08:59:54] Assigning strands to alignments 
[2026-06-08T08:59:57] Annotating alignments 
[2026-06-08T09:00:39] Filtering duplicates (remaining=7365464)
[2026-06-08T09:00:51] 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=6813519)
[2026-06-08T09:00:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6813519)
[2026-06-08T09:01:01] Filtering viral contigs with expression lower than the top 5 (remaining=6813519)
[2026-06-08T09:01:08] Filtering viral contigs with less than 5% coverage (remaining=6813519)
[2026-06-08T09:01:11] Estimating fragment length (mate gap mean=-83.9906, mate gap stddev=30.3525, read length mean=130.155)
[2026-06-08T09:01:11] Filtering read-through fragments with a distance <=10000bp (remaining=6395122)
[2026-06-08T09:01:14] Filtering inconsistently clipped mates (remaining=6268831)
[2026-06-08T09:01:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6081445)
[2026-06-08T09:01:24] Filtering fragments with small insert size (remaining=6080298)
[2026-06-08T09:01:27] Filtering alignments with long gaps (remaining=6080298)
[2026-06-08T09:01:29] Filtering fragments with both mates in the same gene (remaining=6079135)
[2026-06-08T09:01:32] Filtering fusions arising from hairpin structures (remaining=5661648)
[2026-06-08T09:01:36] Filtering reads with a mismatch p-value <=0.01 (remaining=2566186)
[2026-06-08T09:01:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=1105305)
[2026-06-08T09:02:05] Finding fusions and counting supporting reads (total=876004)
[2026-06-08T09:02:39] Merging adjacent fusion breakpoints (remaining=867790)
[2026-06-08T09:02:42] Filtering multi-mapping fusions by alignment score and read support (remaining=518824)
[2026-06-08T09:03:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=514659)
[2026-06-08T09:03:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=308190)
[2026-06-08T09:03:43] Filtering fusions with <2 supporting reads (remaining=33864)
[2026-06-08T09:03:44] Filtering fusions with an e-value >=0.3 (remaining=12805)
[2026-06-08T09:03:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12883)
[2026-06-08T09:03:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12758)
[2026-06-08T09:03:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12758)
[2026-06-08T09:03:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6731)
[2026-06-08T09:04:06] Searching for fusions with spliced split reads (remaining=6870)
[2026-06-08T09:04:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=4018)
[2026-06-08T09:04:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3971)
[2026-06-08T09:04:18] Searching for fusions with >=4 spliced events (remaining=4732)
[2026-06-08T09:04:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1976)
[2026-06-08T09:04:37] Filtering fusions with anchors <=23nt (remaining=1494)
[2026-06-08T09:04:38] Filtering end-to-end fusions with low support (remaining=1439)
[2026-06-08T09:04:39] Filtering fusions with no coverage around the breakpoints (remaining=1402)
[2026-06-08T09:04:40] Indexing gene sequences 
[2026-06-08T09:04:47] Filtering genes with >=30% identity (remaining=397)
[2026-06-08T09:04:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=173)
[2026-06-08T09:04:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=149)
[2026-06-08T09:04:54] Searching for additional isoforms (remaining=198)
[2026-06-08T09:04:56] Assigning confidence scores to events 
[2026-06-08T09:05:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:00] Writing fusions to file 'aih-tih-sc-d963a2-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:02] Writing discarded fusions to file 'aih-tih-sc-d963a2-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:37] Freeing resources
[2026-06-08T09:05:59] Done (elapsed time=00:14:08, CPU time=00:14:06, peak memory=16.5gb)