[2026-06-08T08:48:35] Launching Arriba 2.4.0
[2026-06-08T08:48:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:49] Reading chimeric alignments from 'aih-tih-sc-3270ab-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10359824)
[2026-06-08T08:55:41] Marking multi-mapping alignments (marked=6748513)
[2026-06-08T08:55:46] Detecting strandedness (reverse)
[2026-06-08T08:55:46] Assigning strands to alignments 
[2026-06-08T08:55:48] Annotating alignments 
[2026-06-08T08:56:23] Filtering duplicates (remaining=7088188)
[2026-06-08T08:56:30] 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=6698130)
[2026-06-08T08:56:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6698130)
[2026-06-08T08:56:35] Filtering viral contigs with expression lower than the top 5 (remaining=6698130)
[2026-06-08T08:56:39] Filtering viral contigs with less than 5% coverage (remaining=6698130)
[2026-06-08T08:56:42] Estimating fragment length (mate gap mean=-83.6586, mate gap stddev=30.032, read length mean=130.075)
[2026-06-08T08:56:42] Filtering read-through fragments with a distance <=10000bp (remaining=6331572)
[2026-06-08T08:56:44] Filtering inconsistently clipped mates (remaining=6206815)
[2026-06-08T08:56:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6056900)
[2026-06-08T08:56:51] Filtering fragments with small insert size (remaining=6055671)
[2026-06-08T08:56:53] Filtering alignments with long gaps (remaining=6055671)
[2026-06-08T08:56:56] Filtering fragments with both mates in the same gene (remaining=6054561)
[2026-06-08T08:56:58] Filtering fusions arising from hairpin structures (remaining=5641023)
[2026-06-08T08:57:01] Filtering reads with a mismatch p-value <=0.01 (remaining=2485454)
[2026-06-08T08:57:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=1052722)
[2026-06-08T08:57:27] Finding fusions and counting supporting reads (total=842797)
[2026-06-08T08:57:45] Merging adjacent fusion breakpoints (remaining=835688)
[2026-06-08T08:57:47] Filtering multi-mapping fusions by alignment score and read support (remaining=546441)
[2026-06-08T08:58:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=544133)
[2026-06-08T08:58:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=318727)
[2026-06-08T08:58:31] Filtering fusions with <2 supporting reads (remaining=33090)
[2026-06-08T08:58:32] Filtering fusions with an e-value >=0.3 (remaining=9456)
[2026-06-08T08:58:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9519)
[2026-06-08T08:58:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9432)
[2026-06-08T08:58:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9434)
[2026-06-08T08:58:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6903)
[2026-06-08T08:58:45] Searching for fusions with spliced split reads (remaining=7020)
[2026-06-08T08:58:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=4221)
[2026-06-08T08:58:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4177)
[2026-06-08T08:58:52] Searching for fusions with >=4 spliced events (remaining=5058)
[2026-06-08T08:58:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1967)
[2026-06-08T08:59:10] Filtering fusions with anchors <=23nt (remaining=1501)
[2026-06-08T08:59:11] Filtering end-to-end fusions with low support (remaining=1470)
[2026-06-08T08:59:11] Filtering fusions with no coverage around the breakpoints (remaining=1441)
[2026-06-08T08:59:12] Indexing gene sequences 
[2026-06-08T08:59:18] Filtering genes with >=30% identity (remaining=465)
[2026-06-08T08:59:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=236)
[2026-06-08T08:59:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=195)
[2026-06-08T08:59:30] Searching for additional isoforms (remaining=244)
[2026-06-08T08:59:32] Assigning confidence scores to events 
[2026-06-08T08:59:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:36] Writing fusions to file 'aih-tih-sc-3270ab-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:38] Writing discarded fusions to file 'aih-tih-sc-3270ab-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:12] Freeing resources
[2026-06-08T09:00:29] Done (elapsed time=00:11:54, CPU time=00:11:53, peak memory=15gb)