[2026-06-08T08:48:07] Launching Arriba 2.4.0
[2026-06-08T08:48:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:24] Reading chimeric alignments from 'aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12097141)
[2026-06-08T08:56:06] Marking multi-mapping alignments (marked=7725703)
[2026-06-08T08:56:12] Detecting strandedness (reverse)
[2026-06-08T08:56:12] Assigning strands to alignments 
[2026-06-08T08:56:14] Annotating alignments 
[2026-06-08T08:56:53] Filtering duplicates (remaining=6762331)
[2026-06-08T08:57:02] 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=6439983)
[2026-06-08T08:57:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6439983)
[2026-06-08T08:57:07] Filtering viral contigs with expression lower than the top 5 (remaining=6439983)
[2026-06-08T08:57:13] Filtering viral contigs with less than 5% coverage (remaining=6439983)
[2026-06-08T08:57:16] Estimating fragment length (mate gap mean=-85.0785, mate gap stddev=27.9038, read length mean=129.305)
[2026-06-08T08:57:16] Filtering read-through fragments with a distance <=10000bp (remaining=6101955)
[2026-06-08T08:57:19] Filtering inconsistently clipped mates (remaining=6006024)
[2026-06-08T08:57:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5859912)
[2026-06-08T08:57:26] Filtering fragments with small insert size (remaining=5858936)
[2026-06-08T08:57:29] Filtering alignments with long gaps (remaining=5858936)
[2026-06-08T08:57:31] Filtering fragments with both mates in the same gene (remaining=5857791)
[2026-06-08T08:57:34] Filtering fusions arising from hairpin structures (remaining=5588288)
[2026-06-08T08:57:37] Filtering reads with a mismatch p-value <=0.01 (remaining=2605272)
[2026-06-08T08:57:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=927825)
[2026-06-08T08:58:02] Finding fusions and counting supporting reads (total=663965)
[2026-06-08T08:58:21] Merging adjacent fusion breakpoints (remaining=656309)
[2026-06-08T08:58:24] Filtering multi-mapping fusions by alignment score and read support (remaining=405606)
[2026-06-08T08:59:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=403878)
[2026-06-08T08:59:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=232821)
[2026-06-08T08:59:13] Filtering fusions with <2 supporting reads (remaining=34160)
[2026-06-08T08:59:14] Filtering fusions with an e-value >=0.3 (remaining=10157)
[2026-06-08T08:59:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10219)
[2026-06-08T08:59:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10150)
[2026-06-08T08:59:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10150)
[2026-06-08T08:59:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6571)
[2026-06-08T08:59:27] Searching for fusions with spliced split reads (remaining=6699)
[2026-06-08T08:59:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=4374)
[2026-06-08T08:59:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4321)
[2026-06-08T08:59:35] Searching for fusions with >=4 spliced events (remaining=5095)
[2026-06-08T08:59:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1839)
[2026-06-08T08:59:53] Filtering fusions with anchors <=23nt (remaining=1545)
[2026-06-08T08:59:54] Filtering end-to-end fusions with low support (remaining=1505)
[2026-06-08T08:59:55] Filtering fusions with no coverage around the breakpoints (remaining=1474)
[2026-06-08T08:59:55] Indexing gene sequences 
[2026-06-08T09:00:01] Filtering genes with >=30% identity (remaining=493)
[2026-06-08T09:00:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=234)
[2026-06-08T09:00:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=198)
[2026-06-08T09:00:09] Searching for additional isoforms (remaining=237)
[2026-06-08T09:00:10] Assigning confidence scores to events 
[2026-06-08T09:00:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:14] Writing fusions to file 'aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:15] Writing discarded fusions to file 'aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:46] Freeing resources
[2026-06-08T09:01:07] Done (elapsed time=00:13:00, CPU time=00:12:58, peak memory=16.4gb)