[2026-06-08T08:48:23] Launching Arriba 2.4.0
[2026-06-08T08:48:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:37] Reading chimeric alignments from 'aih-tih-sc-d64bdd-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9371177)
[2026-06-08T08:54:43] Marking multi-mapping alignments (marked=6149125)
[2026-06-08T08:54:46] Detecting strandedness (reverse)
[2026-06-08T08:54:46] Assigning strands to alignments 
[2026-06-08T08:54:48] Annotating alignments 
[2026-06-08T08:55:19] Filtering duplicates (remaining=5379937)
[2026-06-08T08:55:25] 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=5017032)
[2026-06-08T08:55:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5017032)
[2026-06-08T08:55:29] Filtering viral contigs with expression lower than the top 5 (remaining=5017032)
[2026-06-08T08:55:33] Filtering viral contigs with less than 5% coverage (remaining=5017032)
[2026-06-08T08:55:35] Estimating fragment length (mate gap mean=-85.2861, mate gap stddev=30.949, read length mean=134.976)
[2026-06-08T08:55:35] Filtering read-through fragments with a distance <=10000bp (remaining=4759515)
[2026-06-08T08:55:37] Filtering inconsistently clipped mates (remaining=4683657)
[2026-06-08T08:55:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4560859)
[2026-06-08T08:55:43] Filtering fragments with small insert size (remaining=4560310)
[2026-06-08T08:55:45] Filtering alignments with long gaps (remaining=4560310)
[2026-06-08T08:55:47] Filtering fragments with both mates in the same gene (remaining=4559397)
[2026-06-08T08:55:49] Filtering fusions arising from hairpin structures (remaining=4281703)
[2026-06-08T08:55:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2084045)
[2026-06-08T08:56:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=682981)
[2026-06-08T08:56:14] Finding fusions and counting supporting reads (total=546014)
[2026-06-08T08:56:30] Merging adjacent fusion breakpoints (remaining=540578)
[2026-06-08T08:56:32] Filtering multi-mapping fusions by alignment score and read support (remaining=344230)
[2026-06-08T08:57:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=340843)
[2026-06-08T08:57:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=185361)
[2026-06-08T08:57:13] Filtering fusions with <2 supporting reads (remaining=24827)
[2026-06-08T08:57:13] Filtering fusions with an e-value >=0.3 (remaining=9558)
[2026-06-08T08:57:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9606)
[2026-06-08T08:57:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9474)
[2026-06-08T08:57:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9474)
[2026-06-08T08:57:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5580)
[2026-06-08T08:57:23] Searching for fusions with spliced split reads (remaining=5688)
[2026-06-08T08:57:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=3433)
[2026-06-08T08:57:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3389)
[2026-06-08T08:57:30] Searching for fusions with >=4 spliced events (remaining=3882)
[2026-06-08T08:57:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1409)
[2026-06-08T08:57:45] Filtering fusions with anchors <=23nt (remaining=1066)
[2026-06-08T08:57:46] Filtering end-to-end fusions with low support (remaining=1013)
[2026-06-08T08:57:47] Filtering fusions with no coverage around the breakpoints (remaining=969)
[2026-06-08T08:57:47] Indexing gene sequences 
[2026-06-08T08:57:52] Filtering genes with >=30% identity (remaining=302)
[2026-06-08T08:57:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=147)
[2026-06-08T08:57:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=129)
[2026-06-08T08:57:58] Searching for additional isoforms (remaining=181)
[2026-06-08T08:58:00] Assigning confidence scores to events 
[2026-06-08T08:58:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:03] Writing fusions to file 'aih-tih-sc-d64bdd-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:04] Writing discarded fusions to file 'aih-tih-sc-d64bdd-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:31] Freeing resources
[2026-06-08T08:58:46] Done (elapsed time=00:10:23, CPU time=00:10:22, peak memory=13.9gb)