[2026-06-08T08:40:11] Launching Arriba 2.4.0
[2026-06-08T08:40:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:24] Reading chimeric alignments from 'aih-tih-sc-9f6030-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11243687)
[2026-06-08T08:46:08] Marking multi-mapping alignments (marked=7960364)
[2026-06-08T08:46:12] Detecting strandedness (no)
[2026-06-08T08:46:12] Annotating alignments 
[2026-06-08T08:46:59] Filtering duplicates (remaining=3053592)
[2026-06-08T08:47:04] 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=2661627)
[2026-06-08T08:47:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2661627)
[2026-06-08T08:47:08] Filtering viral contigs with expression lower than the top 5 (remaining=2661627)
[2026-06-08T08:47:13] Filtering viral contigs with less than 5% coverage (remaining=2661627)
[2026-06-08T08:47:15] Estimating fragment length (mate gap mean=-85.6721, mate gap stddev=28.268, read length mean=121.404)
[2026-06-08T08:47:15] Filtering read-through fragments with a distance <=10000bp (remaining=2571787)
[2026-06-08T08:47:17] Filtering inconsistently clipped mates (remaining=2511991)
[2026-06-08T08:47:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2418541)
[2026-06-08T08:47:22] Filtering fragments with small insert size (remaining=2417734)
[2026-06-08T08:47:25] Filtering alignments with long gaps (remaining=2417729)
[2026-06-08T08:47:27] Filtering fragments with both mates in the same gene (remaining=2416996)
[2026-06-08T08:47:29] Filtering fusions arising from hairpin structures (remaining=2280562)
[2026-06-08T08:47:31] Filtering reads with a mismatch p-value <=0.01 (remaining=883105)
[2026-06-08T08:47:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=257604)
[2026-06-08T08:47:45] Finding fusions and counting supporting reads (total=216665)
[2026-06-08T08:47:58] Merging adjacent fusion breakpoints (remaining=214587)
[2026-06-08T08:47:59] Filtering multi-mapping fusions by alignment score and read support (remaining=117293)
[2026-06-08T08:48:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=116269)
[2026-06-08T08:48:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=71124)
[2026-06-08T08:48:36] Filtering fusions with <2 supporting reads (remaining=6418)
[2026-06-08T08:48:37] Filtering fusions with an e-value >=0.3 (remaining=1617)
[2026-06-08T08:48:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1642)
[2026-06-08T08:48:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1581)
[2026-06-08T08:48:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1581)
[2026-06-08T08:48:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1526)
[2026-06-08T08:48:45] Searching for fusions with spliced split reads (remaining=1661)
[2026-06-08T08:48:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=1246)
[2026-06-08T08:48:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1214)
[2026-06-08T08:48:50] Searching for fusions with >=4 spliced events (remaining=1348)
[2026-06-08T08:48:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=432)
[2026-06-08T08:49:03] Filtering fusions with anchors <=23nt (remaining=359)
[2026-06-08T08:49:03] Filtering end-to-end fusions with low support (remaining=348)
[2026-06-08T08:49:04] Filtering fusions with no coverage around the breakpoints (remaining=336)
[2026-06-08T08:49:04] Indexing gene sequences 
[2026-06-08T08:49:06] Filtering genes with >=30% identity (remaining=98)
[2026-06-08T08:49:07] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=45)
[2026-06-08T08:49:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=42)
[2026-06-08T08:49:08] Searching for additional isoforms (remaining=50)
[2026-06-08T08:49:09] Assigning confidence scores to events 
[2026-06-08T08:49:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:11] Writing fusions to file 'aih-tih-sc-9f6030-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:11] Writing discarded fusions to file 'aih-tih-sc-9f6030-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:25] Freeing resources
[2026-06-08T08:49:41] Done (elapsed time=00:09:30, CPU time=00:09:29, peak memory=15.6gb)