[2026-06-08T08:40:05] Launching Arriba 2.4.0
[2026-06-08T08:40:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:14] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:17] Reading chimeric alignments from 'aih-tih-sc-82e8c1-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10780606)
[2026-06-08T08:46:38] Marking multi-mapping alignments (marked=6396474)
[2026-06-08T08:46:42] Detecting strandedness (reverse)
[2026-06-08T08:46:42] Assigning strands to alignments 
[2026-06-08T08:46:45] Annotating alignments 
[2026-06-08T08:47:18] Filtering duplicates (remaining=6982238)
[2026-06-08T08:47:25] 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=6750529)
[2026-06-08T08:47:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6750529)
[2026-06-08T08:47:29] Filtering viral contigs with expression lower than the top 5 (remaining=6750529)
[2026-06-08T08:47:34] Filtering viral contigs with less than 5% coverage (remaining=6750529)
[2026-06-08T08:47:36] Estimating fragment length (mate gap mean=-86.1896, mate gap stddev=28.2635, read length mean=132.686)
[2026-06-08T08:47:36] Filtering read-through fragments with a distance <=10000bp (remaining=6425815)
[2026-06-08T08:47:38] Filtering inconsistently clipped mates (remaining=6353998)
[2026-06-08T08:47:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6206334)
[2026-06-08T08:47:45] Filtering fragments with small insert size (remaining=6205677)
[2026-06-08T08:47:47] Filtering alignments with long gaps (remaining=6205677)
[2026-06-08T08:47:49] Filtering fragments with both mates in the same gene (remaining=6204602)
[2026-06-08T08:47:51] Filtering fusions arising from hairpin structures (remaining=6002698)
[2026-06-08T08:47:54] Filtering reads with a mismatch p-value <=0.01 (remaining=3185920)
[2026-06-08T08:48:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=1412904)
[2026-06-08T08:48:21] Finding fusions and counting supporting reads (total=779336)
[2026-06-08T08:48:36] Merging adjacent fusion breakpoints (remaining=774132)
[2026-06-08T08:48:38] Filtering multi-mapping fusions by alignment score and read support (remaining=499938)
[2026-06-08T08:49:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=498131)
[2026-06-08T08:49:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=312488)
[2026-06-08T08:49:19] Filtering fusions with <2 supporting reads (remaining=50099)
[2026-06-08T08:49:20] Filtering fusions with an e-value >=0.3 (remaining=11525)
[2026-06-08T08:49:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11553)
[2026-06-08T08:49:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11477)
[2026-06-08T08:49:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11477)
[2026-06-08T08:49:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10864)
[2026-06-08T08:49:31] Searching for fusions with spliced split reads (remaining=10923)
[2026-06-08T08:49:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=5783)
[2026-06-08T08:49:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5713)
[2026-06-08T08:49:39] Searching for fusions with >=4 spliced events (remaining=7135)
[2026-06-08T08:49:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2497)
[2026-06-08T08:49:56] Filtering fusions with anchors <=23nt (remaining=2107)
[2026-06-08T08:49:57] Filtering end-to-end fusions with low support (remaining=2066)
[2026-06-08T08:49:58] Filtering fusions with no coverage around the breakpoints (remaining=2036)
[2026-06-08T08:49:58] Indexing gene sequences 
[2026-06-08T08:50:05] Filtering genes with >=30% identity (remaining=580)
[2026-06-08T08:50:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=298)
[2026-06-08T08:50:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=265)
[2026-06-08T08:50:17] Searching for additional isoforms (remaining=321)
[2026-06-08T08:50:19] Assigning confidence scores to events 
[2026-06-08T08:50:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:22] Writing fusions to file 'aih-tih-sc-82e8c1-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:25] Writing discarded fusions to file 'aih-tih-sc-82e8c1-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:52] Freeing resources
[2026-06-08T08:51:20] Done (elapsed time=00:11:15, CPU time=00:11:14, peak memory=15.2gb)