[2026-06-08T08:39:06] Launching Arriba 2.4.0
[2026-06-08T08:39:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:19] Reading chimeric alignments from 'aih-tih-sc-b845f7-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11707277)
[2026-06-08T08:45:50] Marking multi-mapping alignments (marked=7716862)
[2026-06-08T08:45:55] Detecting strandedness (reverse)
[2026-06-08T08:45:55] Assigning strands to alignments 
[2026-06-08T08:45:57] Annotating alignments 
[2026-06-08T08:46:34] Filtering duplicates (remaining=6708114)
[2026-06-08T08:46:42] 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=6359598)
[2026-06-08T08:46:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6359598)
[2026-06-08T08:46:46] Filtering viral contigs with expression lower than the top 5 (remaining=6359598)
[2026-06-08T08:46:52] Filtering viral contigs with less than 5% coverage (remaining=6359598)
[2026-06-08T08:46:55] Estimating fragment length (mate gap mean=-87.8683, mate gap stddev=28.2453, read length mean=132.858)
[2026-06-08T08:46:55] Filtering read-through fragments with a distance <=10000bp (remaining=6026793)
[2026-06-08T08:46:57] Filtering inconsistently clipped mates (remaining=5925978)
[2026-06-08T08:46:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5750535)
[2026-06-08T08:47:04] Filtering fragments with small insert size (remaining=5749889)
[2026-06-08T08:47:06] Filtering alignments with long gaps (remaining=5749889)
[2026-06-08T08:47:09] Filtering fragments with both mates in the same gene (remaining=5748897)
[2026-06-08T08:47:11] Filtering fusions arising from hairpin structures (remaining=5462367)
[2026-06-08T08:47:14] Filtering reads with a mismatch p-value <=0.01 (remaining=2628040)
[2026-06-08T08:47:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=875360)
[2026-06-08T08:47:39] Finding fusions and counting supporting reads (total=658949)
[2026-06-08T08:47:57] Merging adjacent fusion breakpoints (remaining=652884)
[2026-06-08T08:47:59] Filtering multi-mapping fusions by alignment score and read support (remaining=381556)
[2026-06-08T08:48:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=379289)
[2026-06-08T08:48:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=219615)
[2026-06-08T08:48:45] Filtering fusions with <2 supporting reads (remaining=25247)
[2026-06-08T08:48:46] Filtering fusions with an e-value >=0.3 (remaining=7182)
[2026-06-08T08:48:47] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7252)
[2026-06-08T08:48:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7137)
[2026-06-08T08:48:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7137)
[2026-06-08T08:48:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6420)
[2026-06-08T08:48:58] Searching for fusions with spliced split reads (remaining=6535)
[2026-06-08T08:49:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=4117)
[2026-06-08T08:49:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4054)
[2026-06-08T08:49:06] Searching for fusions with >=4 spliced events (remaining=4621)
[2026-06-08T08:49:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1833)
[2026-06-08T08:49:25] Filtering fusions with anchors <=23nt (remaining=1476)
[2026-06-08T08:49:26] Filtering end-to-end fusions with low support (remaining=1413)
[2026-06-08T08:49:27] Filtering fusions with no coverage around the breakpoints (remaining=1372)
[2026-06-08T08:49:27] Indexing gene sequences 
[2026-06-08T08:49:33] Filtering genes with >=30% identity (remaining=494)
[2026-06-08T08:49:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=245)
[2026-06-08T08:49:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=220)
[2026-06-08T08:49:43] Searching for additional isoforms (remaining=273)
[2026-06-08T08:49:45] Assigning confidence scores to events 
[2026-06-08T08:49:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:48] Writing fusions to file 'aih-tih-sc-b845f7-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:50] Writing discarded fusions to file 'aih-tih-sc-b845f7-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:19] Freeing resources
[2026-06-08T08:50:36] Done (elapsed time=00:11:30, CPU time=00:11:28, peak memory=16.1gb)