[2026-06-08T08:51:06] Launching Arriba 2.4.0
[2026-06-08T08:51:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:21] Reading chimeric alignments from 'aih-tih-sc-ac6a71-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10217725)
[2026-06-08T08:58:42] Marking multi-mapping alignments (marked=6246052)
[2026-06-08T08:58:46] Detecting strandedness (reverse)
[2026-06-08T08:58:46] Assigning strands to alignments 
[2026-06-08T08:58:49] Annotating alignments 
[2026-06-08T08:59:25] Filtering duplicates (remaining=6658750)
[2026-06-08T08:59:34] 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=6427207)
[2026-06-08T08:59:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6427207)
[2026-06-08T08:59:38] Filtering viral contigs with expression lower than the top 5 (remaining=6427207)
[2026-06-08T08:59:43] Filtering viral contigs with less than 5% coverage (remaining=6427207)
[2026-06-08T08:59:46] Estimating fragment length (mate gap mean=-86.0414, mate gap stddev=29.5709, read length mean=136.106)
[2026-06-08T08:59:46] Filtering read-through fragments with a distance <=10000bp (remaining=6094496)
[2026-06-08T08:59:48] Filtering inconsistently clipped mates (remaining=6023830)
[2026-06-08T08:59:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5898653)
[2026-06-08T08:59:55] Filtering fragments with small insert size (remaining=5898053)
[2026-06-08T08:59:57] Filtering alignments with long gaps (remaining=5898053)
[2026-06-08T08:59:59] Filtering fragments with both mates in the same gene (remaining=5896837)
[2026-06-08T09:00:02] Filtering fusions arising from hairpin structures (remaining=5663430)
[2026-06-08T09:00:05] Filtering reads with a mismatch p-value <=0.01 (remaining=2875291)
[2026-06-08T09:00:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=998839)
[2026-06-08T09:00:33] Finding fusions and counting supporting reads (total=659928)
[2026-06-08T09:00:50] Merging adjacent fusion breakpoints (remaining=654625)
[2026-06-08T09:00:52] Filtering multi-mapping fusions by alignment score and read support (remaining=437506)
[2026-06-08T09:01:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=435657)
[2026-06-08T09:01:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=253893)
[2026-06-08T09:01:36] Filtering fusions with <2 supporting reads (remaining=38735)
[2026-06-08T09:01:37] Filtering fusions with an e-value >=0.3 (remaining=11705)
[2026-06-08T09:01:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11771)
[2026-06-08T09:01:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11713)
[2026-06-08T09:01:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11713)
[2026-06-08T09:01:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8900)
[2026-06-08T09:01:50] Searching for fusions with spliced split reads (remaining=8927)
[2026-06-08T09:01:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=5164)
[2026-06-08T09:01:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5097)
[2026-06-08T09:01:57] Searching for fusions with >=4 spliced events (remaining=5986)
[2026-06-08T09:01:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1962)
[2026-06-08T09:02:15] Filtering fusions with anchors <=23nt (remaining=1562)
[2026-06-08T09:02:16] Filtering end-to-end fusions with low support (remaining=1520)
[2026-06-08T09:02:16] Filtering fusions with no coverage around the breakpoints (remaining=1482)
[2026-06-08T09:02:17] Indexing gene sequences 
[2026-06-08T09:02:23] Filtering genes with >=30% identity (remaining=424)
[2026-06-08T09:02:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=186)
[2026-06-08T09:02:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=181)
[2026-06-08T09:02:33] Searching for additional isoforms (remaining=221)
[2026-06-08T09:02:35] Assigning confidence scores to events 
[2026-06-08T09:02:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:38] Writing fusions to file 'aih-tih-sc-ac6a71-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:02:40] Writing discarded fusions to file 'aih-tih-sc-ac6a71-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:11] Freeing resources
[2026-06-08T09:03:28] Done (elapsed time=00:12:22, CPU time=00:12:21, peak memory=14.4gb)