[2026-06-08T08:51:04] Launching Arriba 2.4.0
[2026-06-08T08:51:04] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:19] Reading chimeric alignments from 'aih-tih-sc-3b3c1e-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11559896)
[2026-06-08T08:58:03] Marking multi-mapping alignments (marked=7595639)
[2026-06-08T08:58:08] Detecting strandedness (reverse)
[2026-06-08T08:58:08] Assigning strands to alignments 
[2026-06-08T08:58:11] Annotating alignments 
[2026-06-08T08:58:50] Filtering duplicates (remaining=5655894)
[2026-06-08T08:58:57] 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=5371657)
[2026-06-08T08:59:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5371657)
[2026-06-08T08:59:02] Filtering viral contigs with expression lower than the top 5 (remaining=5371657)
[2026-06-08T08:59:07] Filtering viral contigs with less than 5% coverage (remaining=5371657)
[2026-06-08T08:59:10] Estimating fragment length (mate gap mean=-86.3046, mate gap stddev=27.9579, read length mean=128.587)
[2026-06-08T08:59:10] Filtering read-through fragments with a distance <=10000bp (remaining=5119529)
[2026-06-08T08:59:13] Filtering inconsistently clipped mates (remaining=5044661)
[2026-06-08T08:59:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4891744)
[2026-06-08T08:59:20] Filtering fragments with small insert size (remaining=4891090)
[2026-06-08T08:59:22] Filtering alignments with long gaps (remaining=4891090)
[2026-06-08T08:59:25] Filtering fragments with both mates in the same gene (remaining=4889957)
[2026-06-08T08:59:27] Filtering fusions arising from hairpin structures (remaining=4698732)
[2026-06-08T08:59:30] Filtering reads with a mismatch p-value <=0.01 (remaining=2145324)
[2026-06-08T08:59:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=681649)
[2026-06-08T08:59:53] Finding fusions and counting supporting reads (total=487626)
[2026-06-08T09:00:11] Merging adjacent fusion breakpoints (remaining=482812)
[2026-06-08T09:00:12] Filtering multi-mapping fusions by alignment score and read support (remaining=280365)
[2026-06-08T09:00:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=279121)
[2026-06-08T09:00:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=170080)
[2026-06-08T09:00:59] Filtering fusions with <2 supporting reads (remaining=23566)
[2026-06-08T09:01:00] Filtering fusions with an e-value >=0.3 (remaining=6303)
[2026-06-08T09:01:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6354)
[2026-06-08T09:01:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6269)
[2026-06-08T09:01:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6269)
[2026-06-08T09:01:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6014)
[2026-06-08T09:01:12] Searching for fusions with spliced split reads (remaining=6102)
[2026-06-08T09:01:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=3992)
[2026-06-08T09:01:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3941)
[2026-06-08T09:01:19] Searching for fusions with >=4 spliced events (remaining=4536)
[2026-06-08T09:01:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1494)
[2026-06-08T09:01:37] Filtering fusions with anchors <=23nt (remaining=1216)
[2026-06-08T09:01:37] Filtering end-to-end fusions with low support (remaining=1194)
[2026-06-08T09:01:38] Filtering fusions with no coverage around the breakpoints (remaining=1180)
[2026-06-08T09:01:39] Indexing gene sequences 
[2026-06-08T09:01:44] Filtering genes with >=30% identity (remaining=336)
[2026-06-08T09:01:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=173)
[2026-06-08T09:01:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=170)
[2026-06-08T09:01:51] Searching for additional isoforms (remaining=201)
[2026-06-08T09:01:53] Assigning confidence scores to events 
[2026-06-08T09:01:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:56] Writing fusions to file 'aih-tih-sc-3b3c1e-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:57] Writing discarded fusions to file 'aih-tih-sc-3b3c1e-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:02:23] Freeing resources
[2026-06-08T09:02:41] Done (elapsed time=00:11:37, CPU time=00:11:36, peak memory=15.8gb)