[2026-06-03T20:10:08] Launching Arriba 2.4.0
[2026-06-03T20:10:08] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:10:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:10:22] Reading chimeric alignments from 'aih-tih-sc-69be7e-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11796079)
[2026-06-03T20:17:41] Marking multi-mapping alignments (marked=8144060)
[2026-06-03T20:17:45] Detecting strandedness (reverse)
[2026-06-03T20:17:45] Assigning strands to alignments 
[2026-06-03T20:17:48] Annotating alignments 
[2026-06-03T20:18:27] Filtering duplicates (remaining=6865853)
[2026-06-03T20:18:35] 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=6303503)
[2026-06-03T20:18:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6303503)
[2026-06-03T20:18:40] Filtering viral contigs with expression lower than the top 5 (remaining=6303503)
[2026-06-03T20:18:45] Filtering viral contigs with less than 5% coverage (remaining=6303503)
[2026-06-03T20:18:48] Estimating fragment length (mate gap mean=-84.1359, mate gap stddev=29.531, read length mean=126.604)
[2026-06-03T20:18:48] Filtering read-through fragments with a distance <=10000bp (remaining=6001184)
[2026-06-03T20:18:50] Filtering inconsistently clipped mates (remaining=5861728)
[2026-06-03T20:18:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5681369)
[2026-06-03T20:18:57] Filtering fragments with small insert size (remaining=5679941)
[2026-06-03T20:18:59] Filtering alignments with long gaps (remaining=5679941)
[2026-06-03T20:19:02] Filtering fragments with both mates in the same gene (remaining=5678625)
[2026-06-03T20:19:04] Filtering fusions arising from hairpin structures (remaining=5264948)
[2026-06-03T20:19:07] Filtering reads with a mismatch p-value <=0.01 (remaining=2186927)
[2026-06-03T20:19:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=939134)
[2026-06-03T20:19:32] Finding fusions and counting supporting reads (total=726926)
[2026-06-03T20:19:51] Merging adjacent fusion breakpoints (remaining=720429)
[2026-06-03T20:19:53] Filtering multi-mapping fusions by alignment score and read support (remaining=431328)
[2026-06-03T20:20:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:20:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=428596)
[2026-06-03T20:20:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=251602)
[2026-06-03T20:20:40] Filtering fusions with <2 supporting reads (remaining=29966)
[2026-06-03T20:20:40] Filtering fusions with an e-value >=0.3 (remaining=8847)
[2026-06-03T20:20:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8915)
[2026-06-03T20:20:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8775)
[2026-06-03T20:20:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8775)
[2026-06-03T20:20:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6299)
[2026-06-03T20:20:54] Searching for fusions with spliced split reads (remaining=6423)
[2026-06-03T20:20:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=4104)
[2026-06-03T20:21:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4047)
[2026-06-03T20:21:02] Searching for fusions with >=4 spliced events (remaining=4727)
[2026-06-03T20:21:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1768)
[2026-06-03T20:21:18] Filtering fusions with anchors <=23nt (remaining=1398)
[2026-06-03T20:21:19] Filtering end-to-end fusions with low support (remaining=1356)
[2026-06-03T20:21:20] Filtering fusions with no coverage around the breakpoints (remaining=1324)
[2026-06-03T20:21:21] Indexing gene sequences 
[2026-06-03T20:21:27] Filtering genes with >=30% identity (remaining=451)
[2026-06-03T20:21:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=218)
[2026-06-03T20:21:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-03T20:21:33] Searching for additional isoforms (remaining=272)
[2026-06-03T20:21:34] Assigning confidence scores to events 
[2026-06-03T20:21:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:21:38] Writing fusions to file 'aih-tih-sc-69be7e-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:21:41] Writing discarded fusions to file 'aih-tih-sc-69be7e-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:22:11] Freeing resources
[2026-06-03T20:22:29] Done (elapsed time=00:12:21, CPU time=00:12:20, peak memory=16.6gb)