[2026-06-08T09:10:22] Launching Arriba 2.4.0
[2026-06-08T09:10:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:10:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:10:34] Reading chimeric alignments from 'aih-tih-sc-af602e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10212079)
[2026-06-08T09:17:25] Marking multi-mapping alignments (marked=6250511)
[2026-06-08T09:17:29] Detecting strandedness (reverse)
[2026-06-08T09:17:29] Assigning strands to alignments 
[2026-06-08T09:17:31] Annotating alignments 
[2026-06-08T09:18:06] Filtering duplicates (remaining=5567242)
[2026-06-08T09:18:12] 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=5359094)
[2026-06-08T09:18:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5359094)
[2026-06-08T09:18:16] Filtering viral contigs with expression lower than the top 5 (remaining=5359094)
[2026-06-08T09:18:20] Filtering viral contigs with less than 5% coverage (remaining=5359094)
[2026-06-08T09:18:23] Estimating fragment length (mate gap mean=-87.3558, mate gap stddev=28.7863, read length mean=133.614)
[2026-06-08T09:18:23] Filtering read-through fragments with a distance <=10000bp (remaining=5026304)
[2026-06-08T09:18:25] Filtering inconsistently clipped mates (remaining=4934380)
[2026-06-08T09:18:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4802046)
[2026-06-08T09:18:31] Filtering fragments with small insert size (remaining=4801196)
[2026-06-08T09:18:33] Filtering alignments with long gaps (remaining=4801196)
[2026-06-08T09:18:35] Filtering fragments with both mates in the same gene (remaining=4800145)
[2026-06-08T09:18:37] Filtering fusions arising from hairpin structures (remaining=4504578)
[2026-06-08T09:18:40] Filtering reads with a mismatch p-value <=0.01 (remaining=2117715)
[2026-06-08T09:18:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=851221)
[2026-06-08T09:19:00] Finding fusions and counting supporting reads (total=663778)
[2026-06-08T09:19:15] Merging adjacent fusion breakpoints (remaining=658083)
[2026-06-08T09:19:16] Filtering multi-mapping fusions by alignment score and read support (remaining=428856)
[2026-06-08T09:19:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:19:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=426896)
[2026-06-08T09:19:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=225855)
[2026-06-08T09:19:55] Filtering fusions with <2 supporting reads (remaining=29964)
[2026-06-08T09:19:56] Filtering fusions with an e-value >=0.3 (remaining=7763)
[2026-06-08T09:19:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7811)
[2026-06-08T09:20:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7758)
[2026-06-08T09:20:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7758)
[2026-06-08T09:20:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6960)
[2026-06-08T09:20:06] Searching for fusions with spliced split reads (remaining=7081)
[2026-06-08T09:20:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=4537)
[2026-06-08T09:20:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4469)
[2026-06-08T09:20:12] Searching for fusions with >=4 spliced events (remaining=5416)
[2026-06-08T09:20:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1938)
[2026-06-08T09:20:27] Filtering fusions with anchors <=23nt (remaining=1657)
[2026-06-08T09:20:28] Filtering end-to-end fusions with low support (remaining=1611)
[2026-06-08T09:20:28] Filtering fusions with no coverage around the breakpoints (remaining=1567)
[2026-06-08T09:20:29] Indexing gene sequences 
[2026-06-08T09:20:35] Filtering genes with >=30% identity (remaining=521)
[2026-06-08T09:20:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=297)
[2026-06-08T09:20:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=250)
[2026-06-08T09:20:43] Searching for additional isoforms (remaining=311)
[2026-06-08T09:20:44] Assigning confidence scores to events 
[2026-06-08T09:20:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:20:47] Writing fusions to file 'aih-tih-sc-af602e-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:20:49] Writing discarded fusions to file 'aih-tih-sc-af602e-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:21:15] Freeing resources
[2026-06-08T09:21:31] Done (elapsed time=00:11:09, CPU time=00:11:08, peak memory=14.8gb)