[2026-06-08T09:05:24] Launching Arriba 2.4.0
[2026-06-08T09:05:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:05:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:05:37] Reading chimeric alignments from 'aih-tih-sc-669302-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9775658)
[2026-06-08T09:12:36] Marking multi-mapping alignments (marked=6342430)
[2026-06-08T09:12:40] Detecting strandedness (reverse)
[2026-06-08T09:12:40] Assigning strands to alignments 
[2026-06-08T09:12:42] Annotating alignments 
[2026-06-08T09:13:12] Filtering duplicates (remaining=5572757)
[2026-06-08T09:13:18] 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=5360871)
[2026-06-08T09:13:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5360871)
[2026-06-08T09:13:21] Filtering viral contigs with expression lower than the top 5 (remaining=5360871)
[2026-06-08T09:13:26] Filtering viral contigs with less than 5% coverage (remaining=5360871)
[2026-06-08T09:13:28] Estimating fragment length (mate gap mean=-83.8731, mate gap stddev=31.3501, read length mean=135.86)
[2026-06-08T09:13:28] Filtering read-through fragments with a distance <=10000bp (remaining=5086664)
[2026-06-08T09:13:30] Filtering inconsistently clipped mates (remaining=5011366)
[2026-06-08T09:13:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4848415)
[2026-06-08T09:13:35] Filtering fragments with small insert size (remaining=4847811)
[2026-06-08T09:13:37] Filtering alignments with long gaps (remaining=4847811)
[2026-06-08T09:13:39] Filtering fragments with both mates in the same gene (remaining=4846928)
[2026-06-08T09:13:41] Filtering fusions arising from hairpin structures (remaining=4577264)
[2026-06-08T09:13:44] Filtering reads with a mismatch p-value <=0.01 (remaining=2232284)
[2026-06-08T09:13:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=744181)
[2026-06-08T09:14:05] Finding fusions and counting supporting reads (total=584409)
[2026-06-08T09:14:20] Merging adjacent fusion breakpoints (remaining=579556)
[2026-06-08T09:14:21] Filtering multi-mapping fusions by alignment score and read support (remaining=365580)
[2026-06-08T09:14:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:14:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=362883)
[2026-06-08T09:14:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=199803)
[2026-06-08T09:15:00] Filtering fusions with <2 supporting reads (remaining=26919)
[2026-06-08T09:15:01] Filtering fusions with an e-value >=0.3 (remaining=10195)
[2026-06-08T09:15:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10238)
[2026-06-08T09:15:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10184)
[2026-06-08T09:15:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10184)
[2026-06-08T09:15:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6510)
[2026-06-08T09:15:11] Searching for fusions with spliced split reads (remaining=6648)
[2026-06-08T09:15:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=3923)
[2026-06-08T09:15:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3884)
[2026-06-08T09:15:17] Searching for fusions with >=4 spliced events (remaining=4479)
[2026-06-08T09:15:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1644)
[2026-06-08T09:15:33] Filtering fusions with anchors <=23nt (remaining=1288)
[2026-06-08T09:15:33] Filtering end-to-end fusions with low support (remaining=1236)
[2026-06-08T09:15:34] Filtering fusions with no coverage around the breakpoints (remaining=1202)
[2026-06-08T09:15:34] Indexing gene sequences 
[2026-06-08T09:15:40] Filtering genes with >=30% identity (remaining=411)
[2026-06-08T09:15:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=155)
[2026-06-08T09:15:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=148)
[2026-06-08T09:15:45] Searching for additional isoforms (remaining=197)
[2026-06-08T09:15:46] Assigning confidence scores to events 
[2026-06-08T09:15:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:15:49] Writing fusions to file 'aih-tih-sc-669302-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:15:51] Writing discarded fusions to file 'aih-tih-sc-669302-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:16:15] Freeing resources
[2026-06-08T09:16:32] Done (elapsed time=00:11:08, CPU time=00:11:06, peak memory=14.2gb)