[2026-06-03T20:25:39] Launching Arriba 2.4.0
[2026-06-03T20:25:39] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:25:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:25:51] Reading chimeric alignments from 'aih-tih-sc-ec2fd6-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9791476)
[2026-06-03T20:31:58] Marking multi-mapping alignments (marked=6342145)
[2026-06-03T20:32:01] Detecting strandedness (reverse)
[2026-06-03T20:32:01] Assigning strands to alignments 
[2026-06-03T20:32:03] Annotating alignments 
[2026-06-03T20:32:33] Filtering duplicates (remaining=6572802)
[2026-06-03T20:32:40] 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=6243085)
[2026-06-03T20:32:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6243085)
[2026-06-03T20:32:43] Filtering viral contigs with expression lower than the top 5 (remaining=6243085)
[2026-06-03T20:32:48] Filtering viral contigs with less than 5% coverage (remaining=6243085)
[2026-06-03T20:32:50] Estimating fragment length (mate gap mean=-84.5727, mate gap stddev=27.6603, read length mean=125.186)
[2026-06-03T20:32:50] Filtering read-through fragments with a distance <=10000bp (remaining=5831415)
[2026-06-03T20:32:52] Filtering inconsistently clipped mates (remaining=5705883)
[2026-06-03T20:32:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5547156)
[2026-06-03T20:32:58] Filtering fragments with small insert size (remaining=5546100)
[2026-06-03T20:33:00] Filtering alignments with long gaps (remaining=5546100)
[2026-06-03T20:33:02] Filtering fragments with both mates in the same gene (remaining=5545124)
[2026-06-03T20:33:04] Filtering fusions arising from hairpin structures (remaining=5184607)
[2026-06-03T20:33:06] Filtering reads with a mismatch p-value <=0.01 (remaining=2267089)
[2026-06-03T20:33:19] Filtering reads with low entropy (k-mer content >=60%) (remaining=1155749)
[2026-06-03T20:33:30] Finding fusions and counting supporting reads (total=907062)
[2026-06-03T20:33:45] Merging adjacent fusion breakpoints (remaining=899801)
[2026-06-03T20:33:47] Filtering multi-mapping fusions by alignment score and read support (remaining=559135)
[2026-06-03T20:34:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:34:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=557829)
[2026-06-03T20:34:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=335684)
[2026-06-03T20:34:26] Filtering fusions with <2 supporting reads (remaining=35477)
[2026-06-03T20:34:27] Filtering fusions with an e-value >=0.3 (remaining=7430)
[2026-06-03T20:34:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7486)
[2026-06-03T20:34:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7399)
[2026-06-03T20:34:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7399)
[2026-06-03T20:34:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7126)
[2026-06-03T20:34:38] Searching for fusions with spliced split reads (remaining=7145)
[2026-06-03T20:34:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=4717)
[2026-06-03T20:34:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4678)
[2026-06-03T20:34:46] Searching for fusions with >=4 spliced events (remaining=5688)
[2026-06-03T20:34:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2492)
[2026-06-03T20:35:02] Filtering fusions with anchors <=23nt (remaining=2040)
[2026-06-03T20:35:03] Filtering end-to-end fusions with low support (remaining=1997)
[2026-06-03T20:35:03] Filtering fusions with no coverage around the breakpoints (remaining=1968)
[2026-06-03T20:35:04] Indexing gene sequences 
[2026-06-03T20:35:11] Filtering genes with >=30% identity (remaining=621)
[2026-06-03T20:35:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=315)
[2026-06-03T20:35:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=236)
[2026-06-03T20:35:20] Searching for additional isoforms (remaining=307)
[2026-06-03T20:35:21] Assigning confidence scores to events 
[2026-06-03T20:35:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:35:25] Writing fusions to file 'aih-tih-sc-ec2fd6-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:35:28] Writing discarded fusions to file 'aih-tih-sc-ec2fd6-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:35:57] Freeing resources
[2026-06-03T20:36:14] Done (elapsed time=00:10:35, CPU time=00:10:33, peak memory=14.6gb)