[2026-06-03T20:23:04] Launching Arriba 2.4.0
[2026-06-03T20:23:04] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:23:12] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:23:16] Reading chimeric alignments from 'aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10857995)
[2026-06-03T20:30:15] Marking multi-mapping alignments (marked=7390505)
[2026-06-03T20:30:20] Detecting strandedness (reverse)
[2026-06-03T20:30:20] Assigning strands to alignments 
[2026-06-03T20:30:22] Annotating alignments 
[2026-06-03T20:30:57] Filtering duplicates (remaining=7158209)
[2026-06-03T20:31:05] 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=6749986)
[2026-06-03T20:31:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6749986)
[2026-06-03T20:31:10] Filtering viral contigs with expression lower than the top 5 (remaining=6749986)
[2026-06-03T20:31:15] Filtering viral contigs with less than 5% coverage (remaining=6749986)
[2026-06-03T20:31:17] Estimating fragment length (mate gap mean=-85.0804, mate gap stddev=28.8062, read length mean=126.399)
[2026-06-03T20:31:17] Filtering read-through fragments with a distance <=10000bp (remaining=6187010)
[2026-06-03T20:31:20] Filtering inconsistently clipped mates (remaining=6053384)
[2026-06-03T20:31:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5892336)
[2026-06-03T20:31:26] Filtering fragments with small insert size (remaining=5891355)
[2026-06-03T20:31:28] Filtering alignments with long gaps (remaining=5891355)
[2026-06-03T20:31:31] Filtering fragments with both mates in the same gene (remaining=5890240)
[2026-06-03T20:31:33] Filtering fusions arising from hairpin structures (remaining=5473519)
[2026-06-03T20:31:36] Filtering reads with a mismatch p-value <=0.01 (remaining=2325715)
[2026-06-03T20:31:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=1161936)
[2026-06-03T20:32:00] Finding fusions and counting supporting reads (total=886700)
[2026-06-03T20:32:16] Merging adjacent fusion breakpoints (remaining=875092)
[2026-06-03T20:32:18] Filtering multi-mapping fusions by alignment score and read support (remaining=530697)
[2026-06-03T20:32:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:32:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=528979)
[2026-06-03T20:32:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=292639)
[2026-06-03T20:32:59] Filtering fusions with <2 supporting reads (remaining=30756)
[2026-06-03T20:33:00] Filtering fusions with an e-value >=0.3 (remaining=7726)
[2026-06-03T20:33:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7780)
[2026-06-03T20:33:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7687)
[2026-06-03T20:33:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7687)
[2026-06-03T20:33:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6606)
[2026-06-03T20:33:13] Searching for fusions with spliced split reads (remaining=6724)
[2026-06-03T20:33:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=4421)
[2026-06-03T20:33:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4363)
[2026-06-03T20:33:21] Searching for fusions with >=4 spliced events (remaining=5150)
[2026-06-03T20:33:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2097)
[2026-06-03T20:33:39] Filtering fusions with anchors <=23nt (remaining=1656)
[2026-06-03T20:33:39] Filtering end-to-end fusions with low support (remaining=1612)
[2026-06-03T20:33:40] Filtering fusions with no coverage around the breakpoints (remaining=1579)
[2026-06-03T20:33:41] Indexing gene sequences 
[2026-06-03T20:33:47] Filtering genes with >=30% identity (remaining=496)
[2026-06-03T20:33:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=212)
[2026-06-03T20:33:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-03T20:33:55] Searching for additional isoforms (remaining=202)
[2026-06-03T20:33:56] Assigning confidence scores to events 
[2026-06-03T20:34:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:34:00] Writing fusions to file 'aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:34:02] Writing discarded fusions to file 'aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:34:32] Freeing resources
[2026-06-03T20:34:49] Done (elapsed time=00:11:45, CPU time=00:11:44, peak memory=15.8gb)