[2026-06-08T08:45:29] Launching Arriba 2.4.0
[2026-06-08T08:45:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:41] Reading chimeric alignments from 'aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10857995)
[2026-06-08T08:52:31] Marking multi-mapping alignments (marked=7390505)
[2026-06-08T08:52:35] Detecting strandedness (reverse)
[2026-06-08T08:52:35] Assigning strands to alignments 
[2026-06-08T08:52:37] Annotating alignments 
[2026-06-08T08:53:11] Filtering duplicates (remaining=7158209)
[2026-06-08T08:53:18] 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=6749986)
[2026-06-08T08:53:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6749986)
[2026-06-08T08:53:22] Filtering viral contigs with expression lower than the top 5 (remaining=6749986)
[2026-06-08T08:53:26] Filtering viral contigs with less than 5% coverage (remaining=6749986)
[2026-06-08T08:53:29] Estimating fragment length (mate gap mean=-85.0804, mate gap stddev=28.8062, read length mean=126.399)
[2026-06-08T08:53:29] Filtering read-through fragments with a distance <=10000bp (remaining=6187010)
[2026-06-08T08:53:31] Filtering inconsistently clipped mates (remaining=6053384)
[2026-06-08T08:53:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5892336)
[2026-06-08T08:53:37] Filtering fragments with small insert size (remaining=5891355)
[2026-06-08T08:53:39] Filtering alignments with long gaps (remaining=5891355)
[2026-06-08T08:53:41] Filtering fragments with both mates in the same gene (remaining=5890240)
[2026-06-08T08:53:44] Filtering fusions arising from hairpin structures (remaining=5473519)
[2026-06-08T08:53:46] Filtering reads with a mismatch p-value <=0.01 (remaining=2325715)
[2026-06-08T08:54:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=1161936)
[2026-06-08T08:54:11] Finding fusions and counting supporting reads (total=886700)
[2026-06-08T08:54:29] Merging adjacent fusion breakpoints (remaining=875092)
[2026-06-08T08:54:31] Filtering multi-mapping fusions by alignment score and read support (remaining=530697)
[2026-06-08T08:55:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:55:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=528979)
[2026-06-08T08:55:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=292639)
[2026-06-08T08:55:16] Filtering fusions with <2 supporting reads (remaining=30756)
[2026-06-08T08:55:17] Filtering fusions with an e-value >=0.3 (remaining=7726)
[2026-06-08T08:55:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7780)
[2026-06-08T08:55:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7687)
[2026-06-08T08:55:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7687)
[2026-06-08T08:55:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6606)
[2026-06-08T08:55:30] Searching for fusions with spliced split reads (remaining=6724)
[2026-06-08T08:55:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=4421)
[2026-06-08T08:55:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4363)
[2026-06-08T08:55:38] Searching for fusions with >=4 spliced events (remaining=5150)
[2026-06-08T08:55:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2097)
[2026-06-08T08:55:57] Filtering fusions with anchors <=23nt (remaining=1656)
[2026-06-08T08:55:58] Filtering end-to-end fusions with low support (remaining=1612)
[2026-06-08T08:55:58] Filtering fusions with no coverage around the breakpoints (remaining=1579)
[2026-06-08T08:55:59] Indexing gene sequences 
[2026-06-08T08:56:06] Filtering genes with >=30% identity (remaining=496)
[2026-06-08T08:56:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=212)
[2026-06-08T08:56:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-08T08:56:14] Searching for additional isoforms (remaining=202)
[2026-06-08T08:56:16] Assigning confidence scores to events 
[2026-06-08T08:56:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:20] Writing fusions to file 'aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:22] Writing discarded fusions to file 'aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:00] Freeing resources
[2026-06-08T08:57:18] Done (elapsed time=00:11:49, CPU time=00:11:48, peak memory=15.7gb)