[2026-06-08T08:06:32] Launching Arriba 2.4.0
[2026-06-08T08:06:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:06:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:06:53] Reading chimeric alignments from 'aih-tih-sc-a558c6-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7149121)
[2026-06-08T08:10:58] Marking multi-mapping alignments (marked=5230993)
[2026-06-08T08:11:01] Detecting strandedness (reverse)
[2026-06-08T08:11:01] Assigning strands to alignments 
[2026-06-08T08:11:02] Annotating alignments 
[2026-06-08T08:11:26] Filtering duplicates (remaining=2959530)
[2026-06-08T08:11:30] 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=2654936)
[2026-06-08T08:11:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2654936)
[2026-06-08T08:11:32] Filtering viral contigs with expression lower than the top 5 (remaining=2654936)
[2026-06-08T08:11:35] Filtering viral contigs with less than 5% coverage (remaining=2654936)
[2026-06-08T08:11:37] Estimating fragment length (mate gap mean=-79.9726, mate gap stddev=27.8061, read length mean=114.254)
[2026-06-08T08:11:37] Filtering read-through fragments with a distance <=10000bp (remaining=2544397)
[2026-06-08T08:11:39] Filtering inconsistently clipped mates (remaining=2476915)
[2026-06-08T08:11:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2370080)
[2026-06-08T08:11:42] Filtering fragments with small insert size (remaining=2369217)
[2026-06-08T08:11:44] Filtering alignments with long gaps (remaining=2369217)
[2026-06-08T08:11:45] Filtering fragments with both mates in the same gene (remaining=2368422)
[2026-06-08T08:11:47] Filtering fusions arising from hairpin structures (remaining=2210454)
[2026-06-08T08:11:48] Filtering reads with a mismatch p-value <=0.01 (remaining=762852)
[2026-06-08T08:11:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=326472)
[2026-06-08T08:11:59] Finding fusions and counting supporting reads (total=285972)
[2026-06-08T08:12:09] Merging adjacent fusion breakpoints (remaining=283515)
[2026-06-08T08:12:10] Filtering multi-mapping fusions by alignment score and read support (remaining=146976)
[2026-06-08T08:12:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:12:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=146194)
[2026-06-08T08:12:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90759)
[2026-06-08T08:12:35] Filtering fusions with <2 supporting reads (remaining=7473)
[2026-06-08T08:12:36] Filtering fusions with an e-value >=0.3 (remaining=1901)
[2026-06-08T08:12:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1952)
[2026-06-08T08:12:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1904)
[2026-06-08T08:12:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1904)
[2026-06-08T08:12:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1893)
[2026-06-08T08:12:42] Searching for fusions with spliced split reads (remaining=2038)
[2026-06-08T08:12:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=1484)
[2026-06-08T08:12:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1464)
[2026-06-08T08:12:46] Searching for fusions with >=4 spliced events (remaining=1635)
[2026-06-08T08:12:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=573)
[2026-06-08T08:13:01] Filtering fusions with anchors <=23nt (remaining=487)
[2026-06-08T08:13:01] Filtering end-to-end fusions with low support (remaining=477)
[2026-06-08T08:13:01] Filtering fusions with no coverage around the breakpoints (remaining=465)
[2026-06-08T08:13:02] Indexing gene sequences 
[2026-06-08T08:13:05] Filtering genes with >=30% identity (remaining=170)
[2026-06-08T08:13:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=103)
[2026-06-08T08:13:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=89)
[2026-06-08T08:13:08] Searching for additional isoforms (remaining=110)
[2026-06-08T08:13:09] Assigning confidence scores to events 
[2026-06-08T08:13:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:13:11] Writing fusions to file 'aih-tih-sc-a558c6-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:13:12] Writing discarded fusions to file 'aih-tih-sc-a558c6-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:13:29] Freeing resources
[2026-06-08T08:13:40] Done (elapsed time=00:07:08, CPU time=00:07:07, peak memory=11.6gb)