[2026-06-08T08:27:11] Launching Arriba 2.4.0
[2026-06-08T08:27:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:27] Reading chimeric alignments from 'aih-tih-sc-242a7d-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11218056)
[2026-06-08T08:32:55] Marking multi-mapping alignments (marked=7876662)
[2026-06-08T08:32:59] Detecting strandedness (reverse)
[2026-06-08T08:32:59] Assigning strands to alignments 
[2026-06-08T08:33:01] Annotating alignments 
[2026-06-08T08:33:32] Filtering duplicates (remaining=3196498)
[2026-06-08T08:33:36] 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=2845244)
[2026-06-08T08:33:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2845244)
[2026-06-08T08:33:40] Filtering viral contigs with expression lower than the top 5 (remaining=2845244)
[2026-06-08T08:33:44] Filtering viral contigs with less than 5% coverage (remaining=2845244)
[2026-06-08T08:33:46] Estimating fragment length (mate gap mean=-81.4657, mate gap stddev=27.9561, read length mean=117.139)
[2026-06-08T08:33:47] Filtering read-through fragments with a distance <=10000bp (remaining=2730089)
[2026-06-08T08:33:48] Filtering inconsistently clipped mates (remaining=2650263)
[2026-06-08T08:33:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2502575)
[2026-06-08T08:33:53] Filtering fragments with small insert size (remaining=2501172)
[2026-06-08T08:33:55] Filtering alignments with long gaps (remaining=2501172)
[2026-06-08T08:33:57] Filtering fragments with both mates in the same gene (remaining=2500194)
[2026-06-08T08:34:00] Filtering fusions arising from hairpin structures (remaining=2324392)
[2026-06-08T08:34:02] Filtering reads with a mismatch p-value <=0.01 (remaining=810615)
[2026-06-08T08:34:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=327432)
[2026-06-08T08:34:14] Finding fusions and counting supporting reads (total=289021)
[2026-06-08T08:34:26] Merging adjacent fusion breakpoints (remaining=285977)
[2026-06-08T08:34:27] Filtering multi-mapping fusions by alignment score and read support (remaining=149205)
[2026-06-08T08:34:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=148207)
[2026-06-08T08:34:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90390)
[2026-06-08T08:34:59] Filtering fusions with <2 supporting reads (remaining=8170)
[2026-06-08T08:34:59] Filtering fusions with an e-value >=0.3 (remaining=1875)
[2026-06-08T08:35:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1902)
[2026-06-08T08:35:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1831)
[2026-06-08T08:35:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1831)
[2026-06-08T08:35:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1815)
[2026-06-08T08:35:07] Searching for fusions with spliced split reads (remaining=1945)
[2026-06-08T08:35:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=1481)
[2026-06-08T08:35:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1451)
[2026-06-08T08:35:12] Searching for fusions with >=4 spliced events (remaining=1600)
[2026-06-08T08:35:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=507)
[2026-06-08T08:35:25] Filtering fusions with anchors <=23nt (remaining=384)
[2026-06-08T08:35:25] Filtering end-to-end fusions with low support (remaining=372)
[2026-06-08T08:35:26] Filtering fusions with no coverage around the breakpoints (remaining=363)
[2026-06-08T08:35:26] Indexing gene sequences 
[2026-06-08T08:35:28] Filtering genes with >=30% identity (remaining=137)
[2026-06-08T08:35:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=88)
[2026-06-08T08:35:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=81)
[2026-06-08T08:35:31] Searching for additional isoforms (remaining=92)
[2026-06-08T08:35:32] Assigning confidence scores to events 
[2026-06-08T08:35:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:33] Writing fusions to file 'aih-tih-sc-242a7d-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:35:34] Writing discarded fusions to file 'aih-tih-sc-242a7d-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:48] Freeing resources
[2026-06-08T08:36:03] Done (elapsed time=00:08:52, CPU time=00:08:52, peak memory=15.7gb)