[2026-06-03T19:50:17] Launching Arriba 2.4.0
[2026-06-03T19:50:17] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:50:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:50:35] Reading chimeric alignments from 'aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7142412)
[2026-06-03T19:55:15] Marking multi-mapping alignments (marked=4887702)
[2026-06-03T19:55:18] Detecting strandedness (reverse)
[2026-06-03T19:55:18] Assigning strands to alignments 
[2026-06-03T19:55:20] Annotating alignments 
[2026-06-03T19:55:46] Filtering duplicates (remaining=3784931)
[2026-06-03T19:55:52] 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=3577203)
[2026-06-03T19:55:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3577203)
[2026-06-03T19:55:54] Filtering viral contigs with expression lower than the top 5 (remaining=3577203)
[2026-06-03T19:55:57] Filtering viral contigs with less than 5% coverage (remaining=3577203)
[2026-06-03T19:55:59] Estimating fragment length (mate gap mean=-78.9317, mate gap stddev=27.2213, read length mean=115.077)
[2026-06-03T19:55:59] Filtering read-through fragments with a distance <=10000bp (remaining=3361179)
[2026-06-03T19:56:01] Filtering inconsistently clipped mates (remaining=3270966)
[2026-06-03T19:56:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3150567)
[2026-06-03T19:56:06] Filtering fragments with small insert size (remaining=3149563)
[2026-06-03T19:56:07] Filtering alignments with long gaps (remaining=3149563)
[2026-06-03T19:56:09] Filtering fragments with both mates in the same gene (remaining=3148660)
[2026-06-03T19:56:10] Filtering fusions arising from hairpin structures (remaining=2926224)
[2026-06-03T19:56:12] Filtering reads with a mismatch p-value <=0.01 (remaining=1129387)
[2026-06-03T19:56:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=519473)
[2026-06-03T19:56:27] Finding fusions and counting supporting reads (total=455944)
[2026-06-03T19:56:42] Merging adjacent fusion breakpoints (remaining=451942)
[2026-06-03T19:56:43] Filtering multi-mapping fusions by alignment score and read support (remaining=253565)
[2026-06-03T19:57:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:57:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=252687)
[2026-06-03T19:57:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=145323)
[2026-06-03T19:57:20] Filtering fusions with <2 supporting reads (remaining=12500)
[2026-06-03T19:57:21] Filtering fusions with an e-value >=0.3 (remaining=3080)
[2026-06-03T19:57:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3144)
[2026-06-03T19:57:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3042)
[2026-06-03T19:57:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3042)
[2026-06-03T19:57:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3015)
[2026-06-03T19:57:29] Searching for fusions with spliced split reads (remaining=3062)
[2026-06-03T19:57:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=2196)
[2026-06-03T19:57:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2166)
[2026-06-03T19:57:34] Searching for fusions with >=4 spliced events (remaining=2553)
[2026-06-03T19:57:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1204)
[2026-06-03T19:57:48] Filtering fusions with anchors <=23nt (remaining=1036)
[2026-06-03T19:57:49] Filtering end-to-end fusions with low support (remaining=1014)
[2026-06-03T19:57:49] Filtering fusions with no coverage around the breakpoints (remaining=996)
[2026-06-03T19:57:50] Indexing gene sequences 
[2026-06-03T19:57:57] Filtering genes with >=30% identity (remaining=414)
[2026-06-03T19:58:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=242)
[2026-06-03T19:58:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-03T19:58:11] Searching for additional isoforms (remaining=221)
[2026-06-03T19:58:11] Assigning confidence scores to events 
[2026-06-03T19:58:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:58:14] Writing fusions to file 'aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:58:16] Writing discarded fusions to file 'aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:58:38] Freeing resources
[2026-06-03T19:58:57] Done (elapsed time=00:08:40, CPU time=00:08:39, peak memory=11.6gb)