[2026-06-08T08:18:05] Launching Arriba 2.4.0
[2026-06-08T08:18:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:18:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:18:22] Reading chimeric alignments from 'aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7142412)
[2026-06-08T08:22:32] Marking multi-mapping alignments (marked=4887702)
[2026-06-08T08:22:35] Detecting strandedness (reverse)
[2026-06-08T08:22:35] Assigning strands to alignments 
[2026-06-08T08:22:36] Annotating alignments 
[2026-06-08T08:22:57] Filtering duplicates (remaining=3784931)
[2026-06-08T08:23:00] 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)
[2026-06-08T08:23:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3577203)
[2026-06-08T08:23:03] Filtering viral contigs with expression lower than the top 5 (remaining=3577203)
[2026-06-08T08:23:06] Filtering viral contigs with less than 5% coverage (remaining=3577203)
[2026-06-08T08:23:07] Estimating fragment length (mate gap mean=-78.9317, mate gap stddev=27.2213, read length mean=115.077)
[2026-06-08T08:23:07] Filtering read-through fragments with a distance <=10000bp (remaining=3361179)
[2026-06-08T08:23:09] Filtering inconsistently clipped mates (remaining=3270966)
[2026-06-08T08:23:10] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3150567)
[2026-06-08T08:23:12] Filtering fragments with small insert size (remaining=3149563)
[2026-06-08T08:23:14] Filtering alignments with long gaps (remaining=3149563)
[2026-06-08T08:23:15] Filtering fragments with both mates in the same gene (remaining=3148660)
[2026-06-08T08:23:16] Filtering fusions arising from hairpin structures (remaining=2926224)
[2026-06-08T08:23:18] Filtering reads with a mismatch p-value <=0.01 (remaining=1129387)
[2026-06-08T08:23:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=519473)
[2026-06-08T08:23:31] Finding fusions and counting supporting reads (total=455944)
[2026-06-08T08:23:42] Merging adjacent fusion breakpoints (remaining=451942)
[2026-06-08T08:23:43] Filtering multi-mapping fusions by alignment score and read support (remaining=253565)
[2026-06-08T08:24:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:24:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=252687)
[2026-06-08T08:24:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=145323)
[2026-06-08T08:24:07] Filtering fusions with <2 supporting reads (remaining=12500)
[2026-06-08T08:24:08] Filtering fusions with an e-value >=0.3 (remaining=3080)
[2026-06-08T08:24:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3144)
[2026-06-08T08:24:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3042)
[2026-06-08T08:24:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3042)
[2026-06-08T08:24:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3015)
[2026-06-08T08:24:15] Searching for fusions with spliced split reads (remaining=3062)
[2026-06-08T08:24:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=2196)
[2026-06-08T08:24:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2166)
[2026-06-08T08:24:19] Searching for fusions with >=4 spliced events (remaining=2553)
[2026-06-08T08:24:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1204)
[2026-06-08T08:24:33] Filtering fusions with anchors <=23nt (remaining=1036)
[2026-06-08T08:24:33] Filtering end-to-end fusions with low support (remaining=1014)
[2026-06-08T08:24:34] Filtering fusions with no coverage around the breakpoints (remaining=996)
[2026-06-08T08:24:34] Indexing gene sequences 
[2026-06-08T08:24:39] Filtering genes with >=30% identity (remaining=414)
[2026-06-08T08:24:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=242)
[2026-06-08T08:24:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-08T08:24:49] Searching for additional isoforms (remaining=221)
[2026-06-08T08:24:49] Assigning confidence scores to events 
[2026-06-08T08:24:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:52] Writing fusions to file 'aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:24:53] Writing discarded fusions to file 'aih-tih-sc-7fa0fb-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:10] Freeing resources
[2026-06-08T08:25:21] Done (elapsed time=00:07:16, CPU time=00:07:14, peak memory=11.6gb)