[2026-06-08T08:48:32] Launching Arriba 2.4.0
[2026-06-08T08:48:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:48] Reading chimeric alignments from 'aih-tih-sc-150e73-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=12722340)
[2026-06-08T08:56:20] Marking multi-mapping alignments (marked=8755426)
[2026-06-08T08:56:26] Detecting strandedness (reverse)
[2026-06-08T08:56:26] Assigning strands to alignments 
[2026-06-08T08:56:28] Annotating alignments 
[2026-06-08T08:57:09] Filtering duplicates (remaining=7102217)
[2026-06-08T08:57:17] 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=6533693)
[2026-06-08T08:57:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6533693)
[2026-06-08T08:57:22] Filtering viral contigs with expression lower than the top 5 (remaining=6533693)
[2026-06-08T08:57:28] Filtering viral contigs with less than 5% coverage (remaining=6533693)
[2026-06-08T08:57:31] Estimating fragment length (mate gap mean=-83.4647, mate gap stddev=29.6909, read length mean=125.207)
[2026-06-08T08:57:31] Filtering read-through fragments with a distance <=10000bp (remaining=6179786)
[2026-06-08T08:57:33] Filtering inconsistently clipped mates (remaining=6051742)
[2026-06-08T08:57:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5874905)
[2026-06-08T08:57:41] Filtering fragments with small insert size (remaining=5873377)
[2026-06-08T08:57:44] Filtering alignments with long gaps (remaining=5873377)
[2026-06-08T08:57:46] Filtering fragments with both mates in the same gene (remaining=5872116)
[2026-06-08T08:57:49] Filtering fusions arising from hairpin structures (remaining=5501951)
[2026-06-08T08:57:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2298478)
[2026-06-08T08:58:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=949023)
[2026-06-08T08:58:17] Finding fusions and counting supporting reads (total=743995)
[2026-06-08T08:58:37] Merging adjacent fusion breakpoints (remaining=736463)
[2026-06-08T08:58:39] Filtering multi-mapping fusions by alignment score and read support (remaining=441462)
[2026-06-08T08:59:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=439441)
[2026-06-08T08:59:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=257880)
[2026-06-08T08:59:27] Filtering fusions with <2 supporting reads (remaining=31872)
[2026-06-08T08:59:28] Filtering fusions with an e-value >=0.3 (remaining=10001)
[2026-06-08T08:59:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10051)
[2026-06-08T08:59:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9954)
[2026-06-08T08:59:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9954)
[2026-06-08T08:59:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6523)
[2026-06-08T08:59:43] Searching for fusions with spliced split reads (remaining=6643)
[2026-06-08T08:59:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=4194)
[2026-06-08T08:59:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4145)
[2026-06-08T08:59:51] Searching for fusions with >=4 spliced events (remaining=4868)
[2026-06-08T08:59:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1743)
[2026-06-08T09:00:09] Filtering fusions with anchors <=23nt (remaining=1401)
[2026-06-08T09:00:10] Filtering end-to-end fusions with low support (remaining=1355)
[2026-06-08T09:00:11] Filtering fusions with no coverage around the breakpoints (remaining=1330)
[2026-06-08T09:00:12] Indexing gene sequences 
[2026-06-08T09:00:18] Filtering genes with >=30% identity (remaining=467)
[2026-06-08T09:00:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=228)
[2026-06-08T09:00:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-08T09:00:25] Searching for additional isoforms (remaining=284)
[2026-06-08T09:00:27] Assigning confidence scores to events 
[2026-06-08T09:00:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:31] Writing fusions to file 'aih-tih-sc-150e73-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:33] Writing discarded fusions to file 'aih-tih-sc-150e73-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:07] Freeing resources
[2026-06-08T09:01:28] Done (elapsed time=00:12:56, CPU time=00:12:55, peak memory=17.4gb)