[2026-06-08T08:19:10] Launching Arriba 2.4.0
[2026-06-08T08:19:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:23] Reading chimeric alignments from 'aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7874496)
[2026-06-08T08:23:46] Marking multi-mapping alignments (marked=5271038)
[2026-06-08T08:23:49] Detecting strandedness (reverse)
[2026-06-08T08:23:49] Assigning strands to alignments 
[2026-06-08T08:23:50] Annotating alignments 
[2026-06-08T08:24:18] Filtering duplicates (remaining=4646963)
[2026-06-08T08:24:23] 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=4369401)
[2026-06-08T08:24:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4369401)
[2026-06-08T08:24:26] Filtering viral contigs with expression lower than the top 5 (remaining=4369401)
[2026-06-08T08:24:29] Filtering viral contigs with less than 5% coverage (remaining=4369401)
[2026-06-08T08:24:31] Estimating fragment length (mate gap mean=-83.8168, mate gap stddev=27.4479, read length mean=121.695)
[2026-06-08T08:24:32] Filtering read-through fragments with a distance <=10000bp (remaining=4107315)
[2026-06-08T08:24:33] Filtering inconsistently clipped mates (remaining=4004152)
[2026-06-08T08:24:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3841017)
[2026-06-08T08:24:39] Filtering fragments with small insert size (remaining=3840102)
[2026-06-08T08:24:40] Filtering alignments with long gaps (remaining=3840101)
[2026-06-08T08:24:42] Filtering fragments with both mates in the same gene (remaining=3839215)
[2026-06-08T08:24:44] Filtering fusions arising from hairpin structures (remaining=3569632)
[2026-06-08T08:24:46] Filtering reads with a mismatch p-value <=0.01 (remaining=1490872)
[2026-06-08T08:24:55] Filtering reads with low entropy (k-mer content >=60%) (remaining=763995)
[2026-06-08T08:25:03] Finding fusions and counting supporting reads (total=610832)
[2026-06-08T08:25:18] Merging adjacent fusion breakpoints (remaining=606673)
[2026-06-08T08:25:20] Filtering multi-mapping fusions by alignment score and read support (remaining=352270)
[2026-06-08T08:25:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:25:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=351004)
[2026-06-08T08:25:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213242)
[2026-06-08T08:25:57] Filtering fusions with <2 supporting reads (remaining=23247)
[2026-06-08T08:25:58] Filtering fusions with an e-value >=0.3 (remaining=5496)
[2026-06-08T08:25:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5556)
[2026-06-08T08:26:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5477)
[2026-06-08T08:26:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5477)
[2026-06-08T08:26:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5411)
[2026-06-08T08:26:07] Searching for fusions with spliced split reads (remaining=5475)
[2026-06-08T08:26:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=3755)
[2026-06-08T08:26:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3721)
[2026-06-08T08:26:13] Searching for fusions with >=4 spliced events (remaining=4300)
[2026-06-08T08:26:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1393)
[2026-06-08T08:26:31] Filtering fusions with anchors <=23nt (remaining=1209)
[2026-06-08T08:26:32] Filtering end-to-end fusions with low support (remaining=1185)
[2026-06-08T08:26:32] Filtering fusions with no coverage around the breakpoints (remaining=1159)
[2026-06-08T08:26:33] Indexing gene sequences 
[2026-06-08T08:26:38] Filtering genes with >=30% identity (remaining=386)
[2026-06-08T08:26:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=185)
[2026-06-08T08:26:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=177)
[2026-06-08T08:26:45] Searching for additional isoforms (remaining=207)
[2026-06-08T08:26:46] Assigning confidence scores to events 
[2026-06-08T08:26:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:26:49] Writing fusions to file 'aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:26:51] Writing discarded fusions to file 'aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:27:22] Freeing resources
[2026-06-08T08:27:36] Done (elapsed time=00:08:26, CPU time=00:08:24, peak memory=12.5gb)