[2026-06-03T19:40:25] Launching Arriba 2.4.0
[2026-06-03T19:40:25] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:40:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:40:44] Reading chimeric alignments from 'aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=7874496)
[2026-06-03T19:48:16] Marking multi-mapping alignments (marked=5271038)
[2026-06-03T19:48:20] Detecting strandedness (reverse)
[2026-06-03T19:48:20] Assigning strands to alignments 
[2026-06-03T19:48:22] Annotating alignments 
[2026-06-03T19:49:00] Filtering duplicates (remaining=4646963)
[2026-06-03T19:49:09] 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)
[2026-06-03T19:49:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4369401)
[2026-06-03T19:49:12] Filtering viral contigs with expression lower than the top 5 (remaining=4369401)
[2026-06-03T19:49:16] Filtering viral contigs with less than 5% coverage (remaining=4369401)
[2026-06-03T19:49:18] Estimating fragment length (mate gap mean=-83.8168, mate gap stddev=27.4479, read length mean=121.695)
[2026-06-03T19:49:19] Filtering read-through fragments with a distance <=10000bp (remaining=4107315)
[2026-06-03T19:49:20] Filtering inconsistently clipped mates (remaining=4004152)
[2026-06-03T19:49:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3841017)
[2026-06-03T19:49:26] Filtering fragments with small insert size (remaining=3840102)
[2026-06-03T19:49:28] Filtering alignments with long gaps (remaining=3840101)
[2026-06-03T19:49:30] Filtering fragments with both mates in the same gene (remaining=3839215)
[2026-06-03T19:49:32] Filtering fusions arising from hairpin structures (remaining=3569632)
[2026-06-03T19:49:34] Filtering reads with a mismatch p-value <=0.01 (remaining=1490872)
[2026-06-03T19:49:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=763995)
[2026-06-03T19:49:53] Finding fusions and counting supporting reads (total=610832)
[2026-06-03T19:50:14] Merging adjacent fusion breakpoints (remaining=606673)
[2026-06-03T19:50:16] Filtering multi-mapping fusions by alignment score and read support (remaining=352270)
[2026-06-03T19:50:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:51:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=351004)
[2026-06-03T19:51:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213242)
[2026-06-03T19:51:09] Filtering fusions with <2 supporting reads (remaining=23247)
[2026-06-03T19:51:09] Filtering fusions with an e-value >=0.3 (remaining=5496)
[2026-06-03T19:51:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5556)
[2026-06-03T19:51:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5477)
[2026-06-03T19:51:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5477)
[2026-06-03T19:51:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5411)
[2026-06-03T19:51:22] Searching for fusions with spliced split reads (remaining=5475)
[2026-06-03T19:51:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=3755)
[2026-06-03T19:51:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3721)
[2026-06-03T19:51:30] Searching for fusions with >=4 spliced events (remaining=4300)
[2026-06-03T19:51:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1393)
[2026-06-03T19:51:59] Filtering fusions with anchors <=23nt (remaining=1209)
[2026-06-03T19:52:00] Filtering end-to-end fusions with low support (remaining=1185)
[2026-06-03T19:52:00] Filtering fusions with no coverage around the breakpoints (remaining=1159)
[2026-06-03T19:52:01] Indexing gene sequences 
[2026-06-03T19:52:12] Filtering genes with >=30% identity (remaining=386)
[2026-06-03T19:52:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=185)
[2026-06-03T19:52:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=177)
[2026-06-03T19:52:21] Searching for additional isoforms (remaining=207)
[2026-06-03T19:52:23] Assigning confidence scores to events 
[2026-06-03T19:52:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:52:28] Writing fusions to file 'aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:52:30] Writing discarded fusions to file 'aih-tih-sc-4bcd26-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:53:14] Freeing resources
[2026-06-03T19:53:37] Done (elapsed time=00:13:12, CPU time=00:13:10, peak memory=12.5gb)