[2026-06-08T08:43:10] Launching Arriba 2.4.0
[2026-06-08T08:43:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:23] Reading chimeric alignments from 'aih-tih-sc-9ab390-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9533583)
[2026-06-08T08:49:16] Marking multi-mapping alignments (marked=5966550)
[2026-06-08T08:49:20] Detecting strandedness (reverse)
[2026-06-08T08:49:20] Assigning strands to alignments 
[2026-06-08T08:49:22] Annotating alignments 
[2026-06-08T08:49:55] Filtering duplicates (remaining=3867196)
[2026-06-08T08:50:00] 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=3671708)
[2026-06-08T08:50:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3671708)
[2026-06-08T08:50:04] Filtering viral contigs with expression lower than the top 5 (remaining=3671708)
[2026-06-08T08:50:07] Filtering viral contigs with less than 5% coverage (remaining=3671708)
[2026-06-08T08:50:10] Estimating fragment length (mate gap mean=-87.9081, mate gap stddev=28.2311, read length mean=128.94)
[2026-06-08T08:50:10] Filtering read-through fragments with a distance <=10000bp (remaining=3442668)
[2026-06-08T08:50:12] Filtering inconsistently clipped mates (remaining=3375400)
[2026-06-08T08:50:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3263262)
[2026-06-08T08:50:17] Filtering fragments with small insert size (remaining=3262673)
[2026-06-08T08:50:19] Filtering alignments with long gaps (remaining=3262673)
[2026-06-08T08:50:21] Filtering fragments with both mates in the same gene (remaining=3261981)
[2026-06-08T08:50:23] Filtering fusions arising from hairpin structures (remaining=3086777)
[2026-06-08T08:50:25] Filtering reads with a mismatch p-value <=0.01 (remaining=1330602)
[2026-06-08T08:50:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=529480)
[2026-06-08T08:50:41] Finding fusions and counting supporting reads (total=448555)
[2026-06-08T08:50:56] Merging adjacent fusion breakpoints (remaining=443906)
[2026-06-08T08:50:57] Filtering multi-mapping fusions by alignment score and read support (remaining=275212)
[2026-06-08T08:51:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=274034)
[2026-06-08T08:51:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=145702)
[2026-06-08T08:51:36] Filtering fusions with <2 supporting reads (remaining=18840)
[2026-06-08T08:51:37] Filtering fusions with an e-value >=0.3 (remaining=5579)
[2026-06-08T08:51:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5622)
[2026-06-08T08:51:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5539)
[2026-06-08T08:51:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5539)
[2026-06-08T08:51:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4063)
[2026-06-08T08:51:46] Searching for fusions with spliced split reads (remaining=4115)
[2026-06-08T08:51:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=2948)
[2026-06-08T08:51:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2893)
[2026-06-08T08:51:52] Searching for fusions with >=4 spliced events (remaining=3228)
[2026-06-08T08:51:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1053)
[2026-06-08T08:52:08] Filtering fusions with anchors <=23nt (remaining=804)
[2026-06-08T08:52:08] Filtering end-to-end fusions with low support (remaining=770)
[2026-06-08T08:52:09] Filtering fusions with no coverage around the breakpoints (remaining=746)
[2026-06-08T08:52:09] Indexing gene sequences 
[2026-06-08T08:52:13] Filtering genes with >=30% identity (remaining=260)
[2026-06-08T08:52:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=136)
[2026-06-08T08:52:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=121)
[2026-06-08T08:52:17] Searching for additional isoforms (remaining=145)
[2026-06-08T08:52:18] Assigning confidence scores to events 
[2026-06-08T08:52:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:21] Writing fusions to file 'aih-tih-sc-9ab390-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:22] Writing discarded fusions to file 'aih-tih-sc-9ab390-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:45] Freeing resources
[2026-06-08T08:53:01] Done (elapsed time=00:09:51, CPU time=00:09:50, peak memory=14.1gb)