[2026-06-08T08:52:21] Launching Arriba 2.4.0
[2026-06-08T08:52:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:34] Reading chimeric alignments from 'aih-tih-sc-4d6599-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9812610)
[2026-06-08T08:59:56] Marking multi-mapping alignments (marked=6089492)
[2026-06-08T09:00:02] Detecting strandedness (reverse)
[2026-06-08T09:00:02] Assigning strands to alignments 
[2026-06-08T09:00:05] Annotating alignments 
[2026-06-08T09:00:48] Filtering duplicates (remaining=5740988)
[2026-06-08T09:00:57] 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=5452457)
[2026-06-08T09:01:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5452457)
[2026-06-08T09:01:02] Filtering viral contigs with expression lower than the top 5 (remaining=5452457)
[2026-06-08T09:01:08] Filtering viral contigs with less than 5% coverage (remaining=5452457)
[2026-06-08T09:01:10] Estimating fragment length (mate gap mean=-87.2623, mate gap stddev=28.8173, read length mean=131.537)
[2026-06-08T09:01:11] Filtering read-through fragments with a distance <=10000bp (remaining=5094844)
[2026-06-08T09:01:13] Filtering inconsistently clipped mates (remaining=4996372)
[2026-06-08T09:01:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4880528)
[2026-06-08T09:01:21] Filtering fragments with small insert size (remaining=4879580)
[2026-06-08T09:01:24] Filtering alignments with long gaps (remaining=4879580)
[2026-06-08T09:01:27] Filtering fragments with both mates in the same gene (remaining=4878622)
[2026-06-08T09:01:31] Filtering fusions arising from hairpin structures (remaining=4554468)
[2026-06-08T09:01:34] Filtering reads with a mismatch p-value <=0.01 (remaining=2128719)
[2026-06-08T09:01:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=952419)
[2026-06-08T09:02:00] Finding fusions and counting supporting reads (total=691966)
[2026-06-08T09:02:23] Merging adjacent fusion breakpoints (remaining=683936)
[2026-06-08T09:02:25] Filtering multi-mapping fusions by alignment score and read support (remaining=439789)
[2026-06-08T09:03:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=437509)
[2026-06-08T09:03:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=232118)
[2026-06-08T09:03:36] Filtering fusions with <2 supporting reads (remaining=37094)
[2026-06-08T09:03:37] Filtering fusions with an e-value >=0.3 (remaining=11949)
[2026-06-08T09:03:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12015)
[2026-06-08T09:03:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11943)
[2026-06-08T09:03:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11944)
[2026-06-08T09:03:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7837)
[2026-06-08T09:03:53] Searching for fusions with spliced split reads (remaining=7988)
[2026-06-08T09:04:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=4889)
[2026-06-08T09:04:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4833)
[2026-06-08T09:04:03] Searching for fusions with >=4 spliced events (remaining=5731)
[2026-06-08T09:04:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2068)
[2026-06-08T09:04:21] Filtering fusions with anchors <=23nt (remaining=1683)
[2026-06-08T09:04:22] Filtering end-to-end fusions with low support (remaining=1636)
[2026-06-08T09:04:23] Filtering fusions with no coverage around the breakpoints (remaining=1613)
[2026-06-08T09:04:24] Indexing gene sequences 
[2026-06-08T09:04:31] Filtering genes with >=30% identity (remaining=469)
[2026-06-08T09:04:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=216)
[2026-06-08T09:04:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=196)
[2026-06-08T09:04:42] Searching for additional isoforms (remaining=247)
[2026-06-08T09:04:43] Assigning confidence scores to events 
[2026-06-08T09:04:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:47] Writing fusions to file 'aih-tih-sc-4d6599-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:49] Writing discarded fusions to file 'aih-tih-sc-4d6599-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:27] Freeing resources
[2026-06-08T09:05:50] Done (elapsed time=00:13:29, CPU time=00:13:28, peak memory=14.5gb)