[2026-06-08T08:47:10] Launching Arriba 2.4.0
[2026-06-08T08:47:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:22] Reading chimeric alignments from 'aih-tih-sc-63b0e7-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10798255)
[2026-06-08T08:53:57] Marking multi-mapping alignments (marked=6753241)
[2026-06-08T08:54:01] Detecting strandedness (reverse)
[2026-06-08T08:54:01] Assigning strands to alignments 
[2026-06-08T08:54:03] Annotating alignments 
[2026-06-08T08:54:39] Filtering duplicates (remaining=6957321)
[2026-06-08T08:54:47] 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=6709583)
[2026-06-08T08:54:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6709583)
[2026-06-08T08:54:51] Filtering viral contigs with expression lower than the top 5 (remaining=6709583)
[2026-06-08T08:54:57] Filtering viral contigs with less than 5% coverage (remaining=6709583)
[2026-06-08T08:54:59] Estimating fragment length (mate gap mean=-86.6324, mate gap stddev=29.0485, read length mean=133.163)
[2026-06-08T08:54:59] Filtering read-through fragments with a distance <=10000bp (remaining=6334910)
[2026-06-08T08:55:01] Filtering inconsistently clipped mates (remaining=6261578)
[2026-06-08T08:55:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6122989)
[2026-06-08T08:55:08] Filtering fragments with small insert size (remaining=6122403)
[2026-06-08T08:55:10] Filtering alignments with long gaps (remaining=6122401)
[2026-06-08T08:55:12] Filtering fragments with both mates in the same gene (remaining=6121271)
[2026-06-08T08:55:15] Filtering fusions arising from hairpin structures (remaining=5907960)
[2026-06-08T08:55:17] Filtering reads with a mismatch p-value <=0.01 (remaining=2961292)
[2026-06-08T08:55:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=1029981)
[2026-06-08T08:55:44] Finding fusions and counting supporting reads (total=747193)
[2026-06-08T08:56:03] Merging adjacent fusion breakpoints (remaining=740084)
[2026-06-08T08:56:05] Filtering multi-mapping fusions by alignment score and read support (remaining=477211)
[2026-06-08T08:56:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=475400)
[2026-06-08T08:56:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=278620)
[2026-06-08T08:56:51] Filtering fusions with <2 supporting reads (remaining=35021)
[2026-06-08T08:56:52] Filtering fusions with an e-value >=0.3 (remaining=9744)
[2026-06-08T08:56:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9788)
[2026-06-08T08:56:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9704)
[2026-06-08T08:56:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9704)
[2026-06-08T08:56:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7932)
[2026-06-08T08:57:05] Searching for fusions with spliced split reads (remaining=7956)
[2026-06-08T08:57:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=4802)
[2026-06-08T08:57:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4725)
[2026-06-08T08:57:12] Searching for fusions with >=4 spliced events (remaining=5704)
[2026-06-08T08:57:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1994)
[2026-06-08T08:57:30] Filtering fusions with anchors <=23nt (remaining=1622)
[2026-06-08T08:57:31] Filtering end-to-end fusions with low support (remaining=1584)
[2026-06-08T08:57:32] Filtering fusions with no coverage around the breakpoints (remaining=1553)
[2026-06-08T08:57:33] Indexing gene sequences 
[2026-06-08T08:57:39] Filtering genes with >=30% identity (remaining=477)
[2026-06-08T08:57:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=221)
[2026-06-08T08:57:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=209)
[2026-06-08T08:57:51] Searching for additional isoforms (remaining=266)
[2026-06-08T08:57:53] Assigning confidence scores to events 
[2026-06-08T08:57:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:56] Writing fusions to file 'aih-tih-sc-63b0e7-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:59] Writing discarded fusions to file 'aih-tih-sc-63b0e7-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:34] Freeing resources
[2026-06-08T08:58:53] Done (elapsed time=00:11:43, CPU time=00:11:42, peak memory=15.1gb)