[2026-06-08T08:28:12] Launching Arriba 2.4.0
[2026-06-08T08:28:12] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:24] Reading chimeric alignments from 'aih-tih-sc-1d9134-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=8232675)
[2026-06-08T08:33:56] Marking multi-mapping alignments (marked=5050908)
[2026-06-08T08:33:59] Detecting strandedness (reverse)
[2026-06-08T08:33:59] Assigning strands to alignments 
[2026-06-08T08:34:01] Annotating alignments 
[2026-06-08T08:34:26] Filtering duplicates (remaining=5476276)
[2026-06-08T08:34:32] 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=5302410)
[2026-06-08T08:34:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5302410)
[2026-06-08T08:34:35] Filtering viral contigs with expression lower than the top 5 (remaining=5302410)
[2026-06-08T08:34:38] Filtering viral contigs with less than 5% coverage (remaining=5302410)
[2026-06-08T08:34:40] Estimating fragment length (mate gap mean=-86.5564, mate gap stddev=28.2588, read length mean=132.309)
[2026-06-08T08:34:40] Filtering read-through fragments with a distance <=10000bp (remaining=4969938)
[2026-06-08T08:34:42] Filtering inconsistently clipped mates (remaining=4904570)
[2026-06-08T08:34:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4799197)
[2026-06-08T08:34:47] Filtering fragments with small insert size (remaining=4798438)
[2026-06-08T08:34:48] Filtering alignments with long gaps (remaining=4798437)
[2026-06-08T08:34:50] Filtering fragments with both mates in the same gene (remaining=4797561)
[2026-06-08T08:34:52] Filtering fusions arising from hairpin structures (remaining=4603465)
[2026-06-08T08:34:54] Filtering reads with a mismatch p-value <=0.01 (remaining=2299129)
[2026-06-08T08:35:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=894236)
[2026-06-08T08:35:14] Finding fusions and counting supporting reads (total=635658)
[2026-06-08T08:35:28] Merging adjacent fusion breakpoints (remaining=629353)
[2026-06-08T08:35:29] Filtering multi-mapping fusions by alignment score and read support (remaining=400556)
[2026-06-08T08:35:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=399073)
[2026-06-08T08:36:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=235006)
[2026-06-08T08:36:03] Filtering fusions with <2 supporting reads (remaining=29540)
[2026-06-08T08:36:04] Filtering fusions with an e-value >=0.3 (remaining=7775)
[2026-06-08T08:36:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7839)
[2026-06-08T08:36:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7785)
[2026-06-08T08:36:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7785)
[2026-06-08T08:36:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6182)
[2026-06-08T08:36:13] Searching for fusions with spliced split reads (remaining=6290)
[2026-06-08T08:36:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=4028)
[2026-06-08T08:36:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3988)
[2026-06-08T08:36:19] Searching for fusions with >=4 spliced events (remaining=4649)
[2026-06-08T08:36:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1714)
[2026-06-08T08:36:35] Filtering fusions with anchors <=23nt (remaining=1425)
[2026-06-08T08:36:35] Filtering end-to-end fusions with low support (remaining=1390)
[2026-06-08T08:36:36] Filtering fusions with no coverage around the breakpoints (remaining=1364)
[2026-06-08T08:36:37] Indexing gene sequences 
[2026-06-08T08:36:41] Filtering genes with >=30% identity (remaining=401)
[2026-06-08T08:36:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=171)
[2026-06-08T08:36:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=165)
[2026-06-08T08:36:48] Searching for additional isoforms (remaining=201)
[2026-06-08T08:36:50] Assigning confidence scores to events 
[2026-06-08T08:36:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:52] Writing fusions to file 'aih-tih-sc-1d9134-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:54] Writing discarded fusions to file 'aih-tih-sc-1d9134-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:19] Freeing resources
[2026-06-08T08:37:33] Done (elapsed time=00:09:21, CPU time=00:09:19, peak memory=12.5gb)