[2026-06-08T08:19:58] Launching Arriba 2.4.0
[2026-06-08T08:19:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:14] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:18] Reading chimeric alignments from 'aih-tih-sc-f39d87-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=9558169)
[2026-06-08T08:26:44] Marking multi-mapping alignments (marked=6465866)
[2026-06-08T08:26:48] Detecting strandedness (reverse)
[2026-06-08T08:26:48] Assigning strands to alignments 
[2026-06-08T08:26:50] Annotating alignments 
[2026-06-08T08:27:22] Filtering duplicates (remaining=5408324)
[2026-06-08T08:27:29] 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=5130434)
[2026-06-08T08:27:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5130434)
[2026-06-08T08:27:32] Filtering viral contigs with expression lower than the top 5 (remaining=5130434)
[2026-06-08T08:27:37] Filtering viral contigs with less than 5% coverage (remaining=5130434)
[2026-06-08T08:27:39] Estimating fragment length (mate gap mean=-83.8387, mate gap stddev=27.1436, read length mean=123.307)
[2026-06-08T08:27:39] Filtering read-through fragments with a distance <=10000bp (remaining=4867595)
[2026-06-08T08:27:41] Filtering inconsistently clipped mates (remaining=4801232)
[2026-06-08T08:27:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4695706)
[2026-06-08T08:27:47] Filtering fragments with small insert size (remaining=4695123)
[2026-06-08T08:27:49] Filtering alignments with long gaps (remaining=4695123)
[2026-06-08T08:27:51] Filtering fragments with both mates in the same gene (remaining=4694244)
[2026-06-08T08:27:53] Filtering fusions arising from hairpin structures (remaining=4528202)
[2026-06-08T08:27:55] Filtering reads with a mismatch p-value <=0.01 (remaining=2072714)
[2026-06-08T08:28:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=723835)
[2026-06-08T08:28:15] Finding fusions and counting supporting reads (total=554121)
[2026-06-08T08:28:31] Merging adjacent fusion breakpoints (remaining=547091)
[2026-06-08T08:28:32] Filtering multi-mapping fusions by alignment score and read support (remaining=316899)
[2026-06-08T08:29:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:29:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=315885)
[2026-06-08T08:29:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=198315)
[2026-06-08T08:29:10] Filtering fusions with <2 supporting reads (remaining=21878)
[2026-06-08T08:29:11] Filtering fusions with an e-value >=0.3 (remaining=5063)
[2026-06-08T08:29:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5106)
[2026-06-08T08:29:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5013)
[2026-06-08T08:29:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5013)
[2026-06-08T08:29:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4723)
[2026-06-08T08:29:21] Searching for fusions with spliced split reads (remaining=4798)
[2026-06-08T08:29:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=3282)
[2026-06-08T08:29:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3255)
[2026-06-08T08:29:27] Searching for fusions with >=4 spliced events (remaining=3777)
[2026-06-08T08:29:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1560)
[2026-06-08T08:29:47] Filtering fusions with anchors <=23nt (remaining=1328)
[2026-06-08T08:29:48] Filtering end-to-end fusions with low support (remaining=1290)
[2026-06-08T08:29:49] Filtering fusions with no coverage around the breakpoints (remaining=1274)
[2026-06-08T08:29:49] Indexing gene sequences 
[2026-06-08T08:29:55] Filtering genes with >=30% identity (remaining=348)
[2026-06-08T08:29:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=107)
[2026-06-08T08:29:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=106)
[2026-06-08T08:30:01] Searching for additional isoforms (remaining=142)
[2026-06-08T08:30:02] Assigning confidence scores to events 
[2026-06-08T08:30:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:05] Writing fusions to file 'aih-tih-sc-f39d87-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:30:07] Writing discarded fusions to file 'aih-tih-sc-f39d87-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:38] Freeing resources
[2026-06-08T08:30:55] Done (elapsed time=00:10:57, CPU time=00:10:55, peak memory=13.8gb)