[2026-06-08T08:49:37] Launching Arriba 2.4.0
[2026-06-08T08:49:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:52] Reading chimeric alignments from 'aih-tih-sc-51ee59-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10026602)
[2026-06-08T08:56:41] Marking multi-mapping alignments (marked=6214803)
[2026-06-08T08:56:45] Detecting strandedness (reverse)
[2026-06-08T08:56:45] Assigning strands to alignments 
[2026-06-08T08:56:46] Annotating alignments 
[2026-06-08T08:57:19] Filtering duplicates (remaining=6569286)
[2026-06-08T08:57:27] 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=6339790)
[2026-06-08T08:57:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6339790)
[2026-06-08T08:57:30] Filtering viral contigs with expression lower than the top 5 (remaining=6339790)
[2026-06-08T08:57:35] Filtering viral contigs with less than 5% coverage (remaining=6339790)
[2026-06-08T08:57:37] Estimating fragment length (mate gap mean=-87.8697, mate gap stddev=29.688, read length mean=135.837)
[2026-06-08T08:57:37] Filtering read-through fragments with a distance <=10000bp (remaining=6009781)
[2026-06-08T08:57:39] Filtering inconsistently clipped mates (remaining=5940648)
[2026-06-08T08:57:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5808366)
[2026-06-08T08:57:45] Filtering fragments with small insert size (remaining=5807957)
[2026-06-08T08:57:47] Filtering alignments with long gaps (remaining=5807956)
[2026-06-08T08:57:49] Filtering fragments with both mates in the same gene (remaining=5806798)
[2026-06-08T08:57:52] Filtering fusions arising from hairpin structures (remaining=5598452)
[2026-06-08T08:57:54] Filtering reads with a mismatch p-value <=0.01 (remaining=2849235)
[2026-06-08T08:58:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=980462)
[2026-06-08T08:58:20] Finding fusions and counting supporting reads (total=671388)
[2026-06-08T08:58:36] Merging adjacent fusion breakpoints (remaining=664697)
[2026-06-08T08:58:38] Filtering multi-mapping fusions by alignment score and read support (remaining=433678)
[2026-06-08T08:59:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=431565)
[2026-06-08T08:59:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=256803)
[2026-06-08T08:59:19] Filtering fusions with <2 supporting reads (remaining=36676)
[2026-06-08T08:59:20] Filtering fusions with an e-value >=0.3 (remaining=10842)
[2026-06-08T08:59:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10888)
[2026-06-08T08:59:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10798)
[2026-06-08T08:59:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10798)
[2026-06-08T08:59:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8724)
[2026-06-08T08:59:31] Searching for fusions with spliced split reads (remaining=8745)
[2026-06-08T08:59:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=5205)
[2026-06-08T08:59:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5141)
[2026-06-08T08:59:39] Searching for fusions with >=4 spliced events (remaining=6073)
[2026-06-08T08:59:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2064)
[2026-06-08T08:59:57] Filtering fusions with anchors <=23nt (remaining=1649)
[2026-06-08T08:59:58] Filtering end-to-end fusions with low support (remaining=1606)
[2026-06-08T08:59:59] Filtering fusions with no coverage around the breakpoints (remaining=1567)
[2026-06-08T09:00:00] Indexing gene sequences 
[2026-06-08T09:00:07] Filtering genes with >=30% identity (remaining=536)
[2026-06-08T09:00:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=281)
[2026-06-08T09:00:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=247)
[2026-06-08T09:00:20] Searching for additional isoforms (remaining=313)
[2026-06-08T09:00:21] Assigning confidence scores to events 
[2026-06-08T09:00:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:25] Writing fusions to file 'aih-tih-sc-51ee59-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:27] Writing discarded fusions to file 'aih-tih-sc-51ee59-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:56] Freeing resources
[2026-06-08T09:01:12] Done (elapsed time=00:11:35, CPU time=00:11:33, peak memory=14.3gb)