[2026-06-08T07:44:45] Launching Arriba 2.4.0
[2026-06-08T07:44:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:44:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:44:59] Reading chimeric alignments from 'aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=235496)
[2026-06-08T07:45:04] Marking multi-mapping alignments (marked=186673)
[2026-06-08T07:45:05] Detecting strandedness (reverse)
[2026-06-08T07:45:05] Assigning strands to alignments 
[2026-06-08T07:45:05] Annotating alignments 
[2026-06-08T07:45:06] Filtering duplicates (remaining=84410)
[2026-06-08T07:45:06] 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=65687)
[2026-06-08T07:45:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=65687)
[2026-06-08T07:45:06] Filtering viral contigs with expression lower than the top 5 (remaining=65687)
[2026-06-08T07:45:06] Filtering viral contigs with less than 5% coverage (remaining=65687)
[2026-06-08T07:45:06] Estimating fragment length (mate gap mean=-64.911, mate gap stddev=28.4107, read length mean=102.141)
[2026-06-08T07:45:06] Filtering read-through fragments with a distance <=10000bp (remaining=63910)
[2026-06-08T07:45:06] Filtering inconsistently clipped mates (remaining=60782)
[2026-06-08T07:45:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=58536)
[2026-06-08T07:45:07] Filtering fragments with small insert size (remaining=58474)
[2026-06-08T07:45:07] Filtering alignments with long gaps (remaining=58474)
[2026-06-08T07:45:07] Filtering fragments with both mates in the same gene (remaining=58426)
[2026-06-08T07:45:07] Filtering fusions arising from hairpin structures (remaining=52091)
[2026-06-08T07:45:07] Filtering reads with a mismatch p-value <=0.01 (remaining=17193)
[2026-06-08T07:45:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=5941)
[2026-06-08T07:45:07] Finding fusions and counting supporting reads (total=5824)
[2026-06-08T07:45:07] Merging adjacent fusion breakpoints (remaining=5809)
[2026-06-08T07:45:07] Filtering multi-mapping fusions by alignment score and read support (remaining=2733)
[2026-06-08T07:45:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:45:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=2674)
[2026-06-08T07:45:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1628)
[2026-06-08T07:45:08] Filtering fusions with <2 supporting reads (remaining=55)
[2026-06-08T07:45:08] Filtering fusions with an e-value >=0.3 (remaining=35)
[2026-06-08T07:45:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=37)
[2026-06-08T07:45:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=35)
[2026-06-08T07:45:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=35)
[2026-06-08T07:45:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=32)
[2026-06-08T07:45:08] Searching for fusions with spliced split reads (remaining=32)
[2026-06-08T07:45:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=29)
[2026-06-08T07:45:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=27)
[2026-06-08T07:45:08] Searching for fusions with >=4 spliced events (remaining=27)
[2026-06-08T07:45:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6)
[2026-06-08T07:45:20] Filtering fusions with anchors <=23nt (remaining=6)
[2026-06-08T07:45:20] Filtering end-to-end fusions with low support (remaining=6)
[2026-06-08T07:45:20] Filtering fusions with no coverage around the breakpoints (remaining=6)
[2026-06-08T07:45:20] Indexing gene sequences 
[2026-06-08T07:45:20] Filtering genes with >=30% identity (remaining=4)
[2026-06-08T07:45:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=4)
[2026-06-08T07:45:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=4)
[2026-06-08T07:45:20] Searching for additional isoforms (remaining=4)
[2026-06-08T07:45:20] Assigning confidence scores to events 
[2026-06-08T07:45:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:45:20] Writing fusions to file 'aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:45:20] Writing discarded fusions to file 'aih-tih-sc-f2a1b0-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:45:21] Freeing resources
[2026-06-08T07:45:22] Done (elapsed time=00:00:37, CPU time=00:00:37, peak memory=4.31gb)