[2026-06-08T07:43:46] Launching Arriba 2.4.0
[2026-06-08T07:43:46] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:43:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:44:04] Reading chimeric alignments from 'aih-tih-sc-331e97-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=82448)
[2026-06-08T07:44:05] Marking multi-mapping alignments (marked=67849)
[2026-06-08T07:44:05] Detecting strandedness (no)
[2026-06-08T07:44:05] Annotating alignments 
[2026-06-08T07:44:06] Filtering duplicates (remaining=29486)
[2026-06-08T07:44:06] 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=22764)
[2026-06-08T07:44:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=22764)
[2026-06-08T07:44:06] Filtering viral contigs with expression lower than the top 5 (remaining=22764)
[2026-06-08T07:44:06] Filtering viral contigs with less than 5% coverage (remaining=22764)
[2026-06-08T07:44:06] Estimating fragment length (mate gap mean=-56.4294, mate gap stddev=27.3706, read length mean=93.2857)
[2026-06-08T07:44:06] Filtering read-through fragments with a distance <=10000bp (remaining=22366)
[2026-06-08T07:44:06] Filtering inconsistently clipped mates (remaining=20600)
[2026-06-08T07:44:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=20043)
[2026-06-08T07:44:06] Filtering fragments with small insert size (remaining=19980)
[2026-06-08T07:44:06] Filtering alignments with long gaps (remaining=19980)
[2026-06-08T07:44:06] Filtering fragments with both mates in the same gene (remaining=19909)
[2026-06-08T07:44:06] Filtering fusions arising from hairpin structures (remaining=17259)
[2026-06-08T07:44:06] Filtering reads with a mismatch p-value <=0.01 (remaining=4399)
[2026-06-08T07:44:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=1439)
[2026-06-08T07:44:07] Finding fusions and counting supporting reads (total=1487)
[2026-06-08T07:44:07] Merging adjacent fusion breakpoints (remaining=1477)
[2026-06-08T07:44:07] Filtering multi-mapping fusions by alignment score and read support (remaining=616)
[2026-06-08T07:44:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:44:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=600)
[2026-06-08T07:44:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=345)
[2026-06-08T07:44:07] Filtering fusions with <2 supporting reads (remaining=14)
[2026-06-08T07:44:07] Filtering fusions with an e-value >=0.3 (remaining=5)
[2026-06-08T07:44:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5)
[2026-06-08T07:44:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5)
[2026-06-08T07:44:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5)
[2026-06-08T07:44:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4)
[2026-06-08T07:44:07] Searching for fusions with spliced split reads (remaining=4)
[2026-06-08T07:44:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=4)
[2026-06-08T07:44:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4)
[2026-06-08T07:44:07] Searching for fusions with >=4 spliced events (remaining=4)
[2026-06-08T07:44:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1)
[2026-06-08T07:44:22] Filtering fusions with anchors <=23nt (remaining=1)
[2026-06-08T07:44:22] Filtering end-to-end fusions with low support (remaining=1)
[2026-06-08T07:44:22] Filtering fusions with no coverage around the breakpoints (remaining=1)
[2026-06-08T07:44:22] Indexing gene sequences 
[2026-06-08T07:44:22] Filtering genes with >=30% identity (remaining=0)
[2026-06-08T07:44:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:44:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:44:22] Searching for additional isoforms (remaining=0)
[2026-06-08T07:44:22] Assigning confidence scores to events 
[2026-06-08T07:44:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:44:22] Writing fusions to file 'aih-tih-sc-331e97-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:44:22] Writing discarded fusions to file 'aih-tih-sc-331e97-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:44:23] Freeing resources
[2026-06-08T07:44:23] Done (elapsed time=00:00:37, CPU time=00:00:37, peak memory=4.15gb)