[2026-06-03T19:06:05] Launching Arriba 2.4.0
[2026-06-03T19:06:05] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:06:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:06:30] Reading chimeric alignments from 'aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=2363022)
[2026-06-03T19:08:10] Marking multi-mapping alignments (marked=1780169)
[2026-06-03T19:08:11] Detecting strandedness (reverse)
[2026-06-03T19:08:11] Assigning strands to alignments 
[2026-06-03T19:08:12] Annotating alignments 
[2026-06-03T19:08:24] Filtering duplicates (remaining=901733)
[2026-06-03T19:08:26] 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=752075)
[2026-06-03T19:08:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=752075)
[2026-06-03T19:08:27] Filtering viral contigs with expression lower than the top 5 (remaining=752075)
[2026-06-03T19:08:28] Filtering viral contigs with less than 5% coverage (remaining=752075)
[2026-06-03T19:08:29] Estimating fragment length (mate gap mean=-66.668, mate gap stddev=27.3578, read length mean=98.1693)
[2026-06-03T19:08:30] Filtering read-through fragments with a distance <=10000bp (remaining=724453)
[2026-06-03T19:08:30] Filtering inconsistently clipped mates (remaining=703289)
[2026-06-03T19:08:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=670570)
[2026-06-03T19:08:32] Filtering fragments with small insert size (remaining=669796)
[2026-06-03T19:08:32] Filtering alignments with long gaps (remaining=669796)
[2026-06-03T19:08:33] Filtering fragments with both mates in the same gene (remaining=669360)
[2026-06-03T19:08:33] Filtering fusions arising from hairpin structures (remaining=633832)
[2026-06-03T19:08:34] Filtering reads with a mismatch p-value <=0.01 (remaining=130511)
[2026-06-03T19:08:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=47772)
[2026-06-03T19:08:37] Finding fusions and counting supporting reads (total=49030)
[2026-06-03T19:08:42] Merging adjacent fusion breakpoints (remaining=48573)
[2026-06-03T19:08:43] Filtering multi-mapping fusions by alignment score and read support (remaining=26731)
[2026-06-03T19:08:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:08:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=26458)
[2026-06-03T19:08:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17186)
[2026-06-03T19:08:55] Filtering fusions with <2 supporting reads (remaining=956)
[2026-06-03T19:08:55] Filtering fusions with an e-value >=0.3 (remaining=364)
[2026-06-03T19:08:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=373)
[2026-06-03T19:08:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=364)
[2026-06-03T19:08:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=364)
[2026-06-03T19:08:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=282)
[2026-06-03T19:08:58] Searching for fusions with spliced split reads (remaining=291)
[2026-06-03T19:09:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=241)
[2026-06-03T19:09:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=240)
[2026-06-03T19:09:01] Searching for fusions with >=4 spliced events (remaining=243)
[2026-06-03T19:09:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=67)
[2026-06-03T19:09:30] Filtering fusions with anchors <=23nt (remaining=23)
[2026-06-03T19:09:30] Filtering end-to-end fusions with low support (remaining=21)
[2026-06-03T19:09:30] Filtering fusions with no coverage around the breakpoints (remaining=19)
[2026-06-03T19:09:30] Indexing gene sequences 
[2026-06-03T19:09:30] Filtering genes with >=30% identity (remaining=11)
[2026-06-03T19:09:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-06-03T19:09:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-06-03T19:09:31] Searching for additional isoforms (remaining=3)
[2026-06-03T19:09:31] Assigning confidence scores to events 
[2026-06-03T19:09:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:09:33] Writing fusions to file 'aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:09:33] Writing discarded fusions to file 'aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:09:42] Freeing resources
[2026-06-03T19:09:49] Done (elapsed time=00:03:44, CPU time=00:03:42, peak memory=6.53gb)