[2026-06-03T19:05:19] Launching Arriba 2.4.0
[2026-06-03T19:05:19] Loading assembly from 'ref_genome.fa' 
[2026-06-03T19:05:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T19:05:46] Reading chimeric alignments from 'aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=2026378)
[2026-06-03T19:07:09] Marking multi-mapping alignments (marked=1547020)
[2026-06-03T19:07:10] Detecting strandedness (no)
[2026-06-03T19:07:10] Annotating alignments 
[2026-06-03T19:07:22] Filtering duplicates (remaining=695583)
[2026-06-03T19:07:24] 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=594393)
[2026-06-03T19:07:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=594393)
[2026-06-03T19:07:25] Filtering viral contigs with expression lower than the top 5 (remaining=594393)
[2026-06-03T19:07:26] Filtering viral contigs with less than 5% coverage (remaining=594393)
[2026-06-03T19:07:27] Estimating fragment length (mate gap mean=-72.2092, mate gap stddev=27.4851, read length mean=105.762)
[2026-06-03T19:07:27] Filtering read-through fragments with a distance <=10000bp (remaining=575125)
[2026-06-03T19:07:27] Filtering inconsistently clipped mates (remaining=553517)
[2026-06-03T19:07:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=519915)
[2026-06-03T19:07:28] Filtering fragments with small insert size (remaining=519328)
[2026-06-03T19:07:29] Filtering alignments with long gaps (remaining=519328)
[2026-06-03T19:07:29] Filtering fragments with both mates in the same gene (remaining=518886)
[2026-06-03T19:07:30] Filtering fusions arising from hairpin structures (remaining=478856)
[2026-06-03T19:07:30] Filtering reads with a mismatch p-value <=0.01 (remaining=127366)
[2026-06-03T19:07:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=59059)
[2026-06-03T19:07:34] Finding fusions and counting supporting reads (total=59942)
[2026-06-03T19:07:38] Merging adjacent fusion breakpoints (remaining=59668)
[2026-06-03T19:07:38] Filtering multi-mapping fusions by alignment score and read support (remaining=27031)
[2026-06-03T19:07:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T19:07:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=26777)
[2026-06-03T19:07:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=18187)
[2026-06-03T19:07:49] Filtering fusions with <2 supporting reads (remaining=637)
[2026-06-03T19:07:50] Filtering fusions with an e-value >=0.3 (remaining=261)
[2026-06-03T19:07:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=274)
[2026-06-03T19:07:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=253)
[2026-06-03T19:07:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=253)
[2026-06-03T19:07:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=240)
[2026-06-03T19:07:52] Searching for fusions with spliced split reads (remaining=251)
[2026-06-03T19:07:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=193)
[2026-06-03T19:07:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=190)
[2026-06-03T19:07:54] Searching for fusions with >=4 spliced events (remaining=190)
[2026-06-03T19:07:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=61)
[2026-06-03T19:08:20] Filtering fusions with anchors <=23nt (remaining=51)
[2026-06-03T19:08:20] Filtering end-to-end fusions with low support (remaining=44)
[2026-06-03T19:08:20] Filtering fusions with no coverage around the breakpoints (remaining=41)
[2026-06-03T19:08:20] Indexing gene sequences 
[2026-06-03T19:08:21] Filtering genes with >=30% identity (remaining=8)
[2026-06-03T19:08:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-06-03T19:08:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-06-03T19:08:22] Searching for additional isoforms (remaining=3)
[2026-06-03T19:08:22] Assigning confidence scores to events 
[2026-06-03T19:08:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T19:08:23] Writing fusions to file 'aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T19:08:23] Writing discarded fusions to file 'aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T19:08:30] Freeing resources
[2026-06-03T19:08:35] Done (elapsed time=00:03:16, CPU time=00:03:15, peak memory=6.18gb)