[2026-06-08T08:50:42] Launching Arriba 2.4.0
[2026-06-08T08:50:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:56] Reading chimeric alignments from 'aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10263574)
[2026-06-08T08:58:28] Marking multi-mapping alignments (marked=6796664)
[2026-06-08T08:58:33] Detecting strandedness (reverse)
[2026-06-08T08:58:33] Assigning strands to alignments 
[2026-06-08T08:58:35] Annotating alignments 
[2026-06-08T08:59:12] Filtering duplicates (remaining=6975293)
[2026-06-08T08:59:20] 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=6668109)
[2026-06-08T08:59:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6668109)
[2026-06-08T08:59:25] Filtering viral contigs with expression lower than the top 5 (remaining=6668109)
[2026-06-08T08:59:30] Filtering viral contigs with less than 5% coverage (remaining=6668109)
[2026-06-08T08:59:33] Estimating fragment length (mate gap mean=-83.0392, mate gap stddev=29.7986, read length mean=130.574)
[2026-06-08T08:59:33] Filtering read-through fragments with a distance <=10000bp (remaining=6214032)
[2026-06-08T08:59:35] Filtering inconsistently clipped mates (remaining=6102763)
[2026-06-08T08:59:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5961729)
[2026-06-08T08:59:42] Filtering fragments with small insert size (remaining=5960814)
[2026-06-08T08:59:45] Filtering alignments with long gaps (remaining=5960814)
[2026-06-08T08:59:47] Filtering fragments with both mates in the same gene (remaining=5959734)
[2026-06-08T08:59:50] Filtering fusions arising from hairpin structures (remaining=5543707)
[2026-06-08T08:59:53] Filtering reads with a mismatch p-value <=0.01 (remaining=2579829)
[2026-06-08T09:00:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=1218428)
[2026-06-08T09:00:21] Finding fusions and counting supporting reads (total=894816)
[2026-06-08T09:00:41] Merging adjacent fusion breakpoints (remaining=885052)
[2026-06-08T09:00:43] Filtering multi-mapping fusions by alignment score and read support (remaining=551586)
[2026-06-08T09:01:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=548777)
[2026-06-08T09:01:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=320708)
[2026-06-08T09:01:35] Filtering fusions with <2 supporting reads (remaining=36801)
[2026-06-08T09:01:36] Filtering fusions with an e-value >=0.3 (remaining=10465)
[2026-06-08T09:01:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10527)
[2026-06-08T09:01:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10454)
[2026-06-08T09:01:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10454)
[2026-06-08T09:01:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8242)
[2026-06-08T09:01:51] Searching for fusions with spliced split reads (remaining=8368)
[2026-06-08T09:01:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=4567)
[2026-06-08T09:01:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4522)
[2026-06-08T09:01:59] Searching for fusions with >=4 spliced events (remaining=5329)
[2026-06-08T09:02:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1825)
[2026-06-08T09:02:16] Filtering fusions with anchors <=23nt (remaining=1423)
[2026-06-08T09:02:17] Filtering end-to-end fusions with low support (remaining=1397)
[2026-06-08T09:02:18] Filtering fusions with no coverage around the breakpoints (remaining=1365)
[2026-06-08T09:02:19] Indexing gene sequences 
[2026-06-08T09:02:25] Filtering genes with >=30% identity (remaining=431)
[2026-06-08T09:02:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=168)
[2026-06-08T09:02:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=157)
[2026-06-08T09:02:33] Searching for additional isoforms (remaining=204)
[2026-06-08T09:02:34] Assigning confidence scores to events 
[2026-06-08T09:02:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:38] Writing fusions to file 'aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:02:40] Writing discarded fusions to file 'aih-tih-sc-e08fa3-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:15] Freeing resources
[2026-06-08T09:03:33] Done (elapsed time=00:12:51, CPU time=00:12:50, peak memory=14.8gb)