[2026-06-08T08:20:36] Launching Arriba 2.4.0
[2026-06-08T08:20:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:49] Reading chimeric alignments from 'tih_rna_sample_00116_23H5VFLT4_s36.Aligned.sortedByCoord.out.bam' (total=12016436)
[2026-06-08T08:27:44] Marking multi-mapping alignments (marked=8055841)
[2026-06-08T08:27:50] Detecting strandedness (reverse)
[2026-06-08T08:27:50] Assigning strands to alignments 
[2026-06-08T08:27:52] Annotating alignments 
[2026-06-08T08:28:38] Filtering duplicates (remaining=7154389)
[2026-06-08T08:28:46] 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=6555548)
[2026-06-08T08:28:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6555548)
[2026-06-08T08:28:51] Filtering viral contigs with expression lower than the top 5 (remaining=6555548)
[2026-06-08T08:28:57] Filtering viral contigs with less than 5% coverage (remaining=6555548)
[2026-06-08T08:28:59] Estimating fragment length (mate gap mean=-83.2216, mate gap stddev=28.3717, read length mean=120.006)
[2026-06-08T08:28:59] Filtering read-through fragments with a distance <=10000bp (remaining=6043129)
[2026-06-08T08:29:02] Filtering inconsistently clipped mates (remaining=5894474)
[2026-06-08T08:29:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5392067)
[2026-06-08T08:29:11] Filtering fragments with small insert size (remaining=5389364)
[2026-06-08T08:29:13] Filtering alignments with long gaps (remaining=5389364)
[2026-06-08T08:29:16] Filtering fragments with both mates in the same gene (remaining=5387505)
[2026-06-08T08:29:18] Filtering fusions arising from hairpin structures (remaining=5018418)
[2026-06-08T08:29:21] Filtering reads with a mismatch p-value <=0.01 (remaining=1910808)
[2026-06-08T08:29:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=1292965)
[2026-06-08T08:29:46] Finding fusions and counting supporting reads (total=1106987)
[2026-06-08T08:30:08] Merging adjacent fusion breakpoints (remaining=1097420)
[2026-06-08T08:30:10] Filtering multi-mapping fusions by alignment score and read support (remaining=601746)
[2026-06-08T08:30:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:31:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=599547)
[2026-06-08T08:31:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=384532)
[2026-06-08T08:31:03] Filtering fusions with <2 supporting reads (remaining=33286)
[2026-06-08T08:31:04] Filtering fusions with an e-value >=0.3 (remaining=6475)
[2026-06-08T08:31:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6537)
[2026-06-08T08:31:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6293)
[2026-06-08T08:31:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6295)
[2026-06-08T08:31:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6185)
[2026-06-08T08:31:19] Searching for fusions with spliced split reads (remaining=6266)
[2026-06-08T08:31:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=4449)
[2026-06-08T08:31:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4389)
[2026-06-08T08:31:29] Searching for fusions with >=4 spliced events (remaining=5304)
[2026-06-08T08:31:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2332)
[2026-06-08T08:31:48] Filtering fusions with anchors <=23nt (remaining=1789)
[2026-06-08T08:31:48] Filtering end-to-end fusions with low support (remaining=1739)
[2026-06-08T08:31:49] Filtering fusions with no coverage around the breakpoints (remaining=1721)
[2026-06-08T08:31:50] Indexing gene sequences 
[2026-06-08T08:31:57] Filtering genes with >=30% identity (remaining=526)
[2026-06-08T08:31:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=153)
[2026-06-08T08:32:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=150)
[2026-06-08T08:32:04] Searching for additional isoforms (remaining=183)
[2026-06-08T08:32:06] Assigning confidence scores to events 
[2026-06-08T08:32:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:11] Writing fusions to file 'tih_rna_sample_00116_23H5VFLT4_s36.arriba.fusions.tsv' 
[2026-06-08T08:32:12] Writing discarded fusions to file 'tih_rna_sample_00116_23H5VFLT4_s36.arriba.fusions.discarded.tsv'
[2026-06-08T08:32:52] Freeing resources
[2026-06-08T08:33:14] Done (elapsed time=00:12:38, CPU time=00:12:36, peak memory=17.4gb)