[2026-06-08T08:21:38] Launching Arriba 2.4.0
[2026-06-08T08:21:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:21:54] Reading chimeric alignments from 'tih_rna_sample_00121_23H5VFLT4_s41.Aligned.sortedByCoord.out.bam' (total=14370406)
[2026-06-08T08:28:59] Marking multi-mapping alignments (marked=10378020)
[2026-06-08T08:29:04] Detecting strandedness (reverse)
[2026-06-08T08:29:04] Assigning strands to alignments 
[2026-06-08T08:29:07] Annotating alignments 
[2026-06-08T08:29:50] Filtering duplicates (remaining=7776608)
[2026-06-08T08:29:59] 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=7016753)
[2026-06-08T08:30:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7016753)
[2026-06-08T08:30:04] Filtering viral contigs with expression lower than the top 5 (remaining=7016753)
[2026-06-08T08:30:10] Filtering viral contigs with less than 5% coverage (remaining=7016753)
[2026-06-08T08:30:13] Estimating fragment length (mate gap mean=-82.1485, mate gap stddev=29.4678, read length mean=120.328)
[2026-06-08T08:30:13] Filtering read-through fragments with a distance <=10000bp (remaining=6647446)
[2026-06-08T08:30:15] Filtering inconsistently clipped mates (remaining=6453643)
[2026-06-08T08:30:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5654238)
[2026-06-08T08:30:24] Filtering fragments with small insert size (remaining=5651169)
[2026-06-08T08:30:27] Filtering alignments with long gaps (remaining=5651168)
[2026-06-08T08:30:30] Filtering fragments with both mates in the same gene (remaining=5649220)
[2026-06-08T08:30:32] Filtering fusions arising from hairpin structures (remaining=5126357)
[2026-06-08T08:30:35] Filtering reads with a mismatch p-value <=0.01 (remaining=1916363)
[2026-06-08T08:30:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=1253936)
[2026-06-08T08:31:00] Finding fusions and counting supporting reads (total=1060582)
[2026-06-08T08:31:21] Merging adjacent fusion breakpoints (remaining=1054194)
[2026-06-08T08:31:23] Filtering multi-mapping fusions by alignment score and read support (remaining=538890)
[2026-06-08T08:32:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=535973)
[2026-06-08T08:32:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=385442)
[2026-06-08T08:32:12] Filtering fusions with <2 supporting reads (remaining=30669)
[2026-06-08T08:32:13] Filtering fusions with an e-value >=0.3 (remaining=5680)
[2026-06-08T08:32:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5785)
[2026-06-08T08:32:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5423)
[2026-06-08T08:32:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5423)
[2026-06-08T08:32:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5091)
[2026-06-08T08:32:28] Searching for fusions with spliced split reads (remaining=5207)
[2026-06-08T08:32:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=3728)
[2026-06-08T08:32:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3683)
[2026-06-08T08:32:37] Searching for fusions with >=4 spliced events (remaining=4364)
[2026-06-08T08:32:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1609)
[2026-06-08T08:32:53] Filtering fusions with anchors <=23nt (remaining=1322)
[2026-06-08T08:32:54] Filtering end-to-end fusions with low support (remaining=1290)
[2026-06-08T08:32:54] Filtering fusions with no coverage around the breakpoints (remaining=1269)
[2026-06-08T08:32:55] Indexing gene sequences 
[2026-06-08T08:33:01] Filtering genes with >=30% identity (remaining=417)
[2026-06-08T08:33:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-08T08:33:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=180)
[2026-06-08T08:33:09] Searching for additional isoforms (remaining=220)
[2026-06-08T08:33:11] Assigning confidence scores to events 
[2026-06-08T08:33:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:15] Writing fusions to file 'tih_rna_sample_00121_23H5VFLT4_s41.arriba.fusions.tsv' 
[2026-06-08T08:33:17] Writing discarded fusions to file 'tih_rna_sample_00121_23H5VFLT4_s41.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:53] Freeing resources
[2026-06-08T08:34:15] Done (elapsed time=00:12:37, CPU time=00:12:35, peak memory=20.1gb)