[2026-06-08T08:44:29] Launching Arriba 2.4.0
[2026-06-08T08:44:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:52] Reading chimeric alignments from 'tih_rna_sample_00669_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11149275)
[2026-06-08T08:54:32] Marking multi-mapping alignments (marked=7320197)
[2026-06-08T08:54:37] Detecting strandedness (reverse)
[2026-06-08T08:54:37] Assigning strands to alignments 
[2026-06-08T08:54:40] Annotating alignments 
[2026-06-08T08:55:28] Filtering duplicates (remaining=6310843)
[2026-06-08T08:55:38] 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=5949234)
[2026-06-08T08:55:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5949234)
[2026-06-08T08:55:44] Filtering viral contigs with expression lower than the top 5 (remaining=5949234)
[2026-06-08T08:55:50] Filtering viral contigs with less than 5% coverage (remaining=5949234)
[2026-06-08T08:55:54] Estimating fragment length (mate gap mean=-87.6147, mate gap stddev=28.0835, read length mean=127.564)
[2026-06-08T08:55:54] Filtering read-through fragments with a distance <=10000bp (remaining=5606430)
[2026-06-08T08:55:57] Filtering inconsistently clipped mates (remaining=5484180)
[2026-06-08T08:56:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5349696)
[2026-06-08T08:56:06] Filtering fragments with small insert size (remaining=5348905)
[2026-06-08T08:56:09] Filtering alignments with long gaps (remaining=5348905)
[2026-06-08T08:56:13] Filtering fragments with both mates in the same gene (remaining=5347850)
[2026-06-08T08:56:16] Filtering fusions arising from hairpin structures (remaining=4985155)
[2026-06-08T08:56:20] Filtering reads with a mismatch p-value <=0.01 (remaining=2265197)
[2026-06-08T08:56:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=763073)
[2026-06-08T08:56:51] Finding fusions and counting supporting reads (total=608643)
[2026-06-08T08:57:23] Merging adjacent fusion breakpoints (remaining=602508)
[2026-06-08T08:57:25] Filtering multi-mapping fusions by alignment score and read support (remaining=364995)
[2026-06-08T08:58:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=363634)
[2026-06-08T08:58:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=202188)
[2026-06-08T08:58:30] Filtering fusions with <2 supporting reads (remaining=23036)
[2026-06-08T08:58:31] Filtering fusions with an e-value >=0.3 (remaining=5863)
[2026-06-08T08:58:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5918)
[2026-06-08T08:58:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5849)
[2026-06-08T08:58:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5850)
[2026-06-08T08:58:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5447)
[2026-06-08T08:58:47] Searching for fusions with spliced split reads (remaining=5570)
[2026-06-08T08:58:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=3758)
[2026-06-08T08:58:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3706)
[2026-06-08T08:58:57] Searching for fusions with >=4 spliced events (remaining=4437)
[2026-06-08T08:58:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2057)
[2026-06-08T08:59:21] Filtering fusions with anchors <=23nt (remaining=1611)
[2026-06-08T08:59:22] Filtering end-to-end fusions with low support (remaining=1560)
[2026-06-08T08:59:23] Filtering fusions with no coverage around the breakpoints (remaining=1526)
[2026-06-08T08:59:24] Indexing gene sequences 
[2026-06-08T08:59:36] Filtering genes with >=30% identity (remaining=503)
[2026-06-08T08:59:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=188)
[2026-06-08T08:59:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=174)
[2026-06-08T08:59:48] Searching for additional isoforms (remaining=217)
[2026-06-08T08:59:49] Assigning confidence scores to events 
[2026-06-08T08:59:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:55] Writing fusions to file 'tih_rna_sample_00669_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:59] Writing discarded fusions to file 'tih_rna_sample_00669_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:55] Freeing resources
[2026-06-08T09:01:33] Done (elapsed time=00:17:04, CPU time=00:17:02, peak memory=15.8gb)