[2026-06-08T08:37:35] Launching Arriba 2.4.0
[2026-06-08T08:37:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:48] Reading chimeric alignments from 'tih_rna_sample_00736_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12689776)
[2026-06-08T08:44:50] Marking multi-mapping alignments (marked=8585602)
[2026-06-08T08:44:56] Detecting strandedness (reverse)
[2026-06-08T08:44:56] Assigning strands to alignments 
[2026-06-08T08:44:58] Annotating alignments 
[2026-06-08T08:45:39] Filtering duplicates (remaining=6931004)
[2026-06-08T08:45:47] 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=6534349)
[2026-06-08T08:45:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6534349)
[2026-06-08T08:45:53] Filtering viral contigs with expression lower than the top 5 (remaining=6534349)
[2026-06-08T08:45:58] Filtering viral contigs with less than 5% coverage (remaining=6534349)
[2026-06-08T08:46:01] Estimating fragment length (mate gap mean=-87.9229, mate gap stddev=28.7325, read length mean=130.568)
[2026-06-08T08:46:01] Filtering read-through fragments with a distance <=10000bp (remaining=6141948)
[2026-06-08T08:46:04] Filtering inconsistently clipped mates (remaining=6037914)
[2026-06-08T08:46:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5905359)
[2026-06-08T08:46:12] Filtering fragments with small insert size (remaining=5904616)
[2026-06-08T08:46:15] Filtering alignments with long gaps (remaining=5904616)
[2026-06-08T08:46:18] Filtering fragments with both mates in the same gene (remaining=5903718)
[2026-06-08T08:46:20] Filtering fusions arising from hairpin structures (remaining=5554700)
[2026-06-08T08:46:23] Filtering reads with a mismatch p-value <=0.01 (remaining=2492803)
[2026-06-08T08:46:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=843706)
[2026-06-08T08:46:50] Finding fusions and counting supporting reads (total=655382)
[2026-06-08T08:47:09] Merging adjacent fusion breakpoints (remaining=648148)
[2026-06-08T08:47:11] Filtering multi-mapping fusions by alignment score and read support (remaining=377477)
[2026-06-08T08:47:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=375832)
[2026-06-08T08:48:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=211511)
[2026-06-08T08:48:02] Filtering fusions with <2 supporting reads (remaining=25400)
[2026-06-08T08:48:03] Filtering fusions with an e-value >=0.3 (remaining=6957)
[2026-06-08T08:48:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7006)
[2026-06-08T08:48:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6896)
[2026-06-08T08:48:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6896)
[2026-06-08T08:48:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6228)
[2026-06-08T08:48:17] Searching for fusions with spliced split reads (remaining=6321)
[2026-06-08T08:48:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=4138)
[2026-06-08T08:48:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4104)
[2026-06-08T08:48:25] Searching for fusions with >=4 spliced events (remaining=4736)
[2026-06-08T08:48:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1922)
[2026-06-08T08:48:43] Filtering fusions with anchors <=23nt (remaining=1378)
[2026-06-08T08:48:44] Filtering end-to-end fusions with low support (remaining=1308)
[2026-06-08T08:48:45] Filtering fusions with no coverage around the breakpoints (remaining=1272)
[2026-06-08T08:48:45] Indexing gene sequences 
[2026-06-08T08:48:51] Filtering genes with >=30% identity (remaining=411)
[2026-06-08T08:48:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=173)
[2026-06-08T08:48:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=167)
[2026-06-08T08:48:58] Searching for additional isoforms (remaining=203)
[2026-06-08T08:49:00] Assigning confidence scores to events 
[2026-06-08T08:49:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:04] Writing fusions to file 'tih_rna_sample_00736_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:05] Writing discarded fusions to file 'tih_rna_sample_00736_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:36] Freeing resources
[2026-06-08T08:49:56] Done (elapsed time=00:12:21, CPU time=00:12:19, peak memory=17.3gb)