[2026-06-08T08:46:25] Launching Arriba 2.4.0
[2026-06-08T08:46:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:44] Reading chimeric alignments from 'tih_rna_sample_00163_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=9637252)
[2026-06-08T08:54:41] Marking multi-mapping alignments (marked=6046437)
[2026-06-08T08:54:45] Detecting strandedness (reverse)
[2026-06-08T08:54:45] Assigning strands to alignments 
[2026-06-08T08:54:47] Annotating alignments 
[2026-06-08T08:55:20] Filtering duplicates (remaining=5142494)
[2026-06-08T08:55:26] 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=4965394)
[2026-06-08T08:55:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4965394)
[2026-06-08T08:55:30] Filtering viral contigs with expression lower than the top 5 (remaining=4965394)
[2026-06-08T08:55:35] Filtering viral contigs with less than 5% coverage (remaining=4965394)
[2026-06-08T08:55:37] Estimating fragment length (mate gap mean=-86.5065, mate gap stddev=28.9956, read length mean=133.298)
[2026-06-08T08:55:37] Filtering read-through fragments with a distance <=10000bp (remaining=4653263)
[2026-06-08T08:55:39] Filtering inconsistently clipped mates (remaining=4583952)
[2026-06-08T08:55:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4454970)
[2026-06-08T08:55:46] Filtering fragments with small insert size (remaining=4454248)
[2026-06-08T08:55:48] Filtering alignments with long gaps (remaining=4454248)
[2026-06-08T08:55:50] Filtering fragments with both mates in the same gene (remaining=4453317)
[2026-06-08T08:55:52] Filtering fusions arising from hairpin structures (remaining=4225481)
[2026-06-08T08:55:54] Filtering reads with a mismatch p-value <=0.01 (remaining=1898757)
[2026-06-08T08:56:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=787933)
[2026-06-08T08:56:15] Finding fusions and counting supporting reads (total=633866)
[2026-06-08T08:56:31] Merging adjacent fusion breakpoints (remaining=628265)
[2026-06-08T08:56:32] Filtering multi-mapping fusions by alignment score and read support (remaining=394587)
[2026-06-08T08:57:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=392119)
[2026-06-08T08:57:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=209067)
[2026-06-08T08:57:14] Filtering fusions with <2 supporting reads (remaining=28881)
[2026-06-08T08:57:15] Filtering fusions with an e-value >=0.3 (remaining=10038)
[2026-06-08T08:57:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10076)
[2026-06-08T08:57:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10009)
[2026-06-08T08:57:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10009)
[2026-06-08T08:57:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6331)
[2026-06-08T08:57:25] Searching for fusions with spliced split reads (remaining=6458)
[2026-06-08T08:57:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=3972)
[2026-06-08T08:57:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3922)
[2026-06-08T08:57:31] Searching for fusions with >=4 spliced events (remaining=4559)
[2026-06-08T08:57:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1736)
[2026-06-08T08:57:46] Filtering fusions with anchors <=23nt (remaining=1470)
[2026-06-08T08:57:47] Filtering end-to-end fusions with low support (remaining=1418)
[2026-06-08T08:57:47] Filtering fusions with no coverage around the breakpoints (remaining=1380)
[2026-06-08T08:57:48] Indexing gene sequences 
[2026-06-08T08:57:54] Filtering genes with >=30% identity (remaining=439)
[2026-06-08T08:57:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=184)
[2026-06-08T08:58:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=168)
[2026-06-08T08:58:12] Searching for additional isoforms (remaining=232)
[2026-06-08T08:58:13] Assigning confidence scores to events 
[2026-06-08T08:58:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:16] Writing fusions to file 'tih_rna_sample_00163_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:58:18] Writing discarded fusions to file 'tih_rna_sample_00163_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:45] Freeing resources
[2026-06-08T08:59:01] Done (elapsed time=00:12:36, CPU time=00:12:34, peak memory=14.1gb)