[2026-06-08T09:36:31] Launching Arriba 2.4.0
[2026-06-08T09:36:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:36:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:36:43] Reading chimeric alignments from 'tih_rna_sample_00636_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11216570)
[2026-06-08T09:42:55] Marking multi-mapping alignments (marked=7214298)
[2026-06-08T09:42:59] Detecting strandedness (no)
[2026-06-08T09:42:59] Annotating alignments 
[2026-06-08T09:43:38] Filtering duplicates (remaining=6725711)
[2026-06-08T09:43:46] 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=6407699)
[2026-06-08T09:43:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6407699)
[2026-06-08T09:43:51] Filtering viral contigs with expression lower than the top 5 (remaining=6407699)
[2026-06-08T09:43:57] Filtering viral contigs with less than 5% coverage (remaining=6407699)
[2026-06-08T09:44:00] Estimating fragment length (mate gap mean=-86.3013, mate gap stddev=28.6589, read length mean=130.543)
[2026-06-08T09:44:00] Filtering read-through fragments with a distance <=10000bp (remaining=6076564)
[2026-06-08T09:44:03] Filtering inconsistently clipped mates (remaining=5956342)
[2026-06-08T09:44:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5807020)
[2026-06-08T09:44:09] Filtering fragments with small insert size (remaining=5806074)
[2026-06-08T09:44:11] Filtering alignments with long gaps (remaining=5806074)
[2026-06-08T09:44:14] Filtering fragments with both mates in the same gene (remaining=5804842)
[2026-06-08T09:44:16] Filtering fusions arising from hairpin structures (remaining=5406763)
[2026-06-08T09:44:19] Filtering reads with a mismatch p-value <=0.01 (remaining=2671050)
[2026-06-08T09:44:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=890033)
[2026-06-08T09:44:42] Finding fusions and counting supporting reads (total=680133)
[2026-06-08T09:44:57] Merging adjacent fusion breakpoints (remaining=672818)
[2026-06-08T09:44:59] Filtering multi-mapping fusions by alignment score and read support (remaining=412192)
[2026-06-08T09:45:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:45:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=410132)
[2026-06-08T09:45:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=218275)
[2026-06-08T09:45:42] Filtering fusions with <2 supporting reads (remaining=28033)
[2026-06-08T09:45:43] Filtering fusions with an e-value >=0.3 (remaining=8044)
[2026-06-08T09:45:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8104)
[2026-06-08T09:45:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7974)
[2026-06-08T09:45:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7974)
[2026-06-08T09:45:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6548)
[2026-06-08T09:45:57] Searching for fusions with spliced split reads (remaining=6666)
[2026-06-08T09:46:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=4300)
[2026-06-08T09:46:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4251)
[2026-06-08T09:46:05] Searching for fusions with >=4 spliced events (remaining=4950)
[2026-06-08T09:46:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1764)
[2026-06-08T09:46:21] Filtering fusions with anchors <=23nt (remaining=1451)
[2026-06-08T09:46:22] Filtering end-to-end fusions with low support (remaining=1407)
[2026-06-08T09:46:23] Filtering fusions with no coverage around the breakpoints (remaining=1367)
[2026-06-08T09:46:24] Indexing gene sequences 
[2026-06-08T09:46:30] Filtering genes with >=30% identity (remaining=399)
[2026-06-08T09:46:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=176)
[2026-06-08T09:46:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=171)
[2026-06-08T09:46:38] Searching for additional isoforms (remaining=196)
[2026-06-08T09:46:40] Assigning confidence scores to events 
[2026-06-08T09:46:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:46:44] Writing fusions to file 'tih_rna_sample_00636_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:46:45] Writing discarded fusions to file 'tih_rna_sample_00636_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:47:12] Freeing resources
[2026-06-08T09:47:30] Done (elapsed time=00:10:59, CPU time=00:10:59, peak memory=15.7gb)