[2026-06-08T08:48:36] Launching Arriba 2.4.0
[2026-06-08T08:48:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:54] Reading chimeric alignments from 'tih_rna_sample_00671_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10821688)
[2026-06-08T08:56:25] Marking multi-mapping alignments (marked=6685784)
[2026-06-08T08:56:30] Detecting strandedness (reverse)
[2026-06-08T08:56:30] Assigning strands to alignments 
[2026-06-08T08:56:32] Annotating alignments 
[2026-06-08T08:57:08] Filtering duplicates (remaining=7599921)
[2026-06-08T08:57:16] 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=7256737)
[2026-06-08T08:57:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7256737)
[2026-06-08T08:57:20] Filtering viral contigs with expression lower than the top 5 (remaining=7256737)
[2026-06-08T08:57:25] Filtering viral contigs with less than 5% coverage (remaining=7256737)
[2026-06-08T08:57:27] Estimating fragment length (mate gap mean=-84.814, mate gap stddev=32.358, read length mean=138.703)
[2026-06-08T08:57:28] Filtering read-through fragments with a distance <=10000bp (remaining=6856636)
[2026-06-08T08:57:30] Filtering inconsistently clipped mates (remaining=6775509)
[2026-06-08T08:57:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6609596)
[2026-06-08T08:57:37] Filtering fragments with small insert size (remaining=6609044)
[2026-06-08T08:57:39] Filtering alignments with long gaps (remaining=6609044)
[2026-06-08T08:57:41] Filtering fragments with both mates in the same gene (remaining=6607929)
[2026-06-08T08:57:43] Filtering fusions arising from hairpin structures (remaining=6277372)
[2026-06-08T08:57:46] Filtering reads with a mismatch p-value <=0.01 (remaining=3280120)
[2026-06-08T08:58:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=1148172)
[2026-06-08T08:58:14] Finding fusions and counting supporting reads (total=852650)
[2026-06-08T08:58:34] Merging adjacent fusion breakpoints (remaining=846394)
[2026-06-08T08:58:36] Filtering multi-mapping fusions by alignment score and read support (remaining=551614)
[2026-06-08T08:59:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=547813)
[2026-06-08T08:59:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=312768)
[2026-06-08T08:59:23] Filtering fusions with <2 supporting reads (remaining=44990)
[2026-06-08T08:59:24] Filtering fusions with an e-value >=0.3 (remaining=16709)
[2026-06-08T08:59:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=16769)
[2026-06-08T08:59:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16680)
[2026-06-08T08:59:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16680)
[2026-06-08T08:59:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9830)
[2026-06-08T08:59:38] Searching for fusions with spliced split reads (remaining=9847)
[2026-06-08T08:59:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=5020)
[2026-06-08T08:59:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4973)
[2026-06-08T08:59:46] Searching for fusions with >=4 spliced events (remaining=6126)
[2026-06-08T08:59:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2359)
[2026-06-08T09:00:03] Filtering fusions with anchors <=23nt (remaining=1840)
[2026-06-08T09:00:04] Filtering end-to-end fusions with low support (remaining=1762)
[2026-06-08T09:00:05] Filtering fusions with no coverage around the breakpoints (remaining=1721)
[2026-06-08T09:00:06] Indexing gene sequences 
[2026-06-08T09:00:13] Filtering genes with >=30% identity (remaining=501)
[2026-06-08T09:00:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=179)
[2026-06-08T09:00:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=141)
[2026-06-08T09:00:22] Searching for additional isoforms (remaining=208)
[2026-06-08T09:00:24] Assigning confidence scores to events 
[2026-06-08T09:00:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:27] Writing fusions to file 'tih_rna_sample_00671_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:29] Writing discarded fusions to file 'tih_rna_sample_00671_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:06] Freeing resources
[2026-06-08T09:01:26] Done (elapsed time=00:12:50, CPU time=00:12:48, peak memory=15.5gb)