[2026-06-08T08:42:34] Launching Arriba 2.4.0
[2026-06-08T08:42:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:46] Reading chimeric alignments from 'tih_rna_sample_00613_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11959007)
[2026-06-08T08:50:02] Marking multi-mapping alignments (marked=7346607)
[2026-06-08T08:50:06] Detecting strandedness (reverse)
[2026-06-08T08:50:06] Assigning strands to alignments 
[2026-06-08T08:50:09] Annotating alignments 
[2026-06-08T08:50:47] Filtering duplicates (remaining=6692063)
[2026-06-08T08:50:55] 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=6411337)
[2026-06-08T08:50:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6411337)
[2026-06-08T08:50:59] Filtering viral contigs with expression lower than the top 5 (remaining=6411337)
[2026-06-08T08:51:05] Filtering viral contigs with less than 5% coverage (remaining=6411337)
[2026-06-08T08:51:08] Estimating fragment length (mate gap mean=-87.1212, mate gap stddev=30.2699, read length mean=134.741)
[2026-06-08T08:51:08] Filtering read-through fragments with a distance <=10000bp (remaining=6031607)
[2026-06-08T08:51:10] Filtering inconsistently clipped mates (remaining=5935222)
[2026-06-08T08:51:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5768314)
[2026-06-08T08:51:18] Filtering fragments with small insert size (remaining=5767529)
[2026-06-08T08:51:20] Filtering alignments with long gaps (remaining=5767527)
[2026-06-08T08:51:23] Filtering fragments with both mates in the same gene (remaining=5766474)
[2026-06-08T08:51:26] Filtering fusions arising from hairpin structures (remaining=5408916)
[2026-06-08T08:51:28] Filtering reads with a mismatch p-value <=0.01 (remaining=2666198)
[2026-06-08T08:51:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=909303)
[2026-06-08T08:51:56] Finding fusions and counting supporting reads (total=663959)
[2026-06-08T08:52:16] Merging adjacent fusion breakpoints (remaining=656768)
[2026-06-08T08:52:18] Filtering multi-mapping fusions by alignment score and read support (remaining=432665)
[2026-06-08T08:52:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=429746)
[2026-06-08T08:53:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=245398)
[2026-06-08T08:53:05] Filtering fusions with <2 supporting reads (remaining=51854)
[2026-06-08T08:53:06] Filtering fusions with an e-value >=0.3 (remaining=27903)
[2026-06-08T08:53:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=27978)
[2026-06-08T08:53:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=27924)
[2026-06-08T08:53:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=27924)
[2026-06-08T08:53:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7297)
[2026-06-08T08:53:19] Searching for fusions with spliced split reads (remaining=7333)
[2026-06-08T08:53:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=4180)
[2026-06-08T08:53:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4122)
[2026-06-08T08:53:26] Searching for fusions with >=4 spliced events (remaining=4927)
[2026-06-08T08:53:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1681)
[2026-06-08T08:53:42] Filtering fusions with anchors <=23nt (remaining=1311)
[2026-06-08T08:53:42] Filtering end-to-end fusions with low support (remaining=1270)
[2026-06-08T08:53:43] Filtering fusions with no coverage around the breakpoints (remaining=1244)
[2026-06-08T08:53:44] Indexing gene sequences 
[2026-06-08T08:53:49] Filtering genes with >=30% identity (remaining=376)
[2026-06-08T08:53:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=201)
[2026-06-08T08:53:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=179)
[2026-06-08T08:53:57] Searching for additional isoforms (remaining=235)
[2026-06-08T08:53:59] Assigning confidence scores to events 
[2026-06-08T08:54:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:02] Writing fusions to file 'tih_rna_sample_00613_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:04] Writing discarded fusions to file 'tih_rna_sample_00613_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:36] Freeing resources
[2026-06-08T08:54:57] Done (elapsed time=00:12:23, CPU time=00:12:22, peak memory=16.5gb)