[2026-06-08T08:41:34] Launching Arriba 2.4.0
[2026-06-08T08:41:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:47] Reading chimeric alignments from 'tih_rna_sample_00629_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11847684)
[2026-06-08T08:48:42] Marking multi-mapping alignments (marked=7322401)
[2026-06-08T08:48:47] Detecting strandedness (reverse)
[2026-06-08T08:48:47] Assigning strands to alignments 
[2026-06-08T08:48:49] Annotating alignments 
[2026-06-08T08:49:28] Filtering duplicates (remaining=7664984)
[2026-06-08T08:49:36] 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=7392116)
[2026-06-08T08:49:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7392116)
[2026-06-08T08:49:41] Filtering viral contigs with expression lower than the top 5 (remaining=7392116)
[2026-06-08T08:49:46] Filtering viral contigs with less than 5% coverage (remaining=7392116)
[2026-06-08T08:49:49] Estimating fragment length (mate gap mean=-85.8865, mate gap stddev=27.9672, read length mean=127.948)
[2026-06-08T08:49:49] Filtering read-through fragments with a distance <=10000bp (remaining=6842668)
[2026-06-08T08:49:51] Filtering inconsistently clipped mates (remaining=6712101)
[2026-06-08T08:49:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6597969)
[2026-06-08T08:49:59] Filtering fragments with small insert size (remaining=6596553)
[2026-06-08T08:50:02] Filtering alignments with long gaps (remaining=6596553)
[2026-06-08T08:50:05] Filtering fragments with both mates in the same gene (remaining=6595449)
[2026-06-08T08:50:08] Filtering fusions arising from hairpin structures (remaining=6227076)
[2026-06-08T08:50:11] Filtering reads with a mismatch p-value <=0.01 (remaining=2949840)
[2026-06-08T08:50:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=1171496)
[2026-06-08T08:50:40] Finding fusions and counting supporting reads (total=878521)
[2026-06-08T08:51:09] Merging adjacent fusion breakpoints (remaining=863679)
[2026-06-08T08:51:11] Filtering multi-mapping fusions by alignment score and read support (remaining=563277)
[2026-06-08T08:51:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=561861)
[2026-06-08T08:52:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=296674)
[2026-06-08T08:52:05] Filtering fusions with <2 supporting reads (remaining=38140)
[2026-06-08T08:52:06] Filtering fusions with an e-value >=0.3 (remaining=8116)
[2026-06-08T08:52:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8191)
[2026-06-08T08:52:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8067)
[2026-06-08T08:52:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8067)
[2026-06-08T08:52:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7282)
[2026-06-08T08:52:21] Searching for fusions with spliced split reads (remaining=7425)
[2026-06-08T08:52:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=4508)
[2026-06-08T08:52:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4449)
[2026-06-08T08:52:30] Searching for fusions with >=4 spliced events (remaining=5701)
[2026-06-08T08:52:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2624)
[2026-06-08T08:52:47] Filtering fusions with anchors <=23nt (remaining=2255)
[2026-06-08T08:52:48] Filtering end-to-end fusions with low support (remaining=2224)
[2026-06-08T08:52:49] Filtering fusions with no coverage around the breakpoints (remaining=2190)
[2026-06-08T08:52:49] Indexing gene sequences 
[2026-06-08T08:52:56] Filtering genes with >=30% identity (remaining=568)
[2026-06-08T08:52:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=157)
[2026-06-08T08:53:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=148)
[2026-06-08T08:53:04] Searching for additional isoforms (remaining=189)
[2026-06-08T08:53:06] Assigning confidence scores to events 
[2026-06-08T08:53:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:10] Writing fusions to file 'tih_rna_sample_00629_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:12] Writing discarded fusions to file 'tih_rna_sample_00629_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:47] Freeing resources
[2026-06-08T08:54:12] Done (elapsed time=00:12:38, CPU time=00:12:36, peak memory=16.4gb)