[2026-06-08T08:20:23] Launching Arriba 2.4.0
[2026-06-08T08:20:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:36] Reading chimeric alignments from 'tih_rna_sample_00638_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11805203)
[2026-06-08T08:26:08] Marking multi-mapping alignments (marked=7950302)
[2026-06-08T08:26:13] Detecting strandedness (reverse)
[2026-06-08T08:26:13] Assigning strands to alignments 
[2026-06-08T08:26:15] Annotating alignments 
[2026-06-08T08:26:53] Filtering duplicates (remaining=5817412)
[2026-06-08T08:26:59] 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=5504076)
[2026-06-08T08:27:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5504076)
[2026-06-08T08:27:04] Filtering viral contigs with expression lower than the top 5 (remaining=5504076)
[2026-06-08T08:27:10] Filtering viral contigs with less than 5% coverage (remaining=5504076)
[2026-06-08T08:27:12] Estimating fragment length (mate gap mean=-82.2043, mate gap stddev=27.2594, read length mean=117.578)
[2026-06-08T08:27:12] Filtering read-through fragments with a distance <=10000bp (remaining=5089735)
[2026-06-08T08:27:14] Filtering inconsistently clipped mates (remaining=4990534)
[2026-06-08T08:27:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4896666)
[2026-06-08T08:27:21] Filtering fragments with small insert size (remaining=4895744)
[2026-06-08T08:27:23] Filtering alignments with long gaps (remaining=4895744)
[2026-06-08T08:27:26] Filtering fragments with both mates in the same gene (remaining=4894800)
[2026-06-08T08:27:28] Filtering fusions arising from hairpin structures (remaining=4645179)
[2026-06-08T08:27:31] Filtering reads with a mismatch p-value <=0.01 (remaining=1915495)
[2026-06-08T08:27:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=784176)
[2026-06-08T08:27:52] Finding fusions and counting supporting reads (total=600645)
[2026-06-08T08:28:09] Merging adjacent fusion breakpoints (remaining=586159)
[2026-06-08T08:28:10] Filtering multi-mapping fusions by alignment score and read support (remaining=344814)
[2026-06-08T08:28:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=343967)
[2026-06-08T08:28:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=193687)
[2026-06-08T08:28:55] Filtering fusions with <2 supporting reads (remaining=25725)
[2026-06-08T08:28:55] Filtering fusions with an e-value >=0.3 (remaining=5495)
[2026-06-08T08:28:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5546)
[2026-06-08T08:29:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5458)
[2026-06-08T08:29:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5458)
[2026-06-08T08:29:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5404)
[2026-06-08T08:29:07] Searching for fusions with spliced split reads (remaining=5490)
[2026-06-08T08:29:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=3555)
[2026-06-08T08:29:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3532)
[2026-06-08T08:29:15] Searching for fusions with >=4 spliced events (remaining=4239)
[2026-06-08T08:29:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1962)
[2026-06-08T08:29:31] Filtering fusions with anchors <=23nt (remaining=1596)
[2026-06-08T08:29:32] Filtering end-to-end fusions with low support (remaining=1554)
[2026-06-08T08:29:33] Filtering fusions with no coverage around the breakpoints (remaining=1527)
[2026-06-08T08:29:33] Indexing gene sequences 
[2026-06-08T08:29:38] Filtering genes with >=30% identity (remaining=412)
[2026-06-08T08:29:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=121)
[2026-06-08T08:29:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=112)
[2026-06-08T08:29:43] Searching for additional isoforms (remaining=133)
[2026-06-08T08:29:44] Assigning confidence scores to events 
[2026-06-08T08:29:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:47] Writing fusions to file 'tih_rna_sample_00638_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:29:48] Writing discarded fusions to file 'tih_rna_sample_00638_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:15] Freeing resources
[2026-06-08T08:30:33] Done (elapsed time=00:10:10, CPU time=00:10:09, peak memory=16.3gb)