[2026-06-08T08:56:32] Launching Arriba 2.4.0
[2026-06-08T08:56:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:56:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:56:45] Reading chimeric alignments from 'tih_rna_sample_00652_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=14441580)
[2026-06-08T09:05:05] Marking multi-mapping alignments (marked=9077164)
[2026-06-08T09:05:12] Detecting strandedness (reverse)
[2026-06-08T09:05:12] Assigning strands to alignments 
[2026-06-08T09:05:19] Annotating alignments 
[2026-06-08T09:06:20] Filtering duplicates (remaining=6074812)
[2026-06-08T09:06:31] 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=5643172)
[2026-06-08T09:06:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5643172)
[2026-06-08T09:06:38] Filtering viral contigs with expression lower than the top 5 (remaining=5643172)
[2026-06-08T09:06:45] Filtering viral contigs with less than 5% coverage (remaining=5643172)
[2026-06-08T09:06:48] Estimating fragment length (mate gap mean=-86.0432, mate gap stddev=30.7084, read length mean=131.989)
[2026-06-08T09:06:49] Filtering read-through fragments with a distance <=10000bp (remaining=5340987)
[2026-06-08T09:06:52] Filtering inconsistently clipped mates (remaining=5259721)
[2026-06-08T09:06:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5062822)
[2026-06-08T09:07:01] Filtering fragments with small insert size (remaining=5062094)
[2026-06-08T09:07:04] Filtering alignments with long gaps (remaining=5062094)
[2026-06-08T09:07:07] Filtering fragments with both mates in the same gene (remaining=5060917)
[2026-06-08T09:07:10] Filtering fusions arising from hairpin structures (remaining=4800224)
[2026-06-08T09:07:13] Filtering reads with a mismatch p-value <=0.01 (remaining=2203477)
[2026-06-08T09:07:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=767894)
[2026-06-08T09:07:41] Finding fusions and counting supporting reads (total=530191)
[2026-06-08T09:08:06] Merging adjacent fusion breakpoints (remaining=524151)
[2026-06-08T09:08:08] Filtering multi-mapping fusions by alignment score and read support (remaining=332717)
[2026-06-08T09:08:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:09:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=330519)
[2026-06-08T09:09:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=208629)
[2026-06-08T09:09:03] Filtering fusions with <2 supporting reads (remaining=62062)
[2026-06-08T09:09:03] Filtering fusions with an e-value >=0.3 (remaining=40522)
[2026-06-08T09:09:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=40580)
[2026-06-08T09:09:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=40479)
[2026-06-08T09:09:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=40479)
[2026-06-08T09:09:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6444)
[2026-06-08T09:09:17] Searching for fusions with spliced split reads (remaining=6486)
[2026-06-08T09:09:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=3795)
[2026-06-08T09:09:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3745)
[2026-06-08T09:09:25] Searching for fusions with >=4 spliced events (remaining=4395)
[2026-06-08T09:09:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1300)
[2026-06-08T09:09:40] Filtering fusions with anchors <=23nt (remaining=1029)
[2026-06-08T09:09:41] Filtering end-to-end fusions with low support (remaining=973)
[2026-06-08T09:09:42] Filtering fusions with no coverage around the breakpoints (remaining=952)
[2026-06-08T09:09:42] Indexing gene sequences 
[2026-06-08T09:09:46] Filtering genes with >=30% identity (remaining=328)
[2026-06-08T09:09:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=218)
[2026-06-08T09:09:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=165)
[2026-06-08T09:09:53] Searching for additional isoforms (remaining=194)
[2026-06-08T09:09:54] Assigning confidence scores to events 
[2026-06-08T09:09:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:57] Writing fusions to file 'tih_rna_sample_00652_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:09:58] Writing discarded fusions to file 'tih_rna_sample_00652_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:26] Freeing resources
[2026-06-08T09:10:48] Done (elapsed time=00:14:16, CPU time=00:14:14, peak memory=18.9gb)