[2026-06-08T08:41:34] Launching Arriba 2.4.0
[2026-06-08T08:41:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:47] Reading chimeric alignments from 'tih_rna_sample_00591_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=13740669)
[2026-06-08T08:48:41] Marking multi-mapping alignments (marked=8910151)
[2026-06-08T08:48:47] Detecting strandedness (reverse)
[2026-06-08T08:48:47] Assigning strands to alignments 
[2026-06-08T08:48:50] Annotating alignments 
[2026-06-08T08:49:37] Filtering duplicates (remaining=7789102)
[2026-06-08T08:49:47] 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=7334969)
[2026-06-08T08:49:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7334969)
[2026-06-08T08:49:53] Filtering viral contigs with expression lower than the top 5 (remaining=7334969)
[2026-06-08T08:49:59] Filtering viral contigs with less than 5% coverage (remaining=7334969)
[2026-06-08T08:50:02] Estimating fragment length (mate gap mean=-85.3924, mate gap stddev=27.4079, read length mean=124.574)
[2026-06-08T08:50:03] Filtering read-through fragments with a distance <=10000bp (remaining=6798371)
[2026-06-08T08:50:05] Filtering inconsistently clipped mates (remaining=6679309)
[2026-06-08T08:50:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6511292)
[2026-06-08T08:50:15] Filtering fragments with small insert size (remaining=6510033)
[2026-06-08T08:50:18] Filtering alignments with long gaps (remaining=6510033)
[2026-06-08T08:50:20] Filtering fragments with both mates in the same gene (remaining=6509039)
[2026-06-08T08:50:23] Filtering fusions arising from hairpin structures (remaining=6166809)
[2026-06-08T08:50:27] Filtering reads with a mismatch p-value <=0.01 (remaining=2825055)
[2026-06-08T08:50:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=1223291)
[2026-06-08T08:50:57] Finding fusions and counting supporting reads (total=948496)
[2026-06-08T08:51:21] Merging adjacent fusion breakpoints (remaining=930125)
[2026-06-08T08:51:23] Filtering multi-mapping fusions by alignment score and read support (remaining=567369)
[2026-06-08T08:52:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=565768)
[2026-06-08T08:52:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=304740)
[2026-06-08T08:52:23] Filtering fusions with <2 supporting reads (remaining=39425)
[2026-06-08T08:52:24] Filtering fusions with an e-value >=0.3 (remaining=8198)
[2026-06-08T08:52:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8257)
[2026-06-08T08:52:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8101)
[2026-06-08T08:52:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8101)
[2026-06-08T08:52:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7882)
[2026-06-08T08:52:39] Searching for fusions with spliced split reads (remaining=7968)
[2026-06-08T08:52:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=5116)
[2026-06-08T08:52:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5081)
[2026-06-08T08:52:49] Searching for fusions with >=4 spliced events (remaining=6237)
[2026-06-08T08:52:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2973)
[2026-06-08T08:53:08] Filtering fusions with anchors <=23nt (remaining=2416)
[2026-06-08T08:53:09] Filtering end-to-end fusions with low support (remaining=2326)
[2026-06-08T08:53:10] Filtering fusions with no coverage around the breakpoints (remaining=2275)
[2026-06-08T08:53:12] Indexing gene sequences 
[2026-06-08T08:53:19] Filtering genes with >=30% identity (remaining=672)
[2026-06-08T08:53:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=176)
[2026-06-08T08:53:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=170)
[2026-06-08T08:53:27] Searching for additional isoforms (remaining=217)
[2026-06-08T08:53:29] Assigning confidence scores to events 
[2026-06-08T08:53:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:33] Writing fusions to file 'tih_rna_sample_00591_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:35] Writing discarded fusions to file 'tih_rna_sample_00591_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:13] Freeing resources
[2026-06-08T08:54:35] Done (elapsed time=00:13:01, CPU time=00:13:00, peak memory=18.5gb)