[2026-06-08T08:51:49] Launching Arriba 2.4.0
[2026-06-08T08:51:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:03] Reading chimeric alignments from 'tih_rna_sample_00473_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=10036190)
[2026-06-08T08:59:32] Marking multi-mapping alignments (marked=6259355)
[2026-06-08T08:59:36] Detecting strandedness (reverse)
[2026-06-08T08:59:36] Assigning strands to alignments 
[2026-06-08T08:59:39] Annotating alignments 
[2026-06-08T09:00:23] Filtering duplicates (remaining=5556943)
[2026-06-08T09:00:34] 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=5344976)
[2026-06-08T09:00:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5344976)
[2026-06-08T09:00:39] Filtering viral contigs with expression lower than the top 5 (remaining=5344976)
[2026-06-08T09:00:45] Filtering viral contigs with less than 5% coverage (remaining=5344976)
[2026-06-08T09:00:48] Estimating fragment length (mate gap mean=-88.433, mate gap stddev=29.2477, read length mean=135.865)
[2026-06-08T09:00:48] Filtering read-through fragments with a distance <=10000bp (remaining=5015827)
[2026-06-08T09:00:51] Filtering inconsistently clipped mates (remaining=4937354)
[2026-06-08T09:00:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4824363)
[2026-06-08T09:00:58] Filtering fragments with small insert size (remaining=4823765)
[2026-06-08T09:01:00] Filtering alignments with long gaps (remaining=4823765)
[2026-06-08T09:01:02] Filtering fragments with both mates in the same gene (remaining=4822988)
[2026-06-08T09:01:05] Filtering fusions arising from hairpin structures (remaining=4572002)
[2026-06-08T09:01:09] Filtering reads with a mismatch p-value <=0.01 (remaining=1958040)
[2026-06-08T09:01:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=872610)
[2026-06-08T09:01:37] Finding fusions and counting supporting reads (total=625702)
[2026-06-08T09:02:08] Merging adjacent fusion breakpoints (remaining=618949)
[2026-06-08T09:02:10] Filtering multi-mapping fusions by alignment score and read support (remaining=417738)
[2026-06-08T09:02:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=415995)
[2026-06-08T09:02:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=215849)
[2026-06-08T09:02:57] Filtering fusions with <2 supporting reads (remaining=37503)
[2026-06-08T09:02:58] Filtering fusions with an e-value >=0.3 (remaining=12170)
[2026-06-08T09:02:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12216)
[2026-06-08T09:03:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12146)
[2026-06-08T09:03:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12146)
[2026-06-08T09:03:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6812)
[2026-06-08T09:03:12] Searching for fusions with spliced split reads (remaining=6852)
[2026-06-08T09:03:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=4182)
[2026-06-08T09:03:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4133)
[2026-06-08T09:03:19] Searching for fusions with >=4 spliced events (remaining=5020)
[2026-06-08T09:03:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1995)
[2026-06-08T09:03:36] Filtering fusions with anchors <=23nt (remaining=1561)
[2026-06-08T09:03:36] Filtering end-to-end fusions with low support (remaining=1507)
[2026-06-08T09:03:37] Filtering fusions with no coverage around the breakpoints (remaining=1477)
[2026-06-08T09:03:38] Indexing gene sequences 
[2026-06-08T09:03:43] Filtering genes with >=30% identity (remaining=452)
[2026-06-08T09:03:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=215)
[2026-06-08T09:03:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-08T09:03:50] Searching for additional isoforms (remaining=235)
[2026-06-08T09:03:52] Assigning confidence scores to events 
[2026-06-08T09:03:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:55] Writing fusions to file 'tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:03:57] Writing discarded fusions to file 'tih_rna_sample_00473_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:30] Freeing resources
[2026-06-08T09:04:49] Done (elapsed time=00:13:00, CPU time=00:12:59, peak memory=14.5gb)