[2026-06-08T08:31:13] Launching Arriba 2.4.0
[2026-06-08T08:31:13] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:26] Reading chimeric alignments from 'tih_rna_sample_00149_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=8961527)
[2026-06-08T08:36:56] Marking multi-mapping alignments (marked=5628086)
[2026-06-08T08:37:00] Detecting strandedness (reverse)
[2026-06-08T08:37:00] Assigning strands to alignments 
[2026-06-08T08:37:01] Annotating alignments 
[2026-06-08T08:37:30] Filtering duplicates (remaining=4515037)
[2026-06-08T08:37:35] 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=4307734)
[2026-06-08T08:37:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4307734)
[2026-06-08T08:37:38] Filtering viral contigs with expression lower than the top 5 (remaining=4307734)
[2026-06-08T08:37:42] Filtering viral contigs with less than 5% coverage (remaining=4307734)
[2026-06-08T08:37:44] Estimating fragment length (mate gap mean=-89.1032, mate gap stddev=27.2648, read length mean=130.447)
[2026-06-08T08:37:44] Filtering read-through fragments with a distance <=10000bp (remaining=3982257)
[2026-06-08T08:37:46] Filtering inconsistently clipped mates (remaining=3911423)
[2026-06-08T08:37:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3792520)
[2026-06-08T08:37:51] Filtering fragments with small insert size (remaining=3791908)
[2026-06-08T08:37:52] Filtering alignments with long gaps (remaining=3791908)
[2026-06-08T08:37:54] Filtering fragments with both mates in the same gene (remaining=3791103)
[2026-06-08T08:37:56] Filtering fusions arising from hairpin structures (remaining=3583274)
[2026-06-08T08:37:58] Filtering reads with a mismatch p-value <=0.01 (remaining=1533480)
[2026-06-08T08:38:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=757620)
[2026-06-08T08:38:14] Finding fusions and counting supporting reads (total=622166)
[2026-06-08T08:38:27] Merging adjacent fusion breakpoints (remaining=616310)
[2026-06-08T08:38:29] Filtering multi-mapping fusions by alignment score and read support (remaining=367536)
[2026-06-08T08:38:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=366004)
[2026-06-08T08:39:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=193675)
[2026-06-08T08:39:03] Filtering fusions with <2 supporting reads (remaining=24362)
[2026-06-08T08:39:04] Filtering fusions with an e-value >=0.3 (remaining=6551)
[2026-06-08T08:39:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6583)
[2026-06-08T08:39:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6481)
[2026-06-08T08:39:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6483)
[2026-06-08T08:39:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5684)
[2026-06-08T08:39:13] Searching for fusions with spliced split reads (remaining=5784)
[2026-06-08T08:39:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=3666)
[2026-06-08T08:39:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3645)
[2026-06-08T08:39:19] Searching for fusions with >=4 spliced events (remaining=4310)
[2026-06-08T08:39:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1706)
[2026-06-08T08:39:33] Filtering fusions with anchors <=23nt (remaining=1412)
[2026-06-08T08:39:33] Filtering end-to-end fusions with low support (remaining=1382)
[2026-06-08T08:39:34] Filtering fusions with no coverage around the breakpoints (remaining=1354)
[2026-06-08T08:39:34] Indexing gene sequences 
[2026-06-08T08:39:39] Filtering genes with >=30% identity (remaining=445)
[2026-06-08T08:39:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=232)
[2026-06-08T08:39:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=177)
[2026-06-08T08:39:46] Searching for additional isoforms (remaining=229)
[2026-06-08T08:39:47] Assigning confidence scores to events 
[2026-06-08T08:39:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:39:49] Writing fusions to file 'tih_rna_sample_00149_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:39:51] Writing discarded fusions to file 'tih_rna_sample_00149_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:13] Freeing resources
[2026-06-08T08:40:27] Done (elapsed time=00:09:14, CPU time=00:09:12, peak memory=13.6gb)