[2026-05-28T00:02:51] Launching Arriba 2.4.0
[2026-05-28T00:02:51] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:02] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:03:07] Reading chimeric alignments from 'tih_rna_sample_00116_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=4047157)
[2026-05-28T00:05:46] Marking multi-mapping alignments (marked=2586615)
[2026-05-28T00:05:48] Detecting strandedness (reverse)
[2026-05-28T00:05:48] Assigning strands to alignments 
[2026-05-28T00:05:49] Annotating alignments 
[2026-05-28T00:06:04] Filtering duplicates (remaining=1959495)
[2026-05-28T00:06:07] 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=1821605)
[2026-05-28T00:06:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1821605)
[2026-05-28T00:06:08] Filtering viral contigs with expression lower than the top 5 (remaining=1821605)
[2026-05-28T00:06:10] Filtering viral contigs with less than 5% coverage (remaining=1821605)
[2026-05-28T00:06:11] Estimating fragment length (mate gap mean=-87.3542, mate gap stddev=27.2104, read length mean=124.285)
[2026-05-28T00:06:11] Filtering read-through fragments with a distance <=10000bp (remaining=1675936)
[2026-05-28T00:06:12] Filtering inconsistently clipped mates (remaining=1643803)
[2026-05-28T00:06:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1598047)
[2026-05-28T00:06:14] Filtering fragments with small insert size (remaining=1597576)
[2026-05-28T00:06:15] Filtering alignments with long gaps (remaining=1597576)
[2026-05-28T00:06:16] Filtering fragments with both mates in the same gene (remaining=1597237)
[2026-05-28T00:06:17] Filtering fusions arising from hairpin structures (remaining=1517420)
[2026-05-28T00:06:18] Filtering reads with a mismatch p-value <=0.01 (remaining=587549)
[2026-05-28T00:06:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=301527)
[2026-05-28T00:06:26] Finding fusions and counting supporting reads (total=275294)
[2026-05-28T00:06:33] Merging adjacent fusion breakpoints (remaining=272211)
[2026-05-28T00:06:34] Filtering multi-mapping fusions by alignment score and read support (remaining=163374)
[2026-05-28T00:06:48] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:06:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=162725)
[2026-05-28T00:06:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=82255)
[2026-05-28T00:06:52] Filtering fusions with <2 supporting reads (remaining=8708)
[2026-05-28T00:06:52] Filtering fusions with an e-value >=0.3 (remaining=2319)
[2026-05-28T00:06:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2348)
[2026-05-28T00:06:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2308)
[2026-05-28T00:06:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2308)
[2026-05-28T00:06:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2235)
[2026-05-28T00:06:56] Searching for fusions with spliced split reads (remaining=2315)
[2026-05-28T00:06:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=1782)
[2026-05-28T00:06:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1759)
[2026-05-28T00:06:59] Searching for fusions with >=4 spliced events (remaining=1915)
[2026-05-28T00:07:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=675)
[2026-05-28T00:07:18] Filtering fusions with anchors <=23nt (remaining=466)
[2026-05-28T00:07:18] Filtering end-to-end fusions with low support (remaining=450)
[2026-05-28T00:07:19] Filtering fusions with no coverage around the breakpoints (remaining=433)
[2026-05-28T00:07:19] Indexing gene sequences 
[2026-05-28T00:07:22] Filtering genes with >=30% identity (remaining=162)
[2026-05-28T00:07:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=67)
[2026-05-28T00:07:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=67)
[2026-05-28T00:07:24] Searching for additional isoforms (remaining=73)
[2026-05-28T00:07:24] Assigning confidence scores to events 
[2026-05-28T00:07:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:26] Writing fusions to file 'tih_rna_sample_00116_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:07:27] Writing discarded fusions to file 'tih_rna_sample_00116_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:07:42] Freeing resources
[2026-05-28T00:07:54] Done (elapsed time=00:05:03, CPU time=00:05:01, peak memory=8.4gb)