[2026-05-28T00:02:00] Launching Arriba 2.4.0
[2026-05-28T00:02:00] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:02:09] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:02:13] Reading chimeric alignments from 'tih_rna_sample_00090_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=4747008)
[2026-05-28T00:04:55] Marking multi-mapping alignments (marked=3367995)
[2026-05-28T00:04:57] Detecting strandedness (no)
[2026-05-28T00:04:57] Annotating alignments 
[2026-05-28T00:05:24] Filtering duplicates (remaining=1969577)
[2026-05-28T00:05:27] 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=1724271)
[2026-05-28T00:05:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1724271)
[2026-05-28T00:05:30] Filtering viral contigs with expression lower than the top 5 (remaining=1724271)
[2026-05-28T00:05:32] Filtering viral contigs with less than 5% coverage (remaining=1724271)
[2026-05-28T00:05:33] Estimating fragment length (mate gap mean=-83.5661, mate gap stddev=28.1895, read length mean=121.166)
[2026-05-28T00:05:33] Filtering read-through fragments with a distance <=10000bp (remaining=1612629)
[2026-05-28T00:05:34] Filtering inconsistently clipped mates (remaining=1576597)
[2026-05-28T00:05:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1506232)
[2026-05-28T00:05:37] Filtering fragments with small insert size (remaining=1505602)
[2026-05-28T00:05:39] Filtering alignments with long gaps (remaining=1505602)
[2026-05-28T00:05:40] Filtering fragments with both mates in the same gene (remaining=1505324)
[2026-05-28T00:05:41] Filtering fusions arising from hairpin structures (remaining=1419432)
[2026-05-28T00:05:42] Filtering reads with a mismatch p-value <=0.01 (remaining=542840)
[2026-05-28T00:05:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=237256)
[2026-05-28T00:05:49] Finding fusions and counting supporting reads (total=214251)
[2026-05-28T00:05:57] Merging adjacent fusion breakpoints (remaining=211935)
[2026-05-28T00:05:57] Filtering multi-mapping fusions by alignment score and read support (remaining=118951)
[2026-05-28T00:06:13] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:06:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=118158)
[2026-05-28T00:06:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=64273)
[2026-05-28T00:06:17] Filtering fusions with <2 supporting reads (remaining=5732)
[2026-05-28T00:06:17] Filtering fusions with an e-value >=0.3 (remaining=1486)
[2026-05-28T00:06:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1511)
[2026-05-28T00:06:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1463)
[2026-05-28T00:06:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1463)
[2026-05-28T00:06:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1379)
[2026-05-28T00:06:22] Searching for fusions with spliced split reads (remaining=1464)
[2026-05-28T00:06:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=1117)
[2026-05-28T00:06:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1104)
[2026-05-28T00:06:25] Searching for fusions with >=4 spliced events (remaining=1172)
[2026-05-28T00:06:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=440)
[2026-05-28T00:06:38] Filtering fusions with anchors <=23nt (remaining=347)
[2026-05-28T00:06:38] Filtering end-to-end fusions with low support (remaining=334)
[2026-05-28T00:06:39] Filtering fusions with no coverage around the breakpoints (remaining=322)
[2026-05-28T00:06:39] Indexing gene sequences 
[2026-05-28T00:06:41] Filtering genes with >=30% identity (remaining=114)
[2026-05-28T00:06:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=36)
[2026-05-28T00:06:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=36)
[2026-05-28T00:06:42] Searching for additional isoforms (remaining=41)
[2026-05-28T00:06:43] Assigning confidence scores to events 
[2026-05-28T00:06:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:06:45] Writing fusions to file 'tih_rna_sample_00090_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:06:45] Writing discarded fusions to file 'tih_rna_sample_00090_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:06:58] Freeing resources
[2026-05-28T00:07:07] Done (elapsed time=00:05:07, CPU time=00:05:06, peak memory=9.06gb)