[2026-06-08T08:50:25] Launching Arriba 2.4.0
[2026-06-08T08:50:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:39] Reading chimeric alignments from 'tih_rna_sample_00096_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=9678419)
[2026-06-08T08:57:34] Marking multi-mapping alignments (marked=6146026)
[2026-06-08T08:57:38] Detecting strandedness (reverse)
[2026-06-08T08:57:38] Assigning strands to alignments 
[2026-06-08T08:57:39] Annotating alignments 
[2026-06-08T08:58:15] Filtering duplicates (remaining=5480937)
[2026-06-08T08:58:21] 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=5234663)
[2026-06-08T08:58:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5234663)
[2026-06-08T08:58:25] Filtering viral contigs with expression lower than the top 5 (remaining=5234663)
[2026-06-08T08:58:29] Filtering viral contigs with less than 5% coverage (remaining=5234663)
[2026-06-08T08:58:32] Estimating fragment length (mate gap mean=-88.0123, mate gap stddev=29.1845, read length mean=134.078)
[2026-06-08T08:58:32] Filtering read-through fragments with a distance <=10000bp (remaining=4881782)
[2026-06-08T08:58:34] Filtering inconsistently clipped mates (remaining=4798585)
[2026-06-08T08:58:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4665759)
[2026-06-08T08:58:40] Filtering fragments with small insert size (remaining=4665161)
[2026-06-08T08:58:42] Filtering alignments with long gaps (remaining=4665161)
[2026-06-08T08:58:44] Filtering fragments with both mates in the same gene (remaining=4664157)
[2026-06-08T08:58:46] Filtering fusions arising from hairpin structures (remaining=4387022)
[2026-06-08T08:58:49] Filtering reads with a mismatch p-value <=0.01 (remaining=1938771)
[2026-06-08T08:59:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=843290)
[2026-06-08T08:59:10] Finding fusions and counting supporting reads (total=680329)
[2026-06-08T08:59:27] Merging adjacent fusion breakpoints (remaining=674584)
[2026-06-08T08:59:29] Filtering multi-mapping fusions by alignment score and read support (remaining=431336)
[2026-06-08T09:00:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=428671)
[2026-06-08T09:00:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=223172)
[2026-06-08T09:00:10] Filtering fusions with <2 supporting reads (remaining=27057)
[2026-06-08T09:00:11] Filtering fusions with an e-value >=0.3 (remaining=9458)
[2026-06-08T09:00:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9511)
[2026-06-08T09:00:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9433)
[2026-06-08T09:00:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9433)
[2026-06-08T09:00:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6043)
[2026-06-08T09:00:22] Searching for fusions with spliced split reads (remaining=6179)
[2026-06-08T09:00:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=3823)
[2026-06-08T09:00:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3770)
[2026-06-08T09:00:28] Searching for fusions with >=4 spliced events (remaining=4586)
[2026-06-08T09:00:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2078)
[2026-06-08T09:00:45] Filtering fusions with anchors <=23nt (remaining=1713)
[2026-06-08T09:00:46] Filtering end-to-end fusions with low support (remaining=1650)
[2026-06-08T09:00:46] Filtering fusions with no coverage around the breakpoints (remaining=1596)
[2026-06-08T09:00:47] Indexing gene sequences 
[2026-06-08T09:00:53] Filtering genes with >=30% identity (remaining=466)
[2026-06-08T09:00:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=208)
[2026-06-08T09:01:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-08T09:01:02] Searching for additional isoforms (remaining=246)
[2026-06-08T09:01:04] Assigning confidence scores to events 
[2026-06-08T09:01:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:07] Writing fusions to file 'tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:01:09] Writing discarded fusions to file 'tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:37] Freeing resources
[2026-06-08T09:01:54] Done (elapsed time=00:11:29, CPU time=00:11:28, peak memory=14.3gb)