[2026-06-08T08:49:20] Launching Arriba 2.4.0
[2026-06-08T08:49:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:37] Reading chimeric alignments from 'tih_rna_sample_00473_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9987296)
[2026-06-08T08:56:17] Marking multi-mapping alignments (marked=6261424)
[2026-06-08T08:56:21] Detecting strandedness (reverse)
[2026-06-08T08:56:21] Assigning strands to alignments 
[2026-06-08T08:56:22] Annotating alignments 
[2026-06-08T08:56:52] Filtering duplicates (remaining=4666431)
[2026-06-08T08:56:58] 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=4467105)
[2026-06-08T08:56:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4467105)
[2026-06-08T08:57:01] Filtering viral contigs with expression lower than the top 5 (remaining=4467105)
[2026-06-08T08:57:05] Filtering viral contigs with less than 5% coverage (remaining=4467105)
[2026-06-08T08:57:07] Estimating fragment length (mate gap mean=-87.2773, mate gap stddev=28.9355, read length mean=133.803)
[2026-06-08T08:57:07] Filtering read-through fragments with a distance <=10000bp (remaining=4224645)
[2026-06-08T08:57:09] Filtering inconsistently clipped mates (remaining=4158992)
[2026-06-08T08:57:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4050456)
[2026-06-08T08:57:14] Filtering fragments with small insert size (remaining=4049874)
[2026-06-08T08:57:16] Filtering alignments with long gaps (remaining=4049874)
[2026-06-08T08:57:18] Filtering fragments with both mates in the same gene (remaining=4049139)
[2026-06-08T08:57:19] Filtering fusions arising from hairpin structures (remaining=3862538)
[2026-06-08T08:57:21] Filtering reads with a mismatch p-value <=0.01 (remaining=1604524)
[2026-06-08T08:57:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=667572)
[2026-06-08T08:57:39] Finding fusions and counting supporting reads (total=493904)
[2026-06-08T08:57:53] Merging adjacent fusion breakpoints (remaining=489130)
[2026-06-08T08:57:54] Filtering multi-mapping fusions by alignment score and read support (remaining=325895)
[2026-06-08T08:58:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=324434)
[2026-06-08T08:58:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=168549)
[2026-06-08T08:58:26] Filtering fusions with <2 supporting reads (remaining=27601)
[2026-06-08T08:58:26] Filtering fusions with an e-value >=0.3 (remaining=8447)
[2026-06-08T08:58:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8485)
[2026-06-08T08:58:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8427)
[2026-06-08T08:58:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8427)
[2026-06-08T08:58:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4860)
[2026-06-08T08:58:35] Searching for fusions with spliced split reads (remaining=4994)
[2026-06-08T08:58:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=3308)
[2026-06-08T08:58:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3268)
[2026-06-08T08:58:40] Searching for fusions with >=4 spliced events (remaining=3804)
[2026-06-08T08:58:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1448)
[2026-06-08T08:58:55] Filtering fusions with anchors <=23nt (remaining=1116)
[2026-06-08T08:58:56] Filtering end-to-end fusions with low support (remaining=1070)
[2026-06-08T08:58:56] Filtering fusions with no coverage around the breakpoints (remaining=1049)
[2026-06-08T08:58:57] Indexing gene sequences 
[2026-06-08T08:59:01] Filtering genes with >=30% identity (remaining=323)
[2026-06-08T08:59:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=163)
[2026-06-08T08:59:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=136)
[2026-06-08T08:59:06] Searching for additional isoforms (remaining=179)
[2026-06-08T08:59:07] Assigning confidence scores to events 
[2026-06-08T08:59:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:09] Writing fusions to file 'tih_rna_sample_00473_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:10] Writing discarded fusions to file 'tih_rna_sample_00473_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:30] Freeing resources
[2026-06-08T08:59:46] Done (elapsed time=00:10:26, CPU time=00:10:24, peak memory=14.5gb)