[2026-06-08T08:25:24] Launching Arriba 2.4.0
[2026-06-08T08:25:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:42] Reading chimeric alignments from 'tih_rna_sample_00624_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9174952)
[2026-06-08T08:31:13] Marking multi-mapping alignments (marked=5917668)
[2026-06-08T08:31:17] Detecting strandedness (no)
[2026-06-08T08:31:17] Annotating alignments 
[2026-06-08T08:31:47] Filtering duplicates (remaining=5727103)
[2026-06-08T08:31:52] 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=5493309)
[2026-06-08T08:31:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5493309)
[2026-06-08T08:31:55] Filtering viral contigs with expression lower than the top 5 (remaining=5493309)
[2026-06-08T08:31:59] Filtering viral contigs with less than 5% coverage (remaining=5493309)
[2026-06-08T08:32:00] Estimating fragment length (mate gap mean=-87.5372, mate gap stddev=28.8497, read length mean=130.104)
[2026-06-08T08:32:00] Filtering read-through fragments with a distance <=10000bp (remaining=5189042)
[2026-06-08T08:32:02] Filtering inconsistently clipped mates (remaining=5072600)
[2026-06-08T08:32:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4948705)
[2026-06-08T08:32:07] Filtering fragments with small insert size (remaining=4948128)
[2026-06-08T08:32:08] Filtering alignments with long gaps (remaining=4948128)
[2026-06-08T08:32:10] Filtering fragments with both mates in the same gene (remaining=4947174)
[2026-06-08T08:32:12] Filtering fusions arising from hairpin structures (remaining=4602966)
[2026-06-08T08:32:14] Filtering reads with a mismatch p-value <=0.01 (remaining=2354514)
[2026-06-08T08:32:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=806436)
[2026-06-08T08:32:34] Finding fusions and counting supporting reads (total=614657)
[2026-06-08T08:32:46] Merging adjacent fusion breakpoints (remaining=607009)
[2026-06-08T08:32:47] Filtering multi-mapping fusions by alignment score and read support (remaining=369194)
[2026-06-08T08:33:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=367081)
[2026-06-08T08:33:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=208919)
[2026-06-08T08:33:19] Filtering fusions with <2 supporting reads (remaining=29308)
[2026-06-08T08:33:20] Filtering fusions with an e-value >=0.3 (remaining=8045)
[2026-06-08T08:33:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8105)
[2026-06-08T08:33:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7974)
[2026-06-08T08:33:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7974)
[2026-06-08T08:33:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6456)
[2026-06-08T08:33:29] Searching for fusions with spliced split reads (remaining=6590)
[2026-06-08T08:33:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=4348)
[2026-06-08T08:33:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4293)
[2026-06-08T08:33:34] Searching for fusions with >=4 spliced events (remaining=5040)
[2026-06-08T08:33:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1831)
[2026-06-08T08:33:50] Filtering fusions with anchors <=23nt (remaining=1556)
[2026-06-08T08:33:51] Filtering end-to-end fusions with low support (remaining=1517)
[2026-06-08T08:33:52] Filtering fusions with no coverage around the breakpoints (remaining=1482)
[2026-06-08T08:33:52] Indexing gene sequences 
[2026-06-08T08:33:58] Filtering genes with >=30% identity (remaining=510)
[2026-06-08T08:34:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=268)
[2026-06-08T08:34:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=213)
[2026-06-08T08:34:04] Searching for additional isoforms (remaining=282)
[2026-06-08T08:34:05] Assigning confidence scores to events 
[2026-06-08T08:34:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:08] Writing fusions to file 'tih_rna_sample_00624_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:10] Writing discarded fusions to file 'tih_rna_sample_00624_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:33] Freeing resources
[2026-06-08T08:34:47] Done (elapsed time=00:09:23, CPU time=00:09:22, peak memory=13.7gb)