[2026-06-08T08:45:49] Launching Arriba 2.4.0
[2026-06-08T08:45:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:46:05] Reading chimeric alignments from 'tih_rna_sample_00087_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=9865436)
[2026-06-08T08:53:11] Marking multi-mapping alignments (marked=6335857)
[2026-06-08T08:53:16] Detecting strandedness (reverse)
[2026-06-08T08:53:16] Assigning strands to alignments 
[2026-06-08T08:53:18] Annotating alignments 
[2026-06-08T08:53:53] Filtering duplicates (remaining=6664735)
[2026-06-08T08:54:01] 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=6410031)
[2026-06-08T08:54:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6410031)
[2026-06-08T08:54:05] Filtering viral contigs with expression lower than the top 5 (remaining=6410031)
[2026-06-08T08:54:09] Filtering viral contigs with less than 5% coverage (remaining=6410031)
[2026-06-08T08:54:12] Estimating fragment length (mate gap mean=-86.8793, mate gap stddev=28.8035, read length mean=132.879)
[2026-06-08T08:54:12] Filtering read-through fragments with a distance <=10000bp (remaining=5977796)
[2026-06-08T08:54:14] Filtering inconsistently clipped mates (remaining=5871497)
[2026-06-08T08:54:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5713185)
[2026-06-08T08:54:21] Filtering fragments with small insert size (remaining=5712100)
[2026-06-08T08:54:23] Filtering alignments with long gaps (remaining=5712100)
[2026-06-08T08:54:25] Filtering fragments with both mates in the same gene (remaining=5710859)
[2026-06-08T08:54:27] Filtering fusions arising from hairpin structures (remaining=5341775)
[2026-06-08T08:54:30] Filtering reads with a mismatch p-value <=0.01 (remaining=2505837)
[2026-06-08T08:54:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=1255308)
[2026-06-08T08:54:57] Finding fusions and counting supporting reads (total=906609)
[2026-06-08T08:55:16] Merging adjacent fusion breakpoints (remaining=895282)
[2026-06-08T08:55:18] Filtering multi-mapping fusions by alignment score and read support (remaining=541663)
[2026-06-08T08:55:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=537706)
[2026-06-08T08:56:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=296857)
[2026-06-08T08:56:04] Filtering fusions with <2 supporting reads (remaining=43661)
[2026-06-08T08:56:04] Filtering fusions with an e-value >=0.3 (remaining=12927)
[2026-06-08T08:56:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12976)
[2026-06-08T08:56:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12822)
[2026-06-08T08:56:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12822)
[2026-06-08T08:56:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10093)
[2026-06-08T08:56:17] Searching for fusions with spliced split reads (remaining=10132)
[2026-06-08T08:56:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=5814)
[2026-06-08T08:56:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5748)
[2026-06-08T08:56:24] Searching for fusions with >=4 spliced events (remaining=6982)
[2026-06-08T08:56:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2717)
[2026-06-08T08:56:41] Filtering fusions with anchors <=23nt (remaining=2302)
[2026-06-08T08:56:42] Filtering end-to-end fusions with low support (remaining=2228)
[2026-06-08T08:56:42] Filtering fusions with no coverage around the breakpoints (remaining=2165)
[2026-06-08T08:56:43] Indexing gene sequences 
[2026-06-08T08:56:50] Filtering genes with >=30% identity (remaining=612)
[2026-06-08T08:56:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=249)
[2026-06-08T08:57:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=230)
[2026-06-08T08:57:02] Searching for additional isoforms (remaining=323)
[2026-06-08T08:57:04] Assigning confidence scores to events 
[2026-06-08T08:57:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:08] Writing fusions to file 'tih_rna_sample_00087_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:57:11] Writing discarded fusions to file 'tih_rna_sample_00087_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:46] Freeing resources
[2026-06-08T08:58:03] Done (elapsed time=00:12:14, CPU time=00:12:11, peak memory=14.6gb)