[2026-05-28T00:03:11] Launching Arriba 2.4.0
[2026-05-28T00:03:11] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:19] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:03:23] Reading chimeric alignments from 'tih_rna_sample_00158_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3778702)
[2026-05-28T00:05:40] Marking multi-mapping alignments (marked=2500668)
[2026-05-28T00:05:42] Detecting strandedness (reverse)
[2026-05-28T00:05:42] Assigning strands to alignments 
[2026-05-28T00:05:42] Annotating alignments 
[2026-05-28T00:05:56] Filtering duplicates (remaining=2052483)
[2026-05-28T00:05:58] 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=1931857)
[2026-05-28T00:05:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1931857)
[2026-05-28T00:05:59] Filtering viral contigs with expression lower than the top 5 (remaining=1931857)
[2026-05-28T00:06:01] Filtering viral contigs with less than 5% coverage (remaining=1931857)
[2026-05-28T00:06:02] Estimating fragment length (mate gap mean=-85.1051, mate gap stddev=29.9522, read length mean=132.562)
[2026-05-28T00:06:02] Filtering read-through fragments with a distance <=10000bp (remaining=1823209)
[2026-05-28T00:06:03] Filtering inconsistently clipped mates (remaining=1793849)
[2026-05-28T00:06:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1742059)
[2026-05-28T00:06:05] Filtering fragments with small insert size (remaining=1741702)
[2026-05-28T00:06:06] Filtering alignments with long gaps (remaining=1741702)
[2026-05-28T00:06:07] Filtering fragments with both mates in the same gene (remaining=1741387)
[2026-05-28T00:06:07] Filtering fusions arising from hairpin structures (remaining=1651476)
[2026-05-28T00:06:08] Filtering reads with a mismatch p-value <=0.01 (remaining=723163)
[2026-05-28T00:06:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=264464)
[2026-05-28T00:06:16] Finding fusions and counting supporting reads (total=221509)
[2026-05-28T00:06:22] Merging adjacent fusion breakpoints (remaining=220210)
[2026-05-28T00:06:23] Filtering multi-mapping fusions by alignment score and read support (remaining=132412)
[2026-05-28T00:06:36] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:06:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=131182)
[2026-05-28T00:06:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=71632)
[2026-05-28T00:06:39] Filtering fusions with <2 supporting reads (remaining=9309)
[2026-05-28T00:06:39] Filtering fusions with an e-value >=0.3 (remaining=3262)
[2026-05-28T00:06:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3288)
[2026-05-28T00:06:41] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3257)
[2026-05-28T00:06:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3258)
[2026-05-28T00:06:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2477)
[2026-05-28T00:06:44] Searching for fusions with spliced split reads (remaining=2623)
[2026-05-28T00:06:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=1801)
[2026-05-28T00:06:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1782)
[2026-05-28T00:06:46] Searching for fusions with >=4 spliced events (remaining=1901)
[2026-05-28T00:06:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=485)
[2026-05-28T00:06:59] Filtering fusions with anchors <=23nt (remaining=368)
[2026-05-28T00:06:59] Filtering end-to-end fusions with low support (remaining=355)
[2026-05-28T00:07:00] Filtering fusions with no coverage around the breakpoints (remaining=344)
[2026-05-28T00:07:00] Indexing gene sequences 
[2026-05-28T00:07:02] Filtering genes with >=30% identity (remaining=94)
[2026-05-28T00:07:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=38)
[2026-05-28T00:07:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=38)
[2026-05-28T00:07:04] Searching for additional isoforms (remaining=51)
[2026-05-28T00:07:04] Assigning confidence scores to events 
[2026-05-28T00:07:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:05] Writing fusions to file 'tih_rna_sample_00158_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:07:06] Writing discarded fusions to file 'tih_rna_sample_00158_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:07:17] Freeing resources
[2026-05-28T00:07:24] Done (elapsed time=00:04:13, CPU time=00:04:12, peak memory=8gb)