[2026-05-28T00:15:41] Launching Arriba 2.4.0
[2026-05-28T00:15:41] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:15:50] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:15:53] Reading chimeric alignments from 'tih_rna_sample_00457_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3344997)
[2026-05-28T00:18:05] Marking multi-mapping alignments (marked=2082149)
[2026-05-28T00:18:06] Detecting strandedness (reverse)
[2026-05-28T00:18:06] Assigning strands to alignments 
[2026-05-28T00:18:07] Annotating alignments 
[2026-05-28T00:18:17] Filtering duplicates (remaining=2179176)
[2026-05-28T00:18:19] 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=2071938)
[2026-05-28T00:18:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2071938)
[2026-05-28T00:18:21] Filtering viral contigs with expression lower than the top 5 (remaining=2071938)
[2026-05-28T00:18:22] Filtering viral contigs with less than 5% coverage (remaining=2071938)
[2026-05-28T00:18:23] Estimating fragment length (mate gap mean=-87.8765, mate gap stddev=29.0586, read length mean=133.55)
[2026-05-28T00:18:23] Filtering read-through fragments with a distance <=10000bp (remaining=1920932)
[2026-05-28T00:18:24] Filtering inconsistently clipped mates (remaining=1892435)
[2026-05-28T00:18:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1851000)
[2026-05-28T00:18:26] Filtering fragments with small insert size (remaining=1850714)
[2026-05-28T00:18:26] Filtering alignments with long gaps (remaining=1850714)
[2026-05-28T00:18:27] Filtering fragments with both mates in the same gene (remaining=1850383)
[2026-05-28T00:18:28] Filtering fusions arising from hairpin structures (remaining=1753570)
[2026-05-28T00:18:28] Filtering reads with a mismatch p-value <=0.01 (remaining=757058)
[2026-05-28T00:18:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=339141)
[2026-05-28T00:18:36] Finding fusions and counting supporting reads (total=284194)
[2026-05-28T00:18:41] Merging adjacent fusion breakpoints (remaining=282654)
[2026-05-28T00:18:42] Filtering multi-mapping fusions by alignment score and read support (remaining=193960)
[2026-05-28T00:18:53] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:18:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=193028)
[2026-05-28T00:18:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=95537)
[2026-05-28T00:18:56] Filtering fusions with <2 supporting reads (remaining=13462)
[2026-05-28T00:18:56] Filtering fusions with an e-value >=0.3 (remaining=4864)
[2026-05-28T00:18:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4905)
[2026-05-28T00:18:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4884)
[2026-05-28T00:18:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4884)
[2026-05-28T00:18:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3058)
[2026-05-28T00:19:01] Searching for fusions with spliced split reads (remaining=3098)
[2026-05-28T00:19:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=2160)
[2026-05-28T00:19:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2124)
[2026-05-28T00:19:03] Searching for fusions with >=4 spliced events (remaining=2283)
[2026-05-28T00:19:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=694)
[2026-05-28T00:19:15] Filtering fusions with anchors <=23nt (remaining=536)
[2026-05-28T00:19:15] Filtering end-to-end fusions with low support (remaining=515)
[2026-05-28T00:19:15] Filtering fusions with no coverage around the breakpoints (remaining=500)
[2026-05-28T00:19:16] Indexing gene sequences 
[2026-05-28T00:19:18] Filtering genes with >=30% identity (remaining=219)
[2026-05-28T00:19:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=154)
[2026-05-28T00:19:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=154)
[2026-05-28T00:19:22] Searching for additional isoforms (remaining=172)
[2026-05-28T00:19:23] Assigning confidence scores to events 
[2026-05-28T00:19:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:19:24] Writing fusions to file 'tih_rna_sample_00457_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:19:25] Writing discarded fusions to file 'tih_rna_sample_00457_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:19:36] Freeing resources
[2026-05-28T00:19:42] Done (elapsed time=00:04:01, CPU time=00:03:59, peak memory=7.69gb)