[2026-06-08T08:38:33] Launching Arriba 2.4.0
[2026-06-08T08:38:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:45] Reading chimeric alignments from 'tih_rna_sample_00740_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12935174)
[2026-06-08T08:45:37] Marking multi-mapping alignments (marked=8427553)
[2026-06-08T08:45:43] Detecting strandedness (reverse)
[2026-06-08T08:45:43] Assigning strands to alignments 
[2026-06-08T08:45:45] Annotating alignments 
[2026-06-08T08:46:27] Filtering duplicates (remaining=7256780)
[2026-06-08T08:46:36] 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=6717095)
[2026-06-08T08:46:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6717095)
[2026-06-08T08:46:41] Filtering viral contigs with expression lower than the top 5 (remaining=6717095)
[2026-06-08T08:46:46] Filtering viral contigs with less than 5% coverage (remaining=6717095)
[2026-06-08T08:46:49] Estimating fragment length (mate gap mean=-87.2009, mate gap stddev=28.8987, read length mean=131.529)
[2026-06-08T08:46:49] Filtering read-through fragments with a distance <=10000bp (remaining=6316434)
[2026-06-08T08:46:52] Filtering inconsistently clipped mates (remaining=6238893)
[2026-06-08T08:46:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6120616)
[2026-06-08T08:47:00] Filtering fragments with small insert size (remaining=6119875)
[2026-06-08T08:47:03] Filtering alignments with long gaps (remaining=6119875)
[2026-06-08T08:47:06] Filtering fragments with both mates in the same gene (remaining=6118787)
[2026-06-08T08:47:09] Filtering fusions arising from hairpin structures (remaining=5874527)
[2026-06-08T08:47:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2795683)
[2026-06-08T08:47:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=1084209)
[2026-06-08T08:47:39] Finding fusions and counting supporting reads (total=729144)
[2026-06-08T08:47:59] Merging adjacent fusion breakpoints (remaining=721101)
[2026-06-08T08:48:01] Filtering multi-mapping fusions by alignment score and read support (remaining=437931)
[2026-06-08T08:48:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=436176)
[2026-06-08T08:48:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=267825)
[2026-06-08T08:48:51] Filtering fusions with <2 supporting reads (remaining=45570)
[2026-06-08T08:48:51] Filtering fusions with an e-value >=0.3 (remaining=11850)
[2026-06-08T08:48:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11910)
[2026-06-08T08:48:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11833)
[2026-06-08T08:48:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11833)
[2026-06-08T08:48:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9359)
[2026-06-08T08:49:05] Searching for fusions with spliced split reads (remaining=9390)
[2026-06-08T08:49:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=5680)
[2026-06-08T08:49:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5611)
[2026-06-08T08:49:13] Searching for fusions with >=4 spliced events (remaining=6790)
[2026-06-08T08:49:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2378)
[2026-06-08T08:49:29] Filtering fusions with anchors <=23nt (remaining=1851)
[2026-06-08T08:49:30] Filtering end-to-end fusions with low support (remaining=1772)
[2026-06-08T08:49:31] Filtering fusions with no coverage around the breakpoints (remaining=1733)
[2026-06-08T08:49:31] Indexing gene sequences 
[2026-06-08T08:49:37] Filtering genes with >=30% identity (remaining=445)
[2026-06-08T08:49:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=145)
[2026-06-08T08:49:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=134)
[2026-06-08T08:49:44] Searching for additional isoforms (remaining=181)
[2026-06-08T08:49:45] Assigning confidence scores to events 
[2026-06-08T08:49:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:49] Writing fusions to file 'tih_rna_sample_00740_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:50] Writing discarded fusions to file 'tih_rna_sample_00740_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:23] Freeing resources
[2026-06-08T08:50:43] Done (elapsed time=00:12:10, CPU time=00:12:09, peak memory=17.7gb)