[2026-06-08T08:53:32] Launching Arriba 2.4.0
[2026-06-08T08:53:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:51] Reading chimeric alignments from 'FFPE_HD789_01_RNA_13_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=13019557)
[2026-06-08T09:02:31] Marking multi-mapping alignments (marked=8369637)
[2026-06-08T09:02:37] Detecting strandedness (reverse)
[2026-06-08T09:02:37] Assigning strands to alignments 
[2026-06-08T09:02:39] Annotating alignments 
[2026-06-08T09:03:24] Filtering duplicates (remaining=9537478)
[2026-06-08T09:03:33] 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=9300557)
[2026-06-08T09:03:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9300557)
[2026-06-08T09:03:38] Filtering viral contigs with expression lower than the top 5 (remaining=9300557)
[2026-06-08T09:03:44] Filtering viral contigs with less than 5% coverage (remaining=9300557)
[2026-06-08T09:03:46] Estimating fragment length (mate gap mean=-73.284, mate gap stddev=43.8434, read length mean=143.38)
[2026-06-08T09:03:46] Filtering read-through fragments with a distance <=10000bp (remaining=9009033)
[2026-06-08T09:03:49] Filtering inconsistently clipped mates (remaining=8915620)
[2026-06-08T09:03:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8578237)
[2026-06-08T09:03:57] Filtering fragments with small insert size (remaining=8577770)
[2026-06-08T09:03:59] Filtering alignments with long gaps (remaining=8577769)
[2026-06-08T09:04:02] Filtering fragments with both mates in the same gene (remaining=8576553)
[2026-06-08T09:04:04] Filtering fusions arising from hairpin structures (remaining=8209123)
[2026-06-08T09:04:07] Filtering reads with a mismatch p-value <=0.01 (remaining=3973163)
[2026-06-08T09:04:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=1206285)
[2026-06-08T09:04:43] Finding fusions and counting supporting reads (total=932837)
[2026-06-08T09:05:05] Merging adjacent fusion breakpoints (remaining=927204)
[2026-06-08T09:05:08] Filtering multi-mapping fusions by alignment score and read support (remaining=615122)
[2026-06-08T09:05:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:06:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=610550)
[2026-06-08T09:06:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=391825)
[2026-06-08T09:06:03] Filtering fusions with <2 supporting reads (remaining=48083)
[2026-06-08T09:06:04] Filtering fusions with an e-value >=0.3 (remaining=18556)
[2026-06-08T09:06:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=18613)
[2026-06-08T09:06:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=18530)
[2026-06-08T09:06:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=18544)
[2026-06-08T09:06:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10552)
[2026-06-08T09:06:20] Searching for fusions with spliced split reads (remaining=10620)
[2026-06-08T09:06:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=4811)
[2026-06-08T09:06:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4768)
[2026-06-08T09:06:30] Searching for fusions with >=4 spliced events (remaining=6278)
[2026-06-08T09:06:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2635)
[2026-06-08T09:06:49] Filtering fusions with anchors <=23nt (remaining=2197)
[2026-06-08T09:06:50] Filtering end-to-end fusions with low support (remaining=2150)
[2026-06-08T09:06:51] Filtering fusions with no coverage around the breakpoints (remaining=2096)
[2026-06-08T09:06:52] Indexing gene sequences 
[2026-06-08T09:07:00] Filtering genes with >=30% identity (remaining=665)
[2026-06-08T09:07:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=394)
[2026-06-08T09:07:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=250)
[2026-06-08T09:07:11] Searching for additional isoforms (remaining=385)
[2026-06-08T09:07:13] Assigning confidence scores to events 
[2026-06-08T09:07:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:07:19] Writing fusions to file 'FFPE_HD789_01_RNA_13_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:07:23] Writing discarded fusions to file 'FFPE_HD789_01_RNA_13_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:09] Freeing resources
[2026-06-08T09:08:33] Done (elapsed time=00:15:01, CPU time=00:15:00, peak memory=17.5gb)