[2026-06-08T08:48:28] Launching Arriba 2.4.0
[2026-06-08T08:48:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:48] Reading chimeric alignments from 'FFPE_HD789_01_RNA_13_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=9885340)
[2026-06-08T08:56:12] Marking multi-mapping alignments (marked=6191410)
[2026-06-08T08:56:16] Detecting strandedness (reverse)
[2026-06-08T08:56:16] Assigning strands to alignments 
[2026-06-08T08:56:18] Annotating alignments 
[2026-06-08T08:56:51] Filtering duplicates (remaining=7030819)
[2026-06-08T08:56:58] 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=6807075)
[2026-06-08T08:57:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6807075)
[2026-06-08T08:57:01] Filtering viral contigs with expression lower than the top 5 (remaining=6807075)
[2026-06-08T08:57:06] Filtering viral contigs with less than 5% coverage (remaining=6807075)
[2026-06-08T08:57:08] Estimating fragment length (mate gap mean=-83.4661, mate gap stddev=34.8402, read length mean=142.905)
[2026-06-08T08:57:08] Filtering read-through fragments with a distance <=10000bp (remaining=6531462)
[2026-06-08T08:57:10] Filtering inconsistently clipped mates (remaining=6464730)
[2026-06-08T08:57:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6269706)
[2026-06-08T08:57:15] Filtering fragments with small insert size (remaining=6269342)
[2026-06-08T08:57:17] Filtering alignments with long gaps (remaining=6269342)
[2026-06-08T08:57:19] Filtering fragments with both mates in the same gene (remaining=6268337)
[2026-06-08T08:57:21] Filtering fusions arising from hairpin structures (remaining=5936126)
[2026-06-08T08:57:24] Filtering reads with a mismatch p-value <=0.01 (remaining=3242005)
[2026-06-08T08:57:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=977404)
[2026-06-08T08:57:52] Finding fusions and counting supporting reads (total=719288)
[2026-06-08T08:58:08] Merging adjacent fusion breakpoints (remaining=715206)
[2026-06-08T08:58:10] Filtering multi-mapping fusions by alignment score and read support (remaining=479618)
[2026-06-08T08:58:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=474331)
[2026-06-08T08:58:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=281638)
[2026-06-08T08:58:51] Filtering fusions with <2 supporting reads (remaining=44692)
[2026-06-08T08:58:51] Filtering fusions with an e-value >=0.3 (remaining=18791)
[2026-06-08T08:58:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=18847)
[2026-06-08T08:58:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=18774)
[2026-06-08T08:58:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=18784)
[2026-06-08T08:58:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10256)
[2026-06-08T08:59:03] Searching for fusions with spliced split reads (remaining=10300)
[2026-06-08T08:59:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=4755)
[2026-06-08T08:59:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4715)
[2026-06-08T08:59:10] Searching for fusions with >=4 spliced events (remaining=6042)
[2026-06-08T08:59:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2461)
[2026-06-08T08:59:28] Filtering fusions with anchors <=23nt (remaining=2054)
[2026-06-08T08:59:28] Filtering end-to-end fusions with low support (remaining=2007)
[2026-06-08T08:59:29] Filtering fusions with no coverage around the breakpoints (remaining=1960)
[2026-06-08T08:59:30] Indexing gene sequences 
[2026-06-08T08:59:37] Filtering genes with >=30% identity (remaining=676)
[2026-06-08T08:59:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=404)
[2026-06-08T08:59:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=261)
[2026-06-08T08:59:48] Searching for additional isoforms (remaining=417)
[2026-06-08T08:59:49] Assigning confidence scores to events 
[2026-06-08T08:59:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:52] Writing fusions to file 'FFPE_HD789_01_RNA_13_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:56] Writing discarded fusions to file 'FFPE_HD789_01_RNA_13_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:27] Freeing resources
[2026-06-08T09:00:43] Done (elapsed time=00:12:15, CPU time=00:12:14, peak memory=14.3gb)