[2026-05-28T22:24:49] Launching Arriba 2.4.0
[2026-05-28T22:24:49] Loading assembly from 'ref_genome.fa' 
[2026-05-28T22:25:09] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T22:25:16] Reading chimeric alignments from 'Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=11446627)
[2026-05-28T22:36:26] Marking multi-mapping alignments (marked=7513721)
[2026-05-28T22:36:32] Detecting strandedness (reverse)
[2026-05-28T22:36:32] Assigning strands to alignments 
[2026-05-28T22:36:35] Annotating alignments 
[2026-05-28T22:37:24] Filtering duplicates (remaining=8369266)
[2026-05-28T22:37:35] 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=7900541)
[2026-05-28T22:37:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7900541)
[2026-05-28T22:37:40] Filtering viral contigs with expression lower than the top 5 (remaining=7900541)
[2026-05-28T22:37:47] Filtering viral contigs with less than 5% coverage (remaining=7900541)
[2026-05-28T22:37:50] Estimating fragment length (mate gap mean=-81.0841, mate gap stddev=34.333, read length mean=126.201)
[2026-05-28T22:37:50] Filtering read-through fragments with a distance <=10000bp (remaining=7539539)
[2026-05-28T22:37:53] Filtering inconsistently clipped mates (remaining=7420693)
[2026-05-28T22:37:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7153744)
[2026-05-28T22:38:03] Filtering fragments with small insert size (remaining=7152579)
[2026-05-28T22:38:05] Filtering alignments with long gaps (remaining=7152579)
[2026-05-28T22:38:08] Filtering fragments with both mates in the same gene (remaining=7151102)
[2026-05-28T22:38:11] Filtering fusions arising from hairpin structures (remaining=6681519)
[2026-05-28T22:38:15] Filtering reads with a mismatch p-value <=0.01 (remaining=3021515)
[2026-05-28T22:38:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=1268285)
[2026-05-28T22:38:54] Finding fusions and counting supporting reads (total=997829)
[2026-05-28T22:39:26] Merging adjacent fusion breakpoints (remaining=989342)
[2026-05-28T22:39:29] Filtering multi-mapping fusions by alignment score and read support (remaining=631551)
[2026-05-28T22:40:24] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T22:40:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=629089)
[2026-05-28T22:40:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=387222)
[2026-05-28T22:40:38] Filtering fusions with <2 supporting reads (remaining=38073)
[2026-05-28T22:40:39] Filtering fusions with an e-value >=0.3 (remaining=8194)
[2026-05-28T22:40:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8248)
[2026-05-28T22:40:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7828)
[2026-05-28T22:40:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7828)
[2026-05-28T22:40:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7035)
[2026-05-28T22:40:57] Searching for fusions with spliced split reads (remaining=7065)
[2026-05-28T22:41:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=4438)
[2026-05-28T22:41:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4403)
[2026-05-28T22:41:08] Searching for fusions with >=4 spliced events (remaining=5666)
[2026-05-28T22:41:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2584)
[2026-05-28T22:41:29] Filtering fusions with anchors <=23nt (remaining=2126)
[2026-05-28T22:41:30] Filtering end-to-end fusions with low support (remaining=2061)
[2026-05-28T22:41:32] Filtering fusions with no coverage around the breakpoints (remaining=2034)
[2026-05-28T22:41:33] Indexing gene sequences 
[2026-05-28T22:41:47] Filtering genes with >=30% identity (remaining=773)
[2026-05-28T22:41:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=422)
[2026-05-28T22:42:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=277)
[2026-05-28T22:42:18] Searching for additional isoforms (remaining=451)
[2026-05-28T22:42:20] Assigning confidence scores to events 
[2026-05-28T22:42:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T22:42:28] Writing fusions to file 'Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T22:42:34] Writing discarded fusions to file 'Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T22:43:40] Freeing resources
[2026-05-28T22:44:08] Done (elapsed time=00:19:19, CPU time=00:19:17, peak memory=16.4gb)