[2026-05-28T21:15:49] Launching Arriba 2.4.0
[2026-05-28T21:15:49] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:16:02] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:16:06] Reading chimeric alignments from 'Hs746T_FFPE_RNA_0001_23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11932485)
[2026-05-28T21:25:28] Marking multi-mapping alignments (marked=7832040)
[2026-05-28T21:25:35] Detecting strandedness (reverse)
[2026-05-28T21:25:35] Assigning strands to alignments 
[2026-05-28T21:25:38] Annotating alignments 
[2026-05-28T21:26:41] Filtering duplicates (remaining=8742491)
[2026-05-28T21:26:56] 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=8211449)
[2026-05-28T21:26:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8211449)
[2026-05-28T21:27:02] Filtering viral contigs with expression lower than the top 5 (remaining=8211449)
[2026-05-28T21:27:09] Filtering viral contigs with less than 5% coverage (remaining=8211449)
[2026-05-28T21:27:12] Estimating fragment length (mate gap mean=-82.7969, mate gap stddev=33.821, read length mean=127.435)
[2026-05-28T21:27:12] Filtering read-through fragments with a distance <=10000bp (remaining=7826113)
[2026-05-28T21:27:15] Filtering inconsistently clipped mates (remaining=7695968)
[2026-05-28T21:27:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7414483)
[2026-05-28T21:27:25] Filtering fragments with small insert size (remaining=7413209)
[2026-05-28T21:27:27] Filtering alignments with long gaps (remaining=7413209)
[2026-05-28T21:27:30] Filtering fragments with both mates in the same gene (remaining=7411796)
[2026-05-28T21:27:34] Filtering fusions arising from hairpin structures (remaining=6881483)
[2026-05-28T21:27:39] Filtering reads with a mismatch p-value <=0.01 (remaining=3134282)
[2026-05-28T21:27:58] Filtering reads with low entropy (k-mer content >=60%) (remaining=1340001)
[2026-05-28T21:28:17] Finding fusions and counting supporting reads (total=1063852)
[2026-05-28T21:28:51] Merging adjacent fusion breakpoints (remaining=1054637)
[2026-05-28T21:28:55] Filtering multi-mapping fusions by alignment score and read support (remaining=664367)
[2026-05-28T21:29:53] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:30:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=661544)
[2026-05-28T21:30:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=405366)
[2026-05-28T21:30:15] Filtering fusions with <2 supporting reads (remaining=40449)
[2026-05-28T21:30:16] Filtering fusions with an e-value >=0.3 (remaining=9703)
[2026-05-28T21:30:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9755)
[2026-05-28T21:30:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8544)
[2026-05-28T21:30:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8545)
[2026-05-28T21:30:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7252)
[2026-05-28T21:30:41] Searching for fusions with spliced split reads (remaining=7281)
[2026-05-28T21:30:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=4628)
[2026-05-28T21:30:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4593)
[2026-05-28T21:30:57] Searching for fusions with >=4 spliced events (remaining=5933)
[2026-05-28T21:31:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2728)
[2026-05-28T21:31:34] Filtering fusions with anchors <=23nt (remaining=2247)
[2026-05-28T21:31:36] Filtering end-to-end fusions with low support (remaining=2184)
[2026-05-28T21:31:37] Filtering fusions with no coverage around the breakpoints (remaining=2142)
[2026-05-28T21:31:39] Indexing gene sequences 
[2026-05-28T21:32:07] Filtering genes with >=30% identity (remaining=834)
[2026-05-28T21:32:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=441)
[2026-05-28T21:32:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=294)
[2026-05-28T21:32:54] Searching for additional isoforms (remaining=472)
[2026-05-28T21:32:56] Assigning confidence scores to events 
[2026-05-28T21:33:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:33:06] Writing fusions to file 'Hs746T_FFPE_RNA_0001_23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:33:17] Writing discarded fusions to file 'Hs746T_FFPE_RNA_0001_23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:34:24] Freeing resources
[2026-05-28T21:34:54] Done (elapsed time=00:19:05, CPU time=00:19:04, peak memory=17.1gb)