[2026-05-28T20:54:12] Launching Arriba 2.4.0
[2026-05-28T20:54:12] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:54:28] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:54:34] Reading chimeric alignments from 'BT-20_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=8262625)
[2026-05-28T20:57:52] Marking multi-mapping alignments (marked=6523031)
[2026-05-28T20:57:55] Detecting strandedness (reverse)
[2026-05-28T20:57:55] Assigning strands to alignments 
[2026-05-28T20:57:57] Annotating alignments 
[2026-05-28T20:58:28] Filtering duplicates (remaining=4347759)
[2026-05-28T20:58:35] 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=3949618)
[2026-05-28T20:58:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3949618)
[2026-05-28T20:58:37] Filtering viral contigs with expression lower than the top 5 (remaining=3949618)
[2026-05-28T20:58:41] Filtering viral contigs with less than 5% coverage (remaining=3949618)
[2026-05-28T20:58:43] Estimating fragment length (mate gap mean=-66.042, mate gap stddev=29.7895, read length mean=99.118)
[2026-05-28T20:58:43] Filtering read-through fragments with a distance <=10000bp (remaining=3876906)
[2026-05-28T20:58:44] Filtering inconsistently clipped mates (remaining=3755643)
[2026-05-28T20:58:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3232547)
[2026-05-28T20:58:49] Filtering fragments with small insert size (remaining=3227193)
[2026-05-28T20:58:50] Filtering alignments with long gaps (remaining=3227193)
[2026-05-28T20:58:52] Filtering fragments with both mates in the same gene (remaining=3225615)
[2026-05-28T20:58:53] Filtering fusions arising from hairpin structures (remaining=3020779)
[2026-05-28T20:58:55] Filtering reads with a mismatch p-value <=0.01 (remaining=672070)
[2026-05-28T20:59:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=322374)
[2026-05-28T20:59:06] Finding fusions and counting supporting reads (total=332074)
[2026-05-28T20:59:17] Merging adjacent fusion breakpoints (remaining=330680)
[2026-05-28T20:59:19] Filtering multi-mapping fusions by alignment score and read support (remaining=142746)
[2026-05-28T20:59:44] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:59:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=141465)
[2026-05-28T20:59:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=119777)
[2026-05-28T20:59:50] Filtering fusions with <2 supporting reads (remaining=3763)
[2026-05-28T20:59:50] Filtering fusions with an e-value >=0.3 (remaining=806)
[2026-05-28T20:59:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=836)
[2026-05-28T20:59:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=717)
[2026-05-28T20:59:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=717)
[2026-05-28T20:59:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=716)
[2026-05-28T20:59:59] Searching for fusions with spliced split reads (remaining=741)
[2026-05-28T21:00:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=591)
[2026-05-28T21:00:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=588)
[2026-05-28T21:00:04] Searching for fusions with >=4 spliced events (remaining=601)
[2026-05-28T21:00:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=172)
[2026-05-28T21:00:20] Filtering fusions with anchors <=23nt (remaining=139)
[2026-05-28T21:00:21] Filtering end-to-end fusions with low support (remaining=131)
[2026-05-28T21:00:21] Filtering fusions with no coverage around the breakpoints (remaining=127)
[2026-05-28T21:00:22] Indexing gene sequences 
[2026-05-28T21:00:23] Filtering genes with >=30% identity (remaining=48)
[2026-05-28T21:00:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=25)
[2026-05-28T21:00:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=25)
[2026-05-28T21:00:26] Searching for additional isoforms (remaining=28)
[2026-05-28T21:00:27] Assigning confidence scores to events 
[2026-05-28T21:00:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:00:30] Writing fusions to file 'BT-20_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T21:00:31] Writing discarded fusions to file 'BT-20_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T21:00:57] Freeing resources
[2026-05-28T21:01:10] Done (elapsed time=00:06:58, CPU time=00:06:57, peak memory=13gb)