[2026-05-28T21:27:52] Launching Arriba 2.4.0
[2026-05-28T21:27:52] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:28:09] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:28:14] Reading chimeric alignments from 'SW780_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=10645676)
[2026-05-28T21:39:50] Marking multi-mapping alignments (marked=7236221)
[2026-05-28T21:39:56] Detecting strandedness (reverse)
[2026-05-28T21:39:56] Assigning strands to alignments 
[2026-05-28T21:39:59] Annotating alignments 
[2026-05-28T21:40:58] Filtering duplicates (remaining=7402563)
[2026-05-28T21:41:10] 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=6919016)
[2026-05-28T21:41:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6919016)
[2026-05-28T21:41:16] Filtering viral contigs with expression lower than the top 5 (remaining=6919016)
[2026-05-28T21:41:22] Filtering viral contigs with less than 5% coverage (remaining=6919016)
[2026-05-28T21:41:25] Estimating fragment length (mate gap mean=-83.0269, mate gap stddev=30.0444, read length mean=126.259)
[2026-05-28T21:41:25] Filtering read-through fragments with a distance <=10000bp (remaining=6626025)
[2026-05-28T21:41:28] Filtering inconsistently clipped mates (remaining=6525169)
[2026-05-28T21:41:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6156280)
[2026-05-28T21:41:36] Filtering fragments with small insert size (remaining=6155097)
[2026-05-28T21:41:39] Filtering alignments with long gaps (remaining=6155097)
[2026-05-28T21:41:42] Filtering fragments with both mates in the same gene (remaining=6153787)
[2026-05-28T21:41:45] Filtering fusions arising from hairpin structures (remaining=5853032)
[2026-05-28T21:41:49] Filtering reads with a mismatch p-value <=0.01 (remaining=2794403)
[2026-05-28T21:42:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=1036828)
[2026-05-28T21:42:28] Finding fusions and counting supporting reads (total=799558)
[2026-05-28T21:43:00] Merging adjacent fusion breakpoints (remaining=795300)
[2026-05-28T21:43:03] Filtering multi-mapping fusions by alignment score and read support (remaining=473548)
[2026-05-28T21:43:50] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:44:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=471407)
[2026-05-28T21:44:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=307919)
[2026-05-28T21:44:09] Filtering fusions with <2 supporting reads (remaining=30390)
[2026-05-28T21:44:10] Filtering fusions with an e-value >=0.3 (remaining=6969)
[2026-05-28T21:44:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7017)
[2026-05-28T21:44:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6783)
[2026-05-28T21:44:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6784)
[2026-05-28T21:44:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5595)
[2026-05-28T21:44:29] Searching for fusions with spliced split reads (remaining=5728)
[2026-05-28T21:44:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=3822)
[2026-05-28T21:44:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3783)
[2026-05-28T21:44:42] Searching for fusions with >=4 spliced events (remaining=4622)
[2026-05-28T21:44:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2053)
[2026-05-28T21:45:06] Filtering fusions with anchors <=23nt (remaining=1671)
[2026-05-28T21:45:07] Filtering end-to-end fusions with low support (remaining=1626)
[2026-05-28T21:45:08] Filtering fusions with no coverage around the breakpoints (remaining=1606)
[2026-05-28T21:45:09] Indexing gene sequences 
[2026-05-28T21:45:25] Filtering genes with >=30% identity (remaining=611)
[2026-05-28T21:45:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=367)
[2026-05-28T21:45:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=268)
[2026-05-28T21:45:45] Searching for additional isoforms (remaining=383)
[2026-05-28T21:45:47] Assigning confidence scores to events 
[2026-05-28T21:45:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:45:55] Writing fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T21:46:03] Writing discarded fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T21:47:10] Freeing resources
[2026-05-28T21:47:40] Done (elapsed time=00:19:48, CPU time=00:19:47, peak memory=15.3gb)