[2026-05-28T21:27:54] Launching Arriba 2.4.0
[2026-05-28T21:27:54] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:28:08] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:28:12] Reading chimeric alignments from 'SW780_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11953072)
[2026-05-28T21:36:45] Marking multi-mapping alignments (marked=8172180)
[2026-05-28T21:36:50] Detecting strandedness (reverse)
[2026-05-28T21:36:50] Assigning strands to alignments 
[2026-05-28T21:36:52] Annotating alignments 
[2026-05-28T21:37:32] Filtering duplicates (remaining=8310521)
[2026-05-28T21:37:41] 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=7740866)
[2026-05-28T21:37:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7740866)
[2026-05-28T21:37:46] Filtering viral contigs with expression lower than the top 5 (remaining=7740866)
[2026-05-28T21:37:52] Filtering viral contigs with less than 5% coverage (remaining=7740866)
[2026-05-28T21:37:55] Estimating fragment length (mate gap mean=-85.0735, mate gap stddev=30.5471, read length mean=127.753)
[2026-05-28T21:37:55] Filtering read-through fragments with a distance <=10000bp (remaining=7388478)
[2026-05-28T21:37:57] Filtering inconsistently clipped mates (remaining=7256467)
[2026-05-28T21:38:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6914836)
[2026-05-28T21:38:06] Filtering fragments with small insert size (remaining=6913605)
[2026-05-28T21:38:08] Filtering alignments with long gaps (remaining=6913605)
[2026-05-28T21:38:11] Filtering fragments with both mates in the same gene (remaining=6912067)
[2026-05-28T21:38:14] Filtering fusions arising from hairpin structures (remaining=6479644)
[2026-05-28T21:38:16] Filtering reads with a mismatch p-value <=0.01 (remaining=3010425)
[2026-05-28T21:38:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=1227079)
[2026-05-28T21:38:48] Finding fusions and counting supporting reads (total=963642)
[2026-05-28T21:39:09] Merging adjacent fusion breakpoints (remaining=957356)
[2026-05-28T21:39:11] Filtering multi-mapping fusions by alignment score and read support (remaining=575827)
[2026-05-28T21:39:48] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:39:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=573489)
[2026-05-28T21:39:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=364159)
[2026-05-28T21:39:58] Filtering fusions with <2 supporting reads (remaining=34720)
[2026-05-28T21:39:59] Filtering fusions with an e-value >=0.3 (remaining=7654)
[2026-05-28T21:40:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7704)
[2026-05-28T21:40:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7528)
[2026-05-28T21:40:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7533)
[2026-05-28T21:40:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6448)
[2026-05-28T21:40:13] Searching for fusions with spliced split reads (remaining=6468)
[2026-05-28T21:40:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=4226)
[2026-05-28T21:40:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4185)
[2026-05-28T21:40:22] Searching for fusions with >=4 spliced events (remaining=5189)
[2026-05-28T21:40:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2403)
[2026-05-28T21:40:41] Filtering fusions with anchors <=23nt (remaining=1922)
[2026-05-28T21:40:43] Filtering end-to-end fusions with low support (remaining=1877)
[2026-05-28T21:40:44] Filtering fusions with no coverage around the breakpoints (remaining=1852)
[2026-05-28T21:40:45] Indexing gene sequences 
[2026-05-28T21:40:54] Filtering genes with >=30% identity (remaining=659)
[2026-05-28T21:40:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=395)
[2026-05-28T21:41:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=283)
[2026-05-28T21:41:08] Searching for additional isoforms (remaining=448)
[2026-05-28T21:41:10] Assigning confidence scores to events 
[2026-05-28T21:41:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:41:15] Writing fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:41:19] Writing discarded fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:41:59] Freeing resources
[2026-05-28T21:42:20] Done (elapsed time=00:14:26, CPU time=00:14:25, peak memory=16.9gb)