[2026-06-08T08:31:10] Launching Arriba 2.4.0
[2026-06-08T08:31:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:27] Reading chimeric alignments from 'SW780_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11953072)
[2026-06-08T08:38:57] Marking multi-mapping alignments (marked=8172180)
[2026-06-08T08:39:02] Detecting strandedness (reverse)
[2026-06-08T08:39:02] Assigning strands to alignments 
[2026-06-08T08:39:04] Annotating alignments 
[2026-06-08T08:39:40] Filtering duplicates (remaining=8310521)
[2026-06-08T08:39:47] 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)
[2026-06-08T08:39:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7740866)
[2026-06-08T08:39:51] Filtering viral contigs with expression lower than the top 5 (remaining=7740866)
[2026-06-08T08:39:56] Filtering viral contigs with less than 5% coverage (remaining=7740866)
[2026-06-08T08:39:58] Estimating fragment length (mate gap mean=-85.0735, mate gap stddev=30.5471, read length mean=127.753)
[2026-06-08T08:39:58] Filtering read-through fragments with a distance <=10000bp (remaining=7388478)
[2026-06-08T08:40:00] Filtering inconsistently clipped mates (remaining=7256467)
[2026-06-08T08:40:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6914836)
[2026-06-08T08:40:08] Filtering fragments with small insert size (remaining=6913605)
[2026-06-08T08:40:10] Filtering alignments with long gaps (remaining=6913605)
[2026-06-08T08:40:13] Filtering fragments with both mates in the same gene (remaining=6912067)
[2026-06-08T08:40:15] Filtering fusions arising from hairpin structures (remaining=6479644)
[2026-06-08T08:40:18] Filtering reads with a mismatch p-value <=0.01 (remaining=3010425)
[2026-06-08T08:40:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=1227079)
[2026-06-08T08:40:47] Finding fusions and counting supporting reads (total=963642)
[2026-06-08T08:41:06] Merging adjacent fusion breakpoints (remaining=957356)
[2026-06-08T08:41:09] Filtering multi-mapping fusions by alignment score and read support (remaining=575827)
[2026-06-08T08:41:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=573489)
[2026-06-08T08:41:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=364159)
[2026-06-08T08:41:56] Filtering fusions with <2 supporting reads (remaining=34720)
[2026-06-08T08:41:56] Filtering fusions with an e-value >=0.3 (remaining=7654)
[2026-06-08T08:41:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7704)
[2026-06-08T08:42:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7528)
[2026-06-08T08:42:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7533)
[2026-06-08T08:42:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6448)
[2026-06-08T08:42:10] Searching for fusions with spliced split reads (remaining=6468)
[2026-06-08T08:42:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=4226)
[2026-06-08T08:42:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4185)
[2026-06-08T08:42:18] Searching for fusions with >=4 spliced events (remaining=5189)
[2026-06-08T08:42:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2403)
[2026-06-08T08:42:36] Filtering fusions with anchors <=23nt (remaining=1922)
[2026-06-08T08:42:37] Filtering end-to-end fusions with low support (remaining=1877)
[2026-06-08T08:42:37] Filtering fusions with no coverage around the breakpoints (remaining=1852)
[2026-06-08T08:42:38] Indexing gene sequences 
[2026-06-08T08:42:46] Filtering genes with >=30% identity (remaining=659)
[2026-06-08T08:42:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=395)
[2026-06-08T08:42:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=283)
[2026-06-08T08:43:00] Searching for additional isoforms (remaining=448)
[2026-06-08T08:43:01] Assigning confidence scores to events 
[2026-06-08T08:43:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:06] Writing fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:10] Writing discarded fusions to file 'SW780_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:45] Freeing resources
[2026-06-08T08:44:04] Done (elapsed time=00:12:54, CPU time=00:12:53, peak memory=16.9gb)