[2026-06-08T08:35:10] Launching Arriba 2.4.0
[2026-06-08T08:35:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:22] Reading chimeric alignments from 'MCF7_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12363051)
[2026-06-08T08:42:31] Marking multi-mapping alignments (marked=8260694)
[2026-06-08T08:42:36] Detecting strandedness (reverse)
[2026-06-08T08:42:36] Assigning strands to alignments 
[2026-06-08T08:42:38] Annotating alignments 
[2026-06-08T08:43:18] Filtering duplicates (remaining=9002802)
[2026-06-08T08:43:27] 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=8378612)
[2026-06-08T08:43:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8378612)
[2026-06-08T08:43:32] Filtering viral contigs with expression lower than the top 5 (remaining=8378612)
[2026-06-08T08:43:37] Filtering viral contigs with less than 5% coverage (remaining=8378612)
[2026-06-08T08:43:40] Estimating fragment length (mate gap mean=-84.4767, mate gap stddev=30.6022, read length mean=130.88)
[2026-06-08T08:43:40] Filtering read-through fragments with a distance <=10000bp (remaining=7942080)
[2026-06-08T08:43:43] Filtering inconsistently clipped mates (remaining=7815912)
[2026-06-08T08:43:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7501693)
[2026-06-08T08:43:50] Filtering fragments with small insert size (remaining=7500358)
[2026-06-08T08:43:53] Filtering alignments with long gaps (remaining=7500358)
[2026-06-08T08:43:55] Filtering fragments with both mates in the same gene (remaining=7498887)
[2026-06-08T08:43:58] Filtering fusions arising from hairpin structures (remaining=7056514)
[2026-06-08T08:44:01] Filtering reads with a mismatch p-value <=0.01 (remaining=3406421)
[2026-06-08T08:44:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=1557717)
[2026-06-08T08:44:31] Finding fusions and counting supporting reads (total=1169665)
[2026-06-08T08:44:50] Merging adjacent fusion breakpoints (remaining=1161795)
[2026-06-08T08:44:52] Filtering multi-mapping fusions by alignment score and read support (remaining=690939)
[2026-06-08T08:45:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=687752)
[2026-06-08T08:45:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=443304)
[2026-06-08T08:45:41] Filtering fusions with <2 supporting reads (remaining=45617)
[2026-06-08T08:45:42] Filtering fusions with an e-value >=0.3 (remaining=11035)
[2026-06-08T08:45:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11077)
[2026-06-08T08:45:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10698)
[2026-06-08T08:45:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10709)
[2026-06-08T08:45:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8475)
[2026-06-08T08:45:58] Searching for fusions with spliced split reads (remaining=8533)
[2026-06-08T08:46:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=4893)
[2026-06-08T08:46:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4847)
[2026-06-08T08:46:07] Searching for fusions with >=4 spliced events (remaining=6489)
[2026-06-08T08:46:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3112)
[2026-06-08T08:46:23] Filtering fusions with anchors <=23nt (remaining=2643)
[2026-06-08T08:46:24] Filtering end-to-end fusions with low support (remaining=2602)
[2026-06-08T08:46:25] Filtering fusions with no coverage around the breakpoints (remaining=2575)
[2026-06-08T08:46:26] Indexing gene sequences 
[2026-06-08T08:46:35] Filtering genes with >=30% identity (remaining=1148)
[2026-06-08T08:46:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=831)
[2026-06-08T08:47:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=479)
[2026-06-08T08:47:05] Searching for additional isoforms (remaining=762)
[2026-06-08T08:47:07] Assigning confidence scores to events 
[2026-06-08T08:47:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:12] Writing fusions to file 'MCF7_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:20] Writing discarded fusions to file 'MCF7_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:59] Freeing resources
[2026-06-08T08:48:19] Done (elapsed time=00:13:09, CPU time=00:13:08, peak memory=17.4gb)