[2026-06-08T08:49:08] Launching Arriba 2.4.0
[2026-06-08T08:49:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:27] Reading chimeric alignments from 'MCF7_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=12687944)
[2026-06-08T08:58:26] Marking multi-mapping alignments (marked=8555829)
[2026-06-08T08:58:31] Detecting strandedness (reverse)
[2026-06-08T08:58:31] Assigning strands to alignments 
[2026-06-08T08:58:34] Annotating alignments 
[2026-06-08T08:59:18] Filtering duplicates (remaining=9226026)
[2026-06-08T08:59:29] 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=8559731)
[2026-06-08T08:59:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8559731)
[2026-06-08T08:59:34] Filtering viral contigs with expression lower than the top 5 (remaining=8559731)
[2026-06-08T08:59:41] Filtering viral contigs with less than 5% coverage (remaining=8559731)
[2026-06-08T08:59:44] Estimating fragment length (mate gap mean=-86.5039, mate gap stddev=29.9994, read length mean=130.63)
[2026-06-08T08:59:44] Filtering read-through fragments with a distance <=10000bp (remaining=8129812)
[2026-06-08T08:59:47] Filtering inconsistently clipped mates (remaining=8003422)
[2026-06-08T08:59:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7689283)
[2026-06-08T08:59:56] Filtering fragments with small insert size (remaining=7687814)
[2026-06-08T08:59:58] Filtering alignments with long gaps (remaining=7687813)
[2026-06-08T09:00:01] Filtering fragments with both mates in the same gene (remaining=7686250)
[2026-06-08T09:00:04] Filtering fusions arising from hairpin structures (remaining=7259603)
[2026-06-08T09:00:08] Filtering reads with a mismatch p-value <=0.01 (remaining=3388446)
[2026-06-08T09:00:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=1547792)
[2026-06-08T09:00:42] Finding fusions and counting supporting reads (total=1164633)
[2026-06-08T09:01:06] Merging adjacent fusion breakpoints (remaining=1157348)
[2026-06-08T09:01:09] Filtering multi-mapping fusions by alignment score and read support (remaining=693949)
[2026-06-08T09:01:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=690907)
[2026-06-08T09:02:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=450752)
[2026-06-08T09:02:04] Filtering fusions with <2 supporting reads (remaining=43884)
[2026-06-08T09:02:05] Filtering fusions with an e-value >=0.3 (remaining=10149)
[2026-06-08T09:02:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10189)
[2026-06-08T09:02:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9961)
[2026-06-08T09:02:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9977)
[2026-06-08T09:02:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8005)
[2026-06-08T09:02:21] Searching for fusions with spliced split reads (remaining=8077)
[2026-06-08T09:02:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=4772)
[2026-06-08T09:02:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4730)
[2026-06-08T09:02:31] Searching for fusions with >=4 spliced events (remaining=6300)
[2026-06-08T09:02:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3075)
[2026-06-08T09:02:51] Filtering fusions with anchors <=23nt (remaining=2604)
[2026-06-08T09:02:52] Filtering end-to-end fusions with low support (remaining=2559)
[2026-06-08T09:02:53] Filtering fusions with no coverage around the breakpoints (remaining=2531)
[2026-06-08T09:02:54] Indexing gene sequences 
[2026-06-08T09:03:06] Filtering genes with >=30% identity (remaining=1124)
[2026-06-08T09:03:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=819)
[2026-06-08T09:03:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=466)
[2026-06-08T09:03:41] Searching for additional isoforms (remaining=732)
[2026-06-08T09:03:43] Assigning confidence scores to events 
[2026-06-08T09:03:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:49] Writing fusions to file 'MCF7_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:04:00] Writing discarded fusions to file 'MCF7_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:47] Freeing resources
[2026-06-08T09:05:10] Done (elapsed time=00:16:02, CPU time=00:16:00, peak memory=17.7gb)