[2026-06-08T07:24:24] Launching Arriba 2.4.0
[2026-06-08T07:24:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:24:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:24:53] Reading chimeric alignments from 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1571685)
[2026-06-08T07:25:31] Marking multi-mapping alignments (marked=1332301)
[2026-06-08T07:25:32] Detecting strandedness (no)
[2026-06-08T07:25:32] Annotating alignments 
[2026-06-08T07:25:41] Filtering duplicates (remaining=746782)
[2026-06-08T07:25:43] 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=620940)
[2026-06-08T07:25:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=620940)
[2026-06-08T07:25:44] Filtering viral contigs with expression lower than the top 5 (remaining=620940)
[2026-06-08T07:25:44] Filtering viral contigs with less than 5% coverage (remaining=620940)
[2026-06-08T07:25:45] Estimating fragment length (mate gap mean=-43.2265, mate gap stddev=29.4148, read length mean=75.5173)
[2026-06-08T07:25:45] Filtering read-through fragments with a distance <=10000bp (remaining=614005)
[2026-06-08T07:25:45] Filtering inconsistently clipped mates (remaining=598131)
[2026-06-08T07:25:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=549851)
[2026-06-08T07:25:47] Filtering fragments with small insert size (remaining=549188)
[2026-06-08T07:25:47] Filtering alignments with long gaps (remaining=549188)
[2026-06-08T07:25:47] Filtering fragments with both mates in the same gene (remaining=548414)
[2026-06-08T07:25:48] Filtering fusions arising from hairpin structures (remaining=527467)
[2026-06-08T07:25:48] Filtering reads with a mismatch p-value <=0.01 (remaining=57590)
[2026-06-08T07:25:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=20720)
[2026-06-08T07:25:51] Finding fusions and counting supporting reads (total=22077)
[2026-06-08T07:25:53] Merging adjacent fusion breakpoints (remaining=21966)
[2026-06-08T07:25:54] Filtering multi-mapping fusions by alignment score and read support (remaining=11117)
[2026-06-08T07:26:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:26:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=10901)
[2026-06-08T07:26:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=9125)
[2026-06-08T07:26:03] Filtering fusions with <2 supporting reads (remaining=177)
[2026-06-08T07:26:03] Filtering fusions with an e-value >=0.3 (remaining=109)
[2026-06-08T07:26:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=111)
[2026-06-08T07:26:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=86)
[2026-06-08T07:26:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=86)
[2026-06-08T07:26:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=76)
[2026-06-08T07:26:05] Searching for fusions with spliced split reads (remaining=76)
[2026-06-08T07:26:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=69)
[2026-06-08T07:26:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=69)
[2026-06-08T07:26:06] Searching for fusions with >=4 spliced events (remaining=69)
[2026-06-08T07:26:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=20)
[2026-06-08T07:26:27] Filtering fusions with anchors <=23nt (remaining=7)
[2026-06-08T07:26:27] Filtering end-to-end fusions with low support (remaining=2)
[2026-06-08T07:26:27] Filtering fusions with no coverage around the breakpoints (remaining=2)
[2026-06-08T07:26:27] Indexing gene sequences 
[2026-06-08T07:26:27] Filtering genes with >=30% identity (remaining=2)
[2026-06-08T07:26:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-06-08T07:26:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-06-08T07:26:28] Searching for additional isoforms (remaining=1)
[2026-06-08T07:26:28] Assigning confidence scores to events 
[2026-06-08T07:26:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:26:29] Writing fusions to file 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:26:29] Writing discarded fusions to file 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:26:35] Freeing resources
[2026-06-08T07:26:40] Done (elapsed time=00:02:16, CPU time=00:02:14, peak memory=5.69gb)