[2026-05-28T20:10:26] Launching Arriba 2.4.0
[2026-05-28T20:10:26] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:10:42] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:10:49] Reading chimeric alignments from 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1571685)
[2026-05-28T20:11:30] Marking multi-mapping alignments (marked=1332301)
[2026-05-28T20:11:31] Detecting strandedness (no)
[2026-05-28T20:11:31] Annotating alignments 
[2026-05-28T20:11:41] Filtering duplicates (remaining=746782)
[2026-05-28T20:11:43] 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)
[2026-05-28T20:11:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=620940)
[2026-05-28T20:11:44] Filtering viral contigs with expression lower than the top 5 (remaining=620940)
[2026-05-28T20:11:45] Filtering viral contigs with less than 5% coverage (remaining=620940)
[2026-05-28T20:11:46] Estimating fragment length (mate gap mean=-43.2265, mate gap stddev=29.4148, read length mean=75.5173)
[2026-05-28T20:11:46] Filtering read-through fragments with a distance <=10000bp (remaining=614005)
[2026-05-28T20:11:46] Filtering inconsistently clipped mates (remaining=598131)
[2026-05-28T20:11:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=549851)
[2026-05-28T20:11:47] Filtering fragments with small insert size (remaining=549188)
[2026-05-28T20:11:48] Filtering alignments with long gaps (remaining=549188)
[2026-05-28T20:11:48] Filtering fragments with both mates in the same gene (remaining=548414)
[2026-05-28T20:11:49] Filtering fusions arising from hairpin structures (remaining=527467)
[2026-05-28T20:11:49] Filtering reads with a mismatch p-value <=0.01 (remaining=57590)
[2026-05-28T20:11:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=20720)
[2026-05-28T20:11:51] Finding fusions and counting supporting reads (total=22077)
[2026-05-28T20:11:54] Merging adjacent fusion breakpoints (remaining=21966)
[2026-05-28T20:11:54] Filtering multi-mapping fusions by alignment score and read support (remaining=11117)
[2026-05-28T20:12:01] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:12:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=10901)
[2026-05-28T20:12:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=9125)
[2026-05-28T20:12:02] Filtering fusions with <2 supporting reads (remaining=177)
[2026-05-28T20:12:02] Filtering fusions with an e-value >=0.3 (remaining=109)
[2026-05-28T20:12:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=111)
[2026-05-28T20:12:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=86)
[2026-05-28T20:12:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=86)
[2026-05-28T20:12:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=76)
[2026-05-28T20:12:04] Searching for fusions with spliced split reads (remaining=76)
[2026-05-28T20:12:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=69)
[2026-05-28T20:12:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=69)
[2026-05-28T20:12:06] Searching for fusions with >=4 spliced events (remaining=69)
[2026-05-28T20:12:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=20)
[2026-05-28T20:12:29] Filtering fusions with anchors <=23nt (remaining=7)
[2026-05-28T20:12:29] Filtering end-to-end fusions with low support (remaining=2)
[2026-05-28T20:12:29] Filtering fusions with no coverage around the breakpoints (remaining=2)
[2026-05-28T20:12:29] Indexing gene sequences 
[2026-05-28T20:12:29] Filtering genes with >=30% identity (remaining=2)
[2026-05-28T20:12:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-05-28T20:12:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-05-28T20:12:30] Searching for additional isoforms (remaining=1)
[2026-05-28T20:12:30] Assigning confidence scores to events 
[2026-05-28T20:12:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:12:31] Writing fusions to file 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:12:31] Writing discarded fusions to file 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:12:38] Freeing resources
[2026-05-28T20:12:42] Done (elapsed time=00:02:16, CPU time=00:02:15, peak memory=5.73gb)