[2026-05-28T21:14:50] Launching Arriba 2.4.0
[2026-05-28T21:14:50] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:15:03] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:15:08] Reading chimeric alignments from 'RT4_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12746012)
[2026-05-28T21:24:42] Marking multi-mapping alignments (marked=8712791)
[2026-05-28T21:24:48] Detecting strandedness (reverse)
[2026-05-28T21:24:48] Assigning strands to alignments 
[2026-05-28T21:24:50] Annotating alignments 
[2026-05-28T21:25:42] Filtering duplicates (remaining=8680119)
[2026-05-28T21:25:54] 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=8005612)
[2026-05-28T21:25:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8005612)
[2026-05-28T21:25:59] Filtering viral contigs with expression lower than the top 5 (remaining=8005612)
[2026-05-28T21:26:05] Filtering viral contigs with less than 5% coverage (remaining=8005612)
[2026-05-28T21:26:08] Estimating fragment length (mate gap mean=-85.7696, mate gap stddev=30.2328, read length mean=128.403)
[2026-05-28T21:26:08] Filtering read-through fragments with a distance <=10000bp (remaining=7640118)
[2026-05-28T21:26:11] Filtering inconsistently clipped mates (remaining=7499830)
[2026-05-28T21:26:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7191185)
[2026-05-28T21:26:19] Filtering fragments with small insert size (remaining=7189609)
[2026-05-28T21:26:22] Filtering alignments with long gaps (remaining=7189609)
[2026-05-28T21:26:24] Filtering fragments with both mates in the same gene (remaining=7188115)
[2026-05-28T21:26:27] Filtering fusions arising from hairpin structures (remaining=6647694)
[2026-05-28T21:26:31] Filtering reads with a mismatch p-value <=0.01 (remaining=3040787)
[2026-05-28T21:26:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=1273526)
[2026-05-28T21:27:03] Finding fusions and counting supporting reads (total=1021782)
[2026-05-28T21:27:25] Merging adjacent fusion breakpoints (remaining=1012473)
[2026-05-28T21:27:28] Filtering multi-mapping fusions by alignment score and read support (remaining=611982)
[2026-05-28T21:28:13] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:28:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=608764)
[2026-05-28T21:28:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=377110)
[2026-05-28T21:28:28] Filtering fusions with <2 supporting reads (remaining=35089)
[2026-05-28T21:28:30] Filtering fusions with an e-value >=0.3 (remaining=8334)
[2026-05-28T21:28:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8386)
[2026-05-28T21:28:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8189)
[2026-05-28T21:28:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8247)
[2026-05-28T21:28:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6504)
[2026-05-28T21:28:47] Searching for fusions with spliced split reads (remaining=6519)
[2026-05-28T21:28:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=4128)
[2026-05-28T21:28:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4102)
[2026-05-28T21:28:58] Searching for fusions with >=4 spliced events (remaining=5114)
[2026-05-28T21:29:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2176)
[2026-05-28T21:29:21] Filtering fusions with anchors <=23nt (remaining=1699)
[2026-05-28T21:29:22] Filtering end-to-end fusions with low support (remaining=1655)
[2026-05-28T21:29:23] Filtering fusions with no coverage around the breakpoints (remaining=1637)
[2026-05-28T21:29:24] Indexing gene sequences 
[2026-05-28T21:29:32] Filtering genes with >=30% identity (remaining=455)
[2026-05-28T21:29:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=183)
[2026-05-28T21:29:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=127)
[2026-05-28T21:29:40] Searching for additional isoforms (remaining=204)
[2026-05-28T21:29:42] Assigning confidence scores to events 
[2026-05-28T21:29:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:29:48] Writing fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:29:50] Writing discarded fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:30:50] Freeing resources
[2026-05-28T21:31:24] Done (elapsed time=00:16:34, CPU time=00:16:33, peak memory=17.8gb)