[2026-06-08T08:49:08] Launching Arriba 2.4.0
[2026-06-08T08:49:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:27] Reading chimeric alignments from 'RT4_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12746012)
[2026-06-08T08:59:42] Marking multi-mapping alignments (marked=8712791)
[2026-06-08T08:59:49] Detecting strandedness (reverse)
[2026-06-08T08:59:49] Assigning strands to alignments 
[2026-06-08T08:59:51] Annotating alignments 
[2026-06-08T09:00:46] Filtering duplicates (remaining=8680119)
[2026-06-08T09:00:59] 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)
[2026-06-08T09:01:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8005612)
[2026-06-08T09:01:05] Filtering viral contigs with expression lower than the top 5 (remaining=8005612)
[2026-06-08T09:01:11] Filtering viral contigs with less than 5% coverage (remaining=8005612)
[2026-06-08T09:01:15] Estimating fragment length (mate gap mean=-85.7696, mate gap stddev=30.2328, read length mean=128.403)
[2026-06-08T09:01:15] Filtering read-through fragments with a distance <=10000bp (remaining=7640118)
[2026-06-08T09:01:18] Filtering inconsistently clipped mates (remaining=7499830)
[2026-06-08T09:01:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7191185)
[2026-06-08T09:01:28] Filtering fragments with small insert size (remaining=7189609)
[2026-06-08T09:01:31] Filtering alignments with long gaps (remaining=7189609)
[2026-06-08T09:01:34] Filtering fragments with both mates in the same gene (remaining=7188115)
[2026-06-08T09:01:38] Filtering fusions arising from hairpin structures (remaining=6647694)
[2026-06-08T09:01:42] Filtering reads with a mismatch p-value <=0.01 (remaining=3040787)
[2026-06-08T09:02:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=1273526)
[2026-06-08T09:02:25] Finding fusions and counting supporting reads (total=1021782)
[2026-06-08T09:02:51] Merging adjacent fusion breakpoints (remaining=1012473)
[2026-06-08T09:02:53] Filtering multi-mapping fusions by alignment score and read support (remaining=611982)
[2026-06-08T09:03:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=608764)
[2026-06-08T09:03:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=377110)
[2026-06-08T09:03:58] Filtering fusions with <2 supporting reads (remaining=35089)
[2026-06-08T09:03:59] Filtering fusions with an e-value >=0.3 (remaining=8334)
[2026-06-08T09:04:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8386)
[2026-06-08T09:04:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8189)
[2026-06-08T09:04:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8247)
[2026-06-08T09:04:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6504)
[2026-06-08T09:04:16] Searching for fusions with spliced split reads (remaining=6519)
[2026-06-08T09:04:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=4128)
[2026-06-08T09:04:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4102)
[2026-06-08T09:04:26] Searching for fusions with >=4 spliced events (remaining=5114)
[2026-06-08T09:04:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2176)
[2026-06-08T09:04:51] Filtering fusions with anchors <=23nt (remaining=1699)
[2026-06-08T09:04:51] Filtering end-to-end fusions with low support (remaining=1655)
[2026-06-08T09:04:52] Filtering fusions with no coverage around the breakpoints (remaining=1637)
[2026-06-08T09:04:53] Indexing gene sequences 
[2026-06-08T09:05:01] Filtering genes with >=30% identity (remaining=455)
[2026-06-08T09:05:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=183)
[2026-06-08T09:05:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=127)
[2026-06-08T09:05:10] Searching for additional isoforms (remaining=204)
[2026-06-08T09:05:12] Assigning confidence scores to events 
[2026-06-08T09:05:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:18] Writing fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:20] Writing discarded fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:10] Freeing resources
[2026-06-08T09:06:33] Done (elapsed time=00:17:25, CPU time=00:17:24, peak memory=17.8gb)