[2026-06-08T08:47:28] Launching Arriba 2.4.0
[2026-06-08T08:47:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:47] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=11291739)
[2026-06-08T08:56:02] Marking multi-mapping alignments (marked=7541137)
[2026-06-08T08:56:07] Detecting strandedness (reverse)
[2026-06-08T08:56:07] Assigning strands to alignments 
[2026-06-08T08:56:09] Annotating alignments 
[2026-06-08T08:56:49] Filtering duplicates (remaining=6163256)
[2026-06-08T08:56:58] 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=5684136)
[2026-06-08T08:57:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5684136)
[2026-06-08T08:57:02] Filtering viral contigs with expression lower than the top 5 (remaining=5684136)
[2026-06-08T08:57:07] Filtering viral contigs with less than 5% coverage (remaining=5684136)
[2026-06-08T08:57:09] Estimating fragment length (mate gap mean=-87.4265, mate gap stddev=32.0261, read length mean=133.651)
[2026-06-08T08:57:09] Filtering read-through fragments with a distance <=10000bp (remaining=5413375)
[2026-06-08T08:57:11] Filtering inconsistently clipped mates (remaining=5309849)
[2026-06-08T08:57:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5129727)
[2026-06-08T08:57:18] Filtering fragments with small insert size (remaining=5129010)
[2026-06-08T08:57:20] Filtering alignments with long gaps (remaining=5129010)
[2026-06-08T08:57:22] Filtering fragments with both mates in the same gene (remaining=5128048)
[2026-06-08T08:57:25] Filtering fusions arising from hairpin structures (remaining=4758440)
[2026-06-08T08:57:27] Filtering reads with a mismatch p-value <=0.01 (remaining=2142294)
[2026-06-08T08:57:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=902832)
[2026-06-08T08:57:52] Finding fusions and counting supporting reads (total=652567)
[2026-06-08T08:58:09] Merging adjacent fusion breakpoints (remaining=643357)
[2026-06-08T08:58:10] Filtering multi-mapping fusions by alignment score and read support (remaining=402193)
[2026-06-08T08:58:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=399145)
[2026-06-08T08:58:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=222563)
[2026-06-08T08:58:56] Filtering fusions with <2 supporting reads (remaining=34452)
[2026-06-08T08:58:56] Filtering fusions with an e-value >=0.3 (remaining=12095)
[2026-06-08T08:58:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12141)
[2026-06-08T08:59:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12019)
[2026-06-08T08:59:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12031)
[2026-06-08T08:59:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8566)
[2026-06-08T08:59:09] Searching for fusions with spliced split reads (remaining=8681)
[2026-06-08T08:59:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=4581)
[2026-06-08T08:59:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4536)
[2026-06-08T08:59:17] Searching for fusions with >=4 spliced events (remaining=5410)
[2026-06-08T08:59:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2178)
[2026-06-08T08:59:36] Filtering fusions with anchors <=23nt (remaining=1605)
[2026-06-08T08:59:37] Filtering end-to-end fusions with low support (remaining=1535)
[2026-06-08T08:59:37] Filtering fusions with no coverage around the breakpoints (remaining=1483)
[2026-06-08T08:59:38] Indexing gene sequences 
[2026-06-08T08:59:43] Filtering genes with >=30% identity (remaining=387)
[2026-06-08T08:59:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=130)
[2026-06-08T08:59:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=125)
[2026-06-08T08:59:49] Searching for additional isoforms (remaining=162)
[2026-06-08T08:59:51] Assigning confidence scores to events 
[2026-06-08T08:59:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:54] Writing fusions to file 'FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:55] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:24] Freeing resources
[2026-06-08T09:00:42] Done (elapsed time=00:13:14, CPU time=00:13:13, peak memory=16gb)