[2026-05-28T20:37:05] Launching Arriba 2.4.0
[2026-05-28T20:37:05] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:37:19] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:37:23] Reading chimeric alignments from 'EndoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=9071719)
[2026-05-28T20:40:43] Marking multi-mapping alignments (marked=7211391)
[2026-05-28T20:40:47] Detecting strandedness (reverse)
[2026-05-28T20:40:47] Assigning strands to alignments 
[2026-05-28T20:40:48] Annotating alignments 
[2026-05-28T20:41:17] Filtering duplicates (remaining=1873054)
[2026-05-28T20:41:21] 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=1483436)
[2026-05-28T20:41:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1483436)
[2026-05-28T20:41:25] Filtering viral contigs with expression lower than the top 5 (remaining=1483436)
[2026-05-28T20:41:28] Filtering viral contigs with less than 5% coverage (remaining=1483436)
[2026-05-28T20:41:30] Estimating fragment length (mate gap mean=-64.8502, mate gap stddev=29.6921, read length mean=100.194)
[2026-05-28T20:41:30] Filtering read-through fragments with a distance <=10000bp (remaining=1451897)
[2026-05-28T20:41:32] Filtering inconsistently clipped mates (remaining=1401027)
[2026-05-28T20:41:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1255940)
[2026-05-28T20:41:35] Filtering fragments with small insert size (remaining=1254026)
[2026-05-28T20:41:37] Filtering alignments with long gaps (remaining=1254026)
[2026-05-28T20:41:39] Filtering fragments with both mates in the same gene (remaining=1252898)
[2026-05-28T20:41:40] Filtering fusions arising from hairpin structures (remaining=1177745)
[2026-05-28T20:41:42] Filtering reads with a mismatch p-value <=0.01 (remaining=294960)
[2026-05-28T20:41:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=104207)
[2026-05-28T20:41:49] Finding fusions and counting supporting reads (total=100653)
[2026-05-28T20:42:00] Merging adjacent fusion breakpoints (remaining=99732)
[2026-05-28T20:42:00] Filtering multi-mapping fusions by alignment score and read support (remaining=39593)
[2026-05-28T20:42:25] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:42:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=38827)
[2026-05-28T20:42:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=30486)
[2026-05-28T20:42:28] Filtering fusions with <2 supporting reads (remaining=1236)
[2026-05-28T20:42:28] Filtering fusions with an e-value >=0.3 (remaining=296)
[2026-05-28T20:42:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=298)
[2026-05-28T20:42:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=223)
[2026-05-28T20:42:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=223)
[2026-05-28T20:42:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=217)
[2026-05-28T20:42:34] Searching for fusions with spliced split reads (remaining=223)
[2026-05-28T20:42:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=191)
[2026-05-28T20:42:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=188)
[2026-05-28T20:42:38] Searching for fusions with >=4 spliced events (remaining=188)
[2026-05-28T20:42:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=32)
[2026-05-28T20:42:53] Filtering fusions with anchors <=23nt (remaining=25)
[2026-05-28T20:42:53] Filtering end-to-end fusions with low support (remaining=24)
[2026-05-28T20:42:54] Filtering fusions with no coverage around the breakpoints (remaining=24)
[2026-05-28T20:42:54] Indexing gene sequences 
[2026-05-28T20:42:54] Filtering genes with >=30% identity (remaining=11)
[2026-05-28T20:42:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=2)
[2026-05-28T20:42:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=2)
[2026-05-28T20:42:55] Searching for additional isoforms (remaining=4)
[2026-05-28T20:42:56] Assigning confidence scores to events 
[2026-05-28T20:42:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:42:57] Writing fusions to file 'EndoN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:42:57] Writing discarded fusions to file 'EndoN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:43:08] Freeing resources
[2026-05-28T20:43:21] Done (elapsed time=00:06:16, CPU time=00:06:15, peak memory=13.2gb)