[2026-05-28T20:18:10] Launching Arriba 2.4.0
[2026-05-28T20:18:10] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:18:30] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:18:37] Reading chimeric alignments from 'EndoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=3761628)
[2026-05-28T20:20:46] Marking multi-mapping alignments (marked=2949140)
[2026-05-28T20:20:48] Detecting strandedness (reverse)
[2026-05-28T20:20:48] Assigning strands to alignments 
[2026-05-28T20:20:49] Annotating alignments 
[2026-05-28T20:21:11] Filtering duplicates (remaining=1045849)
[2026-05-28T20:21:14] 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=808726)
[2026-05-28T20:21:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=808726)
[2026-05-28T20:21:16] Filtering viral contigs with expression lower than the top 5 (remaining=808726)
[2026-05-28T20:21:18] Filtering viral contigs with less than 5% coverage (remaining=808726)
[2026-05-28T20:21:20] Estimating fragment length (mate gap mean=-60.4184, mate gap stddev=27.7447, read length mean=94.6075)
[2026-05-28T20:21:20] Filtering read-through fragments with a distance <=10000bp (remaining=789285)
[2026-05-28T20:21:21] Filtering inconsistently clipped mates (remaining=761147)
[2026-05-28T20:21:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=691148)
[2026-05-28T20:21:23] Filtering fragments with small insert size (remaining=690176)
[2026-05-28T20:21:24] Filtering alignments with long gaps (remaining=690176)
[2026-05-28T20:21:26] Filtering fragments with both mates in the same gene (remaining=689655)
[2026-05-28T20:21:27] Filtering fusions arising from hairpin structures (remaining=649125)
[2026-05-28T20:21:28] Filtering reads with a mismatch p-value <=0.01 (remaining=124956)
[2026-05-28T20:21:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=52834)
[2026-05-28T20:21:32] Finding fusions and counting supporting reads (total=54515)
[2026-05-28T20:21:39] Merging adjacent fusion breakpoints (remaining=54162)
[2026-05-28T20:21:40] Filtering multi-mapping fusions by alignment score and read support (remaining=22038)
[2026-05-28T20:21:55] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:21:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=21578)
[2026-05-28T20:21:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17553)
[2026-05-28T20:21:57] Filtering fusions with <2 supporting reads (remaining=424)
[2026-05-28T20:21:57] Filtering fusions with an e-value >=0.3 (remaining=165)
[2026-05-28T20:21:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=166)
[2026-05-28T20:21:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=129)
[2026-05-28T20:21:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=129)
[2026-05-28T20:21:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=112)
[2026-05-28T20:22:01] Searching for fusions with spliced split reads (remaining=118)
[2026-05-28T20:22:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=95)
[2026-05-28T20:22:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=93)
[2026-05-28T20:22:03] Searching for fusions with >=4 spliced events (remaining=93)
[2026-05-28T20:22:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=23)
[2026-05-28T20:22:19] Filtering fusions with anchors <=23nt (remaining=17)
[2026-05-28T20:22:19] Filtering end-to-end fusions with low support (remaining=16)
[2026-05-28T20:22:19] Filtering fusions with no coverage around the breakpoints (remaining=15)
[2026-05-28T20:22:19] Indexing gene sequences 
[2026-05-28T20:22:20] Filtering genes with >=30% identity (remaining=7)
[2026-05-28T20:22:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-05-28T20:22:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-05-28T20:22:20] Searching for additional isoforms (remaining=1)
[2026-05-28T20:22:21] Assigning confidence scores to events 
[2026-05-28T20:22:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:22:22] Writing fusions to file 'EndoN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:22:22] Writing discarded fusions to file 'EndoN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:22:29] Freeing resources
[2026-05-28T20:22:37] Done (elapsed time=00:04:27, CPU time=00:04:26, peak memory=7.93gb)