[2026-05-28T20:28:05] Launching Arriba 2.4.0
[2026-05-28T20:28:05] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:28:20] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:28:25] Reading chimeric alignments from 'BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=9051231)
[2026-05-28T20:32:01] Marking multi-mapping alignments (marked=7170752)
[2026-05-28T20:32:05] Detecting strandedness (no)
[2026-05-28T20:32:05] Annotating alignments 
[2026-05-28T20:32:43] Filtering duplicates (remaining=4836309)
[2026-05-28T20:32:50] 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=4388705)
[2026-05-28T20:32:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4388705)
[2026-05-28T20:32:53] Filtering viral contigs with expression lower than the top 5 (remaining=4388705)
[2026-05-28T20:32:57] Filtering viral contigs with less than 5% coverage (remaining=4388705)
[2026-05-28T20:32:59] Estimating fragment length (mate gap mean=-64.3281, mate gap stddev=29.7687, read length mean=96.9167)
[2026-05-28T20:32:59] Filtering read-through fragments with a distance <=10000bp (remaining=4308337)
[2026-05-28T20:33:01] Filtering inconsistently clipped mates (remaining=4174876)
[2026-05-28T20:33:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3591635)
[2026-05-28T20:33:07] Filtering fragments with small insert size (remaining=3586253)
[2026-05-28T20:33:09] Filtering alignments with long gaps (remaining=3586253)
[2026-05-28T20:33:11] Filtering fragments with both mates in the same gene (remaining=3584636)
[2026-05-28T20:33:13] Filtering fusions arising from hairpin structures (remaining=3339628)
[2026-05-28T20:33:15] Filtering reads with a mismatch p-value <=0.01 (remaining=738366)
[2026-05-28T20:33:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=362613)
[2026-05-28T20:33:28] Finding fusions and counting supporting reads (total=372424)
[2026-05-28T20:33:43] Merging adjacent fusion breakpoints (remaining=370518)
[2026-05-28T20:33:45] Filtering multi-mapping fusions by alignment score and read support (remaining=158544)
[2026-05-28T20:34:19] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:34:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=157029)
[2026-05-28T20:34:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=131221)
[2026-05-28T20:34:28] Filtering fusions with <2 supporting reads (remaining=4192)
[2026-05-28T20:34:29] Filtering fusions with an e-value >=0.3 (remaining=872)
[2026-05-28T20:34:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=906)
[2026-05-28T20:34:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=785)
[2026-05-28T20:34:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=785)
[2026-05-28T20:34:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=784)
[2026-05-28T20:34:41] Searching for fusions with spliced split reads (remaining=808)
[2026-05-28T20:34:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=652)
[2026-05-28T20:34:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=649)
[2026-05-28T20:34:49] Searching for fusions with >=4 spliced events (remaining=665)
[2026-05-28T20:34:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=186)
[2026-05-28T20:35:13] Filtering fusions with anchors <=23nt (remaining=159)
[2026-05-28T20:35:14] Filtering end-to-end fusions with low support (remaining=154)
[2026-05-28T20:35:15] Filtering fusions with no coverage around the breakpoints (remaining=154)
[2026-05-28T20:35:15] Indexing gene sequences 
[2026-05-28T20:35:18] Filtering genes with >=30% identity (remaining=64)
[2026-05-28T20:35:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=39)
[2026-05-28T20:35:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=39)
[2026-05-28T20:35:22] Searching for additional isoforms (remaining=42)
[2026-05-28T20:35:23] Assigning confidence scores to events 
[2026-05-28T20:35:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:35:28] Writing fusions to file 'BT-20_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:35:28] Writing discarded fusions to file 'BT-20_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:35:57] Freeing resources
[2026-05-28T20:36:14] Done (elapsed time=00:08:09, CPU time=00:08:08, peak memory=13.9gb)