[2026-06-08T08:03:38] Launching Arriba 2.4.0
[2026-06-08T08:03:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:03:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:04:00] Reading chimeric alignments from 'LungN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=13168249)
[2026-06-08T08:09:29] Marking multi-mapping alignments (marked=10111342)
[2026-06-08T08:09:34] Detecting strandedness (reverse)
[2026-06-08T08:09:34] Assigning strands to alignments 
[2026-06-08T08:09:36] Annotating alignments 
[2026-06-08T08:10:18] Filtering duplicates (remaining=3310780)
[2026-06-08T08:10:24] 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=2741628)
[2026-06-08T08:10:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2741628)
[2026-06-08T08:10:29] Filtering viral contigs with expression lower than the top 5 (remaining=2741628)
[2026-06-08T08:10:34] Filtering viral contigs with less than 5% coverage (remaining=2741628)
[2026-06-08T08:10:36] Estimating fragment length (mate gap mean=-68.7338, mate gap stddev=29.9631, read length mean=103.945)
[2026-06-08T08:10:37] Filtering read-through fragments with a distance <=10000bp (remaining=2693319)
[2026-06-08T08:10:39] Filtering inconsistently clipped mates (remaining=2620935)
[2026-06-08T08:10:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2370052)
[2026-06-08T08:10:45] Filtering fragments with small insert size (remaining=2367524)
[2026-06-08T08:10:47] Filtering alignments with long gaps (remaining=2367524)
[2026-06-08T08:10:50] Filtering fragments with both mates in the same gene (remaining=2366237)
[2026-06-08T08:10:52] Filtering fusions arising from hairpin structures (remaining=2257807)
[2026-06-08T08:10:55] Filtering reads with a mismatch p-value <=0.01 (remaining=565288)
[2026-06-08T08:11:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=206304)
[2026-06-08T08:11:07] Finding fusions and counting supporting reads (total=195019)
[2026-06-08T08:11:21] Merging adjacent fusion breakpoints (remaining=193042)
[2026-06-08T08:11:22] Filtering multi-mapping fusions by alignment score and read support (remaining=78935)
[2026-06-08T08:11:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:11:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=77464)
[2026-06-08T08:11:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=63480)
[2026-06-08T08:12:00] Filtering fusions with <2 supporting reads (remaining=2243)
[2026-06-08T08:12:00] Filtering fusions with an e-value >=0.3 (remaining=490)
[2026-06-08T08:12:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=492)
[2026-06-08T08:12:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=402)
[2026-06-08T08:12:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=402)
[2026-06-08T08:12:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=376)
[2026-06-08T08:12:09] Searching for fusions with spliced split reads (remaining=419)
[2026-06-08T08:12:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=294)
[2026-06-08T08:12:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=287)
[2026-06-08T08:12:15] Searching for fusions with >=4 spliced events (remaining=301)
[2026-06-08T08:12:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=88)
[2026-06-08T08:12:30] Filtering fusions with anchors <=23nt (remaining=67)
[2026-06-08T08:12:30] Filtering end-to-end fusions with low support (remaining=64)
[2026-06-08T08:12:31] Filtering fusions with no coverage around the breakpoints (remaining=63)
[2026-06-08T08:12:31] Indexing gene sequences 
[2026-06-08T08:12:32] Filtering genes with >=30% identity (remaining=15)
[2026-06-08T08:12:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=2)
[2026-06-08T08:12:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=2)
[2026-06-08T08:12:34] Searching for additional isoforms (remaining=2)
[2026-06-08T08:12:35] Assigning confidence scores to events 
[2026-06-08T08:12:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:12:37] Writing fusions to file 'LungN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:12:37] Writing discarded fusions to file 'LungN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:12:53] Freeing resources
[2026-06-08T08:13:10] Done (elapsed time=00:09:32, CPU time=00:09:30, peak memory=17.4gb)