[2026-05-28T20:51:16] Launching Arriba 2.4.0
[2026-05-28T20:51:16] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:51:29] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:51:34] Reading chimeric alignments from 'LungN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=13168249)
[2026-05-28T20:56:59] Marking multi-mapping alignments (marked=10111342)
[2026-05-28T20:57:04] Detecting strandedness (reverse)
[2026-05-28T20:57:04] Assigning strands to alignments 
[2026-05-28T20:57:07] Annotating alignments 
[2026-05-28T20:57:54] Filtering duplicates (remaining=3310780)
[2026-05-28T20:58:01] 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)
[2026-05-28T20:58:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2741628)
[2026-05-28T20:58:05] Filtering viral contigs with expression lower than the top 5 (remaining=2741628)
[2026-05-28T20:58:10] Filtering viral contigs with less than 5% coverage (remaining=2741628)
[2026-05-28T20:58:13] Estimating fragment length (mate gap mean=-68.7338, mate gap stddev=29.9631, read length mean=103.945)
[2026-05-28T20:58:13] Filtering read-through fragments with a distance <=10000bp (remaining=2693319)
[2026-05-28T20:58:15] Filtering inconsistently clipped mates (remaining=2620935)
[2026-05-28T20:58:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2370052)
[2026-05-28T20:58:21] Filtering fragments with small insert size (remaining=2367524)
[2026-05-28T20:58:23] Filtering alignments with long gaps (remaining=2367524)
[2026-05-28T20:58:26] Filtering fragments with both mates in the same gene (remaining=2366237)
[2026-05-28T20:58:28] Filtering fusions arising from hairpin structures (remaining=2257807)
[2026-05-28T20:58:30] Filtering reads with a mismatch p-value <=0.01 (remaining=565288)
[2026-05-28T20:58:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=206304)
[2026-05-28T20:58:42] Finding fusions and counting supporting reads (total=195019)
[2026-05-28T20:58:57] Merging adjacent fusion breakpoints (remaining=193042)
[2026-05-28T20:58:58] Filtering multi-mapping fusions by alignment score and read support (remaining=78935)
[2026-05-28T20:59:33] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:59:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=77464)
[2026-05-28T20:59:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=63480)
[2026-05-28T20:59:38] Filtering fusions with <2 supporting reads (remaining=2243)
[2026-05-28T20:59:38] Filtering fusions with an e-value >=0.3 (remaining=490)
[2026-05-28T20:59:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=492)
[2026-05-28T20:59:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=402)
[2026-05-28T20:59:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=402)
[2026-05-28T20:59:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=376)
[2026-05-28T20:59:47] Searching for fusions with spliced split reads (remaining=419)
[2026-05-28T20:59:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=294)
[2026-05-28T20:59:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=287)
[2026-05-28T20:59:53] Searching for fusions with >=4 spliced events (remaining=301)
[2026-05-28T20:59:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=88)
[2026-05-28T21:00:09] Filtering fusions with anchors <=23nt (remaining=67)
[2026-05-28T21:00:09] Filtering end-to-end fusions with low support (remaining=64)
[2026-05-28T21:00:10] Filtering fusions with no coverage around the breakpoints (remaining=63)
[2026-05-28T21:00:10] Indexing gene sequences 
[2026-05-28T21:00:11] Filtering genes with >=30% identity (remaining=15)
[2026-05-28T21:00:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=2)
[2026-05-28T21:00:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=2)
[2026-05-28T21:00:13] Searching for additional isoforms (remaining=2)
[2026-05-28T21:00:14] Assigning confidence scores to events 
[2026-05-28T21:00:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:00:16] Writing fusions to file 'LungN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:00:16] Writing discarded fusions to file 'LungN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:00:34] Freeing resources
[2026-05-28T21:00:53] Done (elapsed time=00:09:37, CPU time=00:09:36, peak memory=17.4gb)