[2026-06-08T08:34:58] Launching Arriba 2.4.0
[2026-06-08T08:34:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:10] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:13] Reading chimeric alignments from 'LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=14429492)
[2026-06-08T08:41:47] Marking multi-mapping alignments (marked=10058940)
[2026-06-08T08:41:52] Detecting strandedness (reverse)
[2026-06-08T08:41:52] Assigning strands to alignments 
[2026-06-08T08:41:55] Annotating alignments 
[2026-06-08T08:42:36] Filtering duplicates (remaining=5383848)
[2026-06-08T08:42:42] 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=4881972)
[2026-06-08T08:42:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4881972)
[2026-06-08T08:42:48] Filtering viral contigs with expression lower than the top 5 (remaining=4881972)
[2026-06-08T08:42:53] Filtering viral contigs with less than 5% coverage (remaining=4881972)
[2026-06-08T08:42:56] Estimating fragment length (mate gap mean=-78.3936, mate gap stddev=28.6869, read length mean=113.588)
[2026-06-08T08:42:56] Filtering read-through fragments with a distance <=10000bp (remaining=4704797)
[2026-06-08T08:42:59] Filtering inconsistently clipped mates (remaining=4595343)
[2026-06-08T08:43:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4305679)
[2026-06-08T08:43:06] Filtering fragments with small insert size (remaining=4303878)
[2026-06-08T08:43:09] Filtering alignments with long gaps (remaining=4303878)
[2026-06-08T08:43:11] Filtering fragments with both mates in the same gene (remaining=4302481)
[2026-06-08T08:43:14] Filtering fusions arising from hairpin structures (remaining=4077891)
[2026-06-08T08:43:17] Filtering reads with a mismatch p-value <=0.01 (remaining=1378778)
[2026-06-08T08:43:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=485328)
[2026-06-08T08:43:36] Finding fusions and counting supporting reads (total=437190)
[2026-06-08T08:43:53] Merging adjacent fusion breakpoints (remaining=432589)
[2026-06-08T08:43:54] Filtering multi-mapping fusions by alignment score and read support (remaining=235918)
[2026-06-08T08:44:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=234232)
[2026-06-08T08:44:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=148142)
[2026-06-08T08:44:39] Filtering fusions with <2 supporting reads (remaining=11285)
[2026-06-08T08:44:40] Filtering fusions with an e-value >=0.3 (remaining=2499)
[2026-06-08T08:44:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2534)
[2026-06-08T08:44:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2436)
[2026-06-08T08:44:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2436)
[2026-06-08T08:44:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2355)
[2026-06-08T08:44:51] Searching for fusions with spliced split reads (remaining=2417)
[2026-06-08T08:44:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=1834)
[2026-06-08T08:44:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1814)
[2026-06-08T08:44:59] Searching for fusions with >=4 spliced events (remaining=2019)
[2026-06-08T08:45:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=684)
[2026-06-08T08:45:13] Filtering fusions with anchors <=23nt (remaining=496)
[2026-06-08T08:45:14] Filtering end-to-end fusions with low support (remaining=485)
[2026-06-08T08:45:14] Filtering fusions with no coverage around the breakpoints (remaining=483)
[2026-06-08T08:45:15] Indexing gene sequences 
[2026-06-08T08:45:18] Filtering genes with >=30% identity (remaining=200)
[2026-06-08T08:45:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=114)
[2026-06-08T08:45:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=101)
[2026-06-08T08:45:22] Searching for additional isoforms (remaining=108)
[2026-06-08T08:45:23] Assigning confidence scores to events 
[2026-06-08T08:45:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:26] Writing fusions to file 'LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:27] Writing discarded fusions to file 'LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:49] Freeing resources
[2026-06-08T08:46:09] Done (elapsed time=00:11:11, CPU time=00:11:10, peak memory=18.9gb)