[2026-05-28T21:19:52] Launching Arriba 2.4.0
[2026-05-28T21:19:52] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:20:00] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:20:04] Reading chimeric alignments from 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=10580291)
[2026-05-28T21:27:20] Marking multi-mapping alignments (marked=6891242)
[2026-05-28T21:27:25] Detecting strandedness (reverse)
[2026-05-28T21:27:25] Assigning strands to alignments 
[2026-05-28T21:27:28] Annotating alignments 
[2026-05-28T21:28:10] Filtering duplicates (remaining=7922844)
[2026-05-28T21:28:20] 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=7514266)
[2026-05-28T21:28:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7514266)
[2026-05-28T21:28:25] Filtering viral contigs with expression lower than the top 5 (remaining=7514266)
[2026-05-28T21:28:31] Filtering viral contigs with less than 5% coverage (remaining=7514266)
[2026-05-28T21:28:34] Estimating fragment length (mate gap mean=-85.5605, mate gap stddev=29.8663, read length mean=130.373)
[2026-05-28T21:28:34] Filtering read-through fragments with a distance <=10000bp (remaining=7085076)
[2026-05-28T21:28:36] Filtering inconsistently clipped mates (remaining=6965550)
[2026-05-28T21:28:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6711660)
[2026-05-28T21:28:45] Filtering fragments with small insert size (remaining=6710550)
[2026-05-28T21:28:47] Filtering alignments with long gaps (remaining=6710549)
[2026-05-28T21:28:50] Filtering fragments with both mates in the same gene (remaining=6709263)
[2026-05-28T21:28:53] Filtering fusions arising from hairpin structures (remaining=6278094)
[2026-05-28T21:28:56] Filtering reads with a mismatch p-value <=0.01 (remaining=3035724)
[2026-05-28T21:29:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=1233525)
[2026-05-28T21:29:26] Finding fusions and counting supporting reads (total=1002046)
[2026-05-28T21:29:48] Merging adjacent fusion breakpoints (remaining=994453)
[2026-05-28T21:29:51] Filtering multi-mapping fusions by alignment score and read support (remaining=619677)
[2026-05-28T21:30:32] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:30:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=617520)
[2026-05-28T21:30:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=373856)
[2026-05-28T21:30:46] Filtering fusions with <2 supporting reads (remaining=29180)
[2026-05-28T21:30:47] Filtering fusions with an e-value >=0.3 (remaining=6875)
[2026-05-28T21:30:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6924)
[2026-05-28T21:30:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6809)
[2026-05-28T21:30:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6810)
[2026-05-28T21:30:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5904)
[2026-05-28T21:31:04] Searching for fusions with spliced split reads (remaining=6042)
[2026-05-28T21:31:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=3762)
[2026-05-28T21:31:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3723)
[2026-05-28T21:31:15] Searching for fusions with >=4 spliced events (remaining=4718)
[2026-05-28T21:31:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2417)
[2026-05-28T21:31:33] Filtering fusions with anchors <=23nt (remaining=1933)
[2026-05-28T21:31:34] Filtering end-to-end fusions with low support (remaining=1892)
[2026-05-28T21:31:35] Filtering fusions with no coverage around the breakpoints (remaining=1861)
[2026-05-28T21:31:36] Indexing gene sequences 
[2026-05-28T21:31:44] Filtering genes with >=30% identity (remaining=638)
[2026-05-28T21:31:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=342)
[2026-05-28T21:32:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=241)
[2026-05-28T21:32:06] Searching for additional isoforms (remaining=321)
[2026-05-28T21:32:08] Assigning confidence scores to events 
[2026-05-28T21:32:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:32:14] Writing fusions to file 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T21:32:17] Writing discarded fusions to file 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T21:33:04] Freeing resources
[2026-05-28T21:33:28] Done (elapsed time=00:13:36, CPU time=00:13:34, peak memory=15.4gb)