[2026-06-08T08:35:07] Launching Arriba 2.4.0
[2026-06-08T08:35:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:26] Reading chimeric alignments from 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=9654637)
[2026-06-08T08:43:32] Marking multi-mapping alignments (marked=6344289)
[2026-06-08T08:43:36] Detecting strandedness (no)
[2026-06-08T08:43:36] Annotating alignments 
[2026-06-08T08:44:11] Filtering duplicates (remaining=7037695)
[2026-06-08T08:44:18] 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=6692644)
[2026-06-08T08:44:20] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6692644)
[2026-06-08T08:44:21] Filtering viral contigs with expression lower than the top 5 (remaining=6692644)
[2026-06-08T08:44:26] Filtering viral contigs with less than 5% coverage (remaining=6692644)
[2026-06-08T08:44:28] Estimating fragment length (mate gap mean=-83.5841, mate gap stddev=29.3667, read length mean=128.491)
[2026-06-08T08:44:28] Filtering read-through fragments with a distance <=10000bp (remaining=6343545)
[2026-06-08T08:44:30] Filtering inconsistently clipped mates (remaining=6253249)
[2026-06-08T08:44:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5994230)
[2026-06-08T08:44:36] Filtering fragments with small insert size (remaining=5993295)
[2026-06-08T08:44:37] Filtering alignments with long gaps (remaining=5993295)
[2026-06-08T08:44:39] Filtering fragments with both mates in the same gene (remaining=5992137)
[2026-06-08T08:44:41] Filtering fusions arising from hairpin structures (remaining=5696563)
[2026-06-08T08:44:44] Filtering reads with a mismatch p-value <=0.01 (remaining=2789434)
[2026-06-08T08:44:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=1009951)
[2026-06-08T08:45:11] Finding fusions and counting supporting reads (total=788597)
[2026-06-08T08:45:26] Merging adjacent fusion breakpoints (remaining=783206)
[2026-06-08T08:45:28] Filtering multi-mapping fusions by alignment score and read support (remaining=487509)
[2026-06-08T08:46:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=485716)
[2026-06-08T08:46:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=295681)
[2026-06-08T08:46:09] Filtering fusions with <2 supporting reads (remaining=24259)
[2026-06-08T08:46:09] Filtering fusions with an e-value >=0.3 (remaining=5941)
[2026-06-08T08:46:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5986)
[2026-06-08T08:46:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5868)
[2026-06-08T08:46:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5869)
[2026-06-08T08:46:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5156)
[2026-06-08T08:46:21] Searching for fusions with spliced split reads (remaining=5296)
[2026-06-08T08:46:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=3444)
[2026-06-08T08:46:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3408)
[2026-06-08T08:46:29] Searching for fusions with >=4 spliced events (remaining=4197)
[2026-06-08T08:46:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2076)
[2026-06-08T08:46:46] Filtering fusions with anchors <=23nt (remaining=1603)
[2026-06-08T08:46:47] Filtering end-to-end fusions with low support (remaining=1585)
[2026-06-08T08:46:47] Filtering fusions with no coverage around the breakpoints (remaining=1561)
[2026-06-08T08:46:48] Indexing gene sequences 
[2026-06-08T08:46:55] Filtering genes with >=30% identity (remaining=592)
[2026-06-08T08:47:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=310)
[2026-06-08T08:47:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=215)
[2026-06-08T08:47:16] Searching for additional isoforms (remaining=298)
[2026-06-08T08:47:17] Assigning confidence scores to events 
[2026-06-08T08:47:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:21] Writing fusions to file 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:47:25] Writing discarded fusions to file 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:56] Freeing resources
[2026-06-08T08:48:13] Done (elapsed time=00:13:06, CPU time=00:13:05, peak memory=14.1gb)