[2026-06-08T08:36:09] Launching Arriba 2.4.0
[2026-06-08T08:36:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:22] Reading chimeric alignments from 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=10841987)
[2026-06-08T08:43:17] Marking multi-mapping alignments (marked=7047451)
[2026-06-08T08:43:20] Detecting strandedness (reverse)
[2026-06-08T08:43:20] Assigning strands to alignments 
[2026-06-08T08:43:23] Annotating alignments 
[2026-06-08T08:43:57] Filtering duplicates (remaining=8161074)
[2026-06-08T08:44:04] 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=7732633)
[2026-06-08T08:44:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7732633)
[2026-06-08T08:44:08] Filtering viral contigs with expression lower than the top 5 (remaining=7732633)
[2026-06-08T08:44:13] Filtering viral contigs with less than 5% coverage (remaining=7732633)
[2026-06-08T08:44:15] Estimating fragment length (mate gap mean=-86.3003, mate gap stddev=29.8556, read length mean=132.107)
[2026-06-08T08:44:15] Filtering read-through fragments with a distance <=10000bp (remaining=7295678)
[2026-06-08T08:44:17] Filtering inconsistently clipped mates (remaining=7172727)
[2026-06-08T08:44:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6900917)
[2026-06-08T08:44:24] Filtering fragments with small insert size (remaining=6899754)
[2026-06-08T08:44:26] Filtering alignments with long gaps (remaining=6899753)
[2026-06-08T08:44:28] Filtering fragments with both mates in the same gene (remaining=6898516)
[2026-06-08T08:44:30] Filtering fusions arising from hairpin structures (remaining=6431613)
[2026-06-08T08:44:33] Filtering reads with a mismatch p-value <=0.01 (remaining=3115100)
[2026-06-08T08:44:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=1296600)
[2026-06-08T08:45:00] Finding fusions and counting supporting reads (total=1068757)
[2026-06-08T08:45:17] Merging adjacent fusion breakpoints (remaining=1060411)
[2026-06-08T08:45:20] Filtering multi-mapping fusions by alignment score and read support (remaining=659237)
[2026-06-08T08:45:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=656808)
[2026-06-08T08:46:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=404921)
[2026-06-08T08:46:03] Filtering fusions with <2 supporting reads (remaining=30746)
[2026-06-08T08:46:04] Filtering fusions with an e-value >=0.3 (remaining=7095)
[2026-06-08T08:46:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7142)
[2026-06-08T08:46:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7012)
[2026-06-08T08:46:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7014)
[2026-06-08T08:46:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6070)
[2026-06-08T08:46:19] Searching for fusions with spliced split reads (remaining=6206)
[2026-06-08T08:46:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=3758)
[2026-06-08T08:46:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3719)
[2026-06-08T08:46:27] Searching for fusions with >=4 spliced events (remaining=4779)
[2026-06-08T08:46:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2400)
[2026-06-08T08:46:42] Filtering fusions with anchors <=23nt (remaining=1903)
[2026-06-08T08:46:43] Filtering end-to-end fusions with low support (remaining=1871)
[2026-06-08T08:46:44] Filtering fusions with no coverage around the breakpoints (remaining=1849)
[2026-06-08T08:46:45] Indexing gene sequences 
[2026-06-08T08:46:51] Filtering genes with >=30% identity (remaining=603)
[2026-06-08T08:46:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=326)
[2026-06-08T08:47:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=227)
[2026-06-08T08:47:12] Searching for additional isoforms (remaining=300)
[2026-06-08T08:47:14] Assigning confidence scores to events 
[2026-06-08T08:47:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:18] Writing fusions to file 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:22] Writing discarded fusions to file 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:55] Freeing resources
[2026-06-08T08:48:15] Done (elapsed time=00:12:06, CPU time=00:12:05, peak memory=15.7gb)