[2026-05-28T21:22:01] Launching Arriba 2.4.0
[2026-05-28T21:22:01] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:22:15] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:22:20] Reading chimeric alignments from 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=10841987)
[2026-05-28T21:30:55] Marking multi-mapping alignments (marked=7047451)
[2026-05-28T21:31:00] Detecting strandedness (reverse)
[2026-05-28T21:31:00] Assigning strands to alignments 
[2026-05-28T21:31:02] Annotating alignments 
[2026-05-28T21:31:39] Filtering duplicates (remaining=8161074)
[2026-05-28T21:31:48] 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)
[2026-05-28T21:31:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7732633)
[2026-05-28T21:31:52] Filtering viral contigs with expression lower than the top 5 (remaining=7732633)
[2026-05-28T21:31:57] Filtering viral contigs with less than 5% coverage (remaining=7732633)
[2026-05-28T21:32:00] Estimating fragment length (mate gap mean=-86.3003, mate gap stddev=29.8556, read length mean=132.107)
[2026-05-28T21:32:00] Filtering read-through fragments with a distance <=10000bp (remaining=7295678)
[2026-05-28T21:32:02] Filtering inconsistently clipped mates (remaining=7172727)
[2026-05-28T21:32:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6900917)
[2026-05-28T21:32:11] Filtering fragments with small insert size (remaining=6899754)
[2026-05-28T21:32:14] Filtering alignments with long gaps (remaining=6899753)
[2026-05-28T21:32:16] Filtering fragments with both mates in the same gene (remaining=6898516)
[2026-05-28T21:32:19] Filtering fusions arising from hairpin structures (remaining=6431613)
[2026-05-28T21:32:22] Filtering reads with a mismatch p-value <=0.01 (remaining=3115100)
[2026-05-28T21:32:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=1296600)
[2026-05-28T21:32:56] Finding fusions and counting supporting reads (total=1068757)
[2026-05-28T21:33:16] Merging adjacent fusion breakpoints (remaining=1060411)
[2026-05-28T21:33:19] Filtering multi-mapping fusions by alignment score and read support (remaining=659237)
[2026-05-28T21:33:55] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:34:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=656808)
[2026-05-28T21:34:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=404921)
[2026-05-28T21:34:06] Filtering fusions with <2 supporting reads (remaining=30746)
[2026-05-28T21:34:07] Filtering fusions with an e-value >=0.3 (remaining=7095)
[2026-05-28T21:34:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7142)
[2026-05-28T21:34:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7012)
[2026-05-28T21:34:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7014)
[2026-05-28T21:34:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6070)
[2026-05-28T21:34:22] Searching for fusions with spliced split reads (remaining=6206)
[2026-05-28T21:34:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=3758)
[2026-05-28T21:34:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3719)
[2026-05-28T21:34:31] Searching for fusions with >=4 spliced events (remaining=4779)
[2026-05-28T21:34:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2400)
[2026-05-28T21:34:49] Filtering fusions with anchors <=23nt (remaining=1903)
[2026-05-28T21:34:50] Filtering end-to-end fusions with low support (remaining=1871)
[2026-05-28T21:34:51] Filtering fusions with no coverage around the breakpoints (remaining=1849)
[2026-05-28T21:34:52] Indexing gene sequences 
[2026-05-28T21:34:59] Filtering genes with >=30% identity (remaining=603)
[2026-05-28T21:35:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=326)
[2026-05-28T21:35:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=227)
[2026-05-28T21:35:23] Searching for additional isoforms (remaining=300)
[2026-05-28T21:35:24] Assigning confidence scores to events 
[2026-05-28T21:35:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:35:29] Writing fusions to file 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:35:33] Writing discarded fusions to file 'NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:36:13] Freeing resources
[2026-05-28T21:36:32] Done (elapsed time=00:14:31, CPU time=00:14:30, peak memory=15.7gb)