[2026-05-28T21:25:47] Launching Arriba 2.4.0
[2026-05-28T21:25:47] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:26:01] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:26:06] Reading chimeric alignments from 'U118MG_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12046934)
[2026-05-28T21:34:45] Marking multi-mapping alignments (marked=7810504)
[2026-05-28T21:34:50] Detecting strandedness (reverse)
[2026-05-28T21:34:50] Assigning strands to alignments 
[2026-05-28T21:34:52] Annotating alignments 
[2026-05-28T21:35:32] Filtering duplicates (remaining=8807729)
[2026-05-28T21:35:41] 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=8146311)
[2026-05-28T21:35:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8146311)
[2026-05-28T21:35:45] Filtering viral contigs with expression lower than the top 5 (remaining=8146311)
[2026-05-28T21:35:51] Filtering viral contigs with less than 5% coverage (remaining=8146311)
[2026-05-28T21:35:53] Estimating fragment length (mate gap mean=-86.5125, mate gap stddev=30.421, read length mean=131.095)
[2026-05-28T21:35:53] Filtering read-through fragments with a distance <=10000bp (remaining=7718469)
[2026-05-28T21:35:56] Filtering inconsistently clipped mates (remaining=7590607)
[2026-05-28T21:35:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7335326)
[2026-05-28T21:36:04] Filtering fragments with small insert size (remaining=7333897)
[2026-05-28T21:36:06] Filtering alignments with long gaps (remaining=7333897)
[2026-05-28T21:36:09] Filtering fragments with both mates in the same gene (remaining=7332319)
[2026-05-28T21:36:11] Filtering fusions arising from hairpin structures (remaining=6814544)
[2026-05-28T21:36:14] Filtering reads with a mismatch p-value <=0.01 (remaining=3127780)
[2026-05-28T21:36:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=1403761)
[2026-05-28T21:36:49] Finding fusions and counting supporting reads (total=1124007)
[2026-05-28T21:37:10] Merging adjacent fusion breakpoints (remaining=1112463)
[2026-05-28T21:37:12] Filtering multi-mapping fusions by alignment score and read support (remaining=724166)
[2026-05-28T21:37:49] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:37:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=720917)
[2026-05-28T21:37:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=420373)
[2026-05-28T21:38:01] Filtering fusions with <2 supporting reads (remaining=39421)
[2026-05-28T21:38:02] Filtering fusions with an e-value >=0.3 (remaining=7725)
[2026-05-28T21:38:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7778)
[2026-05-28T21:38:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7678)
[2026-05-28T21:38:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7683)
[2026-05-28T21:38:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6923)
[2026-05-28T21:38:16] Searching for fusions with spliced split reads (remaining=6947)
[2026-05-28T21:38:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=4194)
[2026-05-28T21:38:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4161)
[2026-05-28T21:38:26] Searching for fusions with >=4 spliced events (remaining=5213)
[2026-05-28T21:38:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2192)
[2026-05-28T21:38:45] Filtering fusions with anchors <=23nt (remaining=1755)
[2026-05-28T21:38:46] Filtering end-to-end fusions with low support (remaining=1711)
[2026-05-28T21:38:47] Filtering fusions with no coverage around the breakpoints (remaining=1691)
[2026-05-28T21:38:48] Indexing gene sequences 
[2026-05-28T21:38:56] Filtering genes with >=30% identity (remaining=609)
[2026-05-28T21:39:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=349)
[2026-05-28T21:39:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=270)
[2026-05-28T21:39:21] Searching for additional isoforms (remaining=371)
[2026-05-28T21:39:23] Assigning confidence scores to events 
[2026-05-28T21:39:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:39:28] Writing fusions to file 'U118MG_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:39:32] Writing discarded fusions to file 'U118MG_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:40:14] Freeing resources
[2026-05-28T21:40:35] Done (elapsed time=00:14:48, CPU time=00:14:48, peak memory=17.1gb)