[2026-06-08T08:36:34] Launching Arriba 2.4.0
[2026-06-08T08:36:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:52] Reading chimeric alignments from '1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=15763028)
[2026-06-08T08:44:38] Marking multi-mapping alignments (marked=10775440)
[2026-06-08T08:44:44] Detecting strandedness (reverse)
[2026-06-08T08:44:44] Assigning strands to alignments 
[2026-06-08T08:44:47] Annotating alignments 
[2026-06-08T08:45:38] Filtering duplicates (remaining=10825288)
[2026-06-08T08:45:50] 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=9752781)
[2026-06-08T08:45:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9752781)
[2026-06-08T08:45:56] Filtering viral contigs with expression lower than the top 5 (remaining=9752781)
[2026-06-08T08:46:03] Filtering viral contigs with less than 5% coverage (remaining=9752781)
[2026-06-08T08:46:07] Estimating fragment length (mate gap mean=-81.4787, mate gap stddev=26.3632, read length mean=122.705)
[2026-06-08T08:46:07] Filtering read-through fragments with a distance <=10000bp (remaining=9391540)
[2026-06-08T08:46:10] Filtering inconsistently clipped mates (remaining=9224851)
[2026-06-08T08:46:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9056320)
[2026-06-08T08:46:20] Filtering fragments with small insert size (remaining=9054959)
[2026-06-08T08:46:23] Filtering alignments with long gaps (remaining=9054958)
[2026-06-08T08:46:27] Filtering fragments with both mates in the same gene (remaining=9053563)
[2026-06-08T08:46:30] Filtering fusions arising from hairpin structures (remaining=8637681)
[2026-06-08T08:46:34] Filtering reads with a mismatch p-value <=0.01 (remaining=4300389)
[2026-06-08T08:46:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=2224787)
[2026-06-08T08:47:13] Finding fusions and counting supporting reads (total=2058010)
[2026-06-08T08:47:42] Merging adjacent fusion breakpoints (remaining=2047140)
[2026-06-08T08:47:45] Filtering multi-mapping fusions by alignment score and read support (remaining=1113932)
[2026-06-08T08:48:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1112876)
[2026-06-08T08:48:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=954974)
[2026-06-08T08:48:52] Filtering fusions with <2 supporting reads (remaining=26082)
[2026-06-08T08:48:53] Filtering fusions with an e-value >=0.3 (remaining=3877)
[2026-06-08T08:48:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3973)
[2026-06-08T08:49:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3905)
[2026-06-08T08:49:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3905)
[2026-06-08T08:49:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3880)
[2026-06-08T08:49:15] Searching for fusions with spliced split reads (remaining=3966)
[2026-06-08T08:49:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=2917)
[2026-06-08T08:49:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2880)
[2026-06-08T08:49:28] Searching for fusions with >=4 spliced events (remaining=3543)
[2026-06-08T08:49:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1539)
[2026-06-08T08:49:49] Filtering fusions with anchors <=23nt (remaining=1262)
[2026-06-08T08:49:50] Filtering end-to-end fusions with low support (remaining=1243)
[2026-06-08T08:49:52] Filtering fusions with no coverage around the breakpoints (remaining=1216)
[2026-06-08T08:49:53] Indexing gene sequences 
[2026-06-08T08:49:59] Filtering genes with >=30% identity (remaining=370)
[2026-06-08T08:50:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=152)
[2026-06-08T08:50:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=140)
[2026-06-08T08:50:13] Searching for additional isoforms (remaining=165)
[2026-06-08T08:50:15] Assigning confidence scores to events 
[2026-06-08T08:50:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:23] Writing fusions to file '1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:25] Writing discarded fusions to file '1173_RPX_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:47] Freeing resources
[2026-06-08T08:52:20] Done (elapsed time=00:15:46, CPU time=00:15:45, peak memory=20.8gb)