[2026-06-08T08:24:25] Launching Arriba 2.4.0
[2026-06-08T08:24:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:38] Reading chimeric alignments from '1173_RDM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=20231375)
[2026-06-08T08:31:31] Marking multi-mapping alignments (marked=14693820)
[2026-06-08T08:31:39] Detecting strandedness (reverse)
[2026-06-08T08:31:39] Assigning strands to alignments 
[2026-06-08T08:31:43] Annotating alignments 
[2026-06-08T08:32:47] Filtering duplicates (remaining=6619257)
[2026-06-08T08:32:59] 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=5771984)
[2026-06-08T08:33:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5771984)
[2026-06-08T08:33:07] Filtering viral contigs with expression lower than the top 5 (remaining=5771984)
[2026-06-08T08:33:16] Filtering viral contigs with less than 5% coverage (remaining=5771984)
[2026-06-08T08:33:20] Estimating fragment length (mate gap mean=-79.3921, mate gap stddev=27.2259, read length mean=116.275)
[2026-06-08T08:33:20] Filtering read-through fragments with a distance <=10000bp (remaining=5594164)
[2026-06-08T08:33:24] Filtering inconsistently clipped mates (remaining=5409429)
[2026-06-08T08:33:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5215168)
[2026-06-08T08:33:34] Filtering fragments with small insert size (remaining=5212189)
[2026-06-08T08:33:38] Filtering alignments with long gaps (remaining=5212188)
[2026-06-08T08:33:43] Filtering fragments with both mates in the same gene (remaining=5210754)
[2026-06-08T08:33:47] Filtering fusions arising from hairpin structures (remaining=4806103)
[2026-06-08T08:33:51] Filtering reads with a mismatch p-value <=0.01 (remaining=1863942)
[2026-06-08T08:34:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=671976)
[2026-06-08T08:34:17] Finding fusions and counting supporting reads (total=606310)
[2026-06-08T08:34:44] Merging adjacent fusion breakpoints (remaining=598690)
[2026-06-08T08:34:45] Filtering multi-mapping fusions by alignment score and read support (remaining=285196)
[2026-06-08T08:35:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=283817)
[2026-06-08T08:35:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=202039)
[2026-06-08T08:35:56] Filtering fusions with <2 supporting reads (remaining=10149)
[2026-06-08T08:35:57] Filtering fusions with an e-value >=0.3 (remaining=2417)
[2026-06-08T08:35:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2531)
[2026-06-08T08:36:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2416)
[2026-06-08T08:36:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2416)
[2026-06-08T08:36:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2416)
[2026-06-08T08:36:14] Searching for fusions with spliced split reads (remaining=2514)
[2026-06-08T08:36:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=1879)
[2026-06-08T08:36:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1864)
[2026-06-08T08:36:25] Searching for fusions with >=4 spliced events (remaining=2027)
[2026-06-08T08:36:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=784)
[2026-06-08T08:36:39] Filtering fusions with anchors <=23nt (remaining=660)
[2026-06-08T08:36:40] Filtering end-to-end fusions with low support (remaining=632)
[2026-06-08T08:36:41] Filtering fusions with no coverage around the breakpoints (remaining=616)
[2026-06-08T08:36:42] Indexing gene sequences 
[2026-06-08T08:36:45] Filtering genes with >=30% identity (remaining=237)
[2026-06-08T08:36:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=123)
[2026-06-08T08:36:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=123)
[2026-06-08T08:36:50] Searching for additional isoforms (remaining=130)
[2026-06-08T08:36:52] Assigning confidence scores to events 
[2026-06-08T08:36:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:55] Writing fusions to file '1173_RDM_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:56] Writing discarded fusions to file '1173_RDM_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:29] Freeing resources
[2026-06-08T08:37:57] Done (elapsed time=00:13:32, CPU time=00:13:31, peak memory=24.6gb)