[2026-06-08T09:00:07] Launching Arriba 2.4.0
[2026-06-08T09:00:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:00:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:00:24] Reading chimeric alignments from '1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=24843920)
[2026-06-08T09:10:28] Marking multi-mapping alignments (marked=17992930)
[2026-06-08T09:10:38] Detecting strandedness (no)
[2026-06-08T09:10:38] Annotating alignments 
[2026-06-08T09:12:25] Filtering duplicates (remaining=11053216)
[2026-06-08T09:12:41] 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=9904744)
[2026-06-08T09:12:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9904744)
[2026-06-08T09:12:51] Filtering viral contigs with expression lower than the top 5 (remaining=9904744)
[2026-06-08T09:13:02] Filtering viral contigs with less than 5% coverage (remaining=9904744)
[2026-06-08T09:13:08] Estimating fragment length (mate gap mean=-86.1049, mate gap stddev=27.6066, read length mean=117.732)
[2026-06-08T09:13:08] Filtering read-through fragments with a distance <=10000bp (remaining=9784249)
[2026-06-08T09:13:13] Filtering inconsistently clipped mates (remaining=9680536)
[2026-06-08T09:13:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9448092)
[2026-06-08T09:13:27] Filtering fragments with small insert size (remaining=9445752)
[2026-06-08T09:13:32] Filtering alignments with long gaps (remaining=9445752)
[2026-06-08T09:13:38] Filtering fragments with both mates in the same gene (remaining=9444481)
[2026-06-08T09:13:43] Filtering fusions arising from hairpin structures (remaining=9118616)
[2026-06-08T09:13:48] Filtering reads with a mismatch p-value <=0.01 (remaining=2889593)
[2026-06-08T09:14:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=1569316)
[2026-06-08T09:14:29] Finding fusions and counting supporting reads (total=1502020)
[2026-06-08T09:15:07] Merging adjacent fusion breakpoints (remaining=1492067)
[2026-06-08T09:15:10] Filtering multi-mapping fusions by alignment score and read support (remaining=892308)
[2026-06-08T09:16:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:16:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=891605)
[2026-06-08T09:16:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=820833)
[2026-06-08T09:16:55] Filtering fusions with <2 supporting reads (remaining=25420)
[2026-06-08T09:16:56] Filtering fusions with an e-value >=0.3 (remaining=2541)
[2026-06-08T09:16:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2567)
[2026-06-08T09:17:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2467)
[2026-06-08T09:17:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2467)
[2026-06-08T09:17:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2451)
[2026-06-08T09:17:22] Searching for fusions with spliced split reads (remaining=2518)
[2026-06-08T09:17:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=2093)
[2026-06-08T09:17:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2079)
[2026-06-08T09:17:39] Searching for fusions with >=4 spliced events (remaining=2328)
[2026-06-08T09:17:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1017)
[2026-06-08T09:17:59] Filtering fusions with anchors <=23nt (remaining=720)
[2026-06-08T09:18:01] Filtering end-to-end fusions with low support (remaining=597)
[2026-06-08T09:18:02] Filtering fusions with no coverage around the breakpoints (remaining=549)
[2026-06-08T09:18:03] Indexing gene sequences 
[2026-06-08T09:18:09] Filtering genes with >=30% identity (remaining=259)
[2026-06-08T09:18:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=152)
[2026-06-08T09:18:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=149)
[2026-06-08T09:18:18] Searching for additional isoforms (remaining=174)
[2026-06-08T09:18:21] Assigning confidence scores to events 
[2026-06-08T09:18:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:18:28] Writing fusions to file '1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:18:31] Writing discarded fusions to file '1173_T46_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:19:32] Freeing resources
[2026-06-08T09:20:16] Done (elapsed time=00:20:09, CPU time=00:20:09, peak memory=30.5gb)