[2026-06-08T08:36:33] Launching Arriba 2.4.0
[2026-06-08T08:36:33] 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_KQG_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=13529067)
[2026-06-08T08:45:33] Marking multi-mapping alignments (marked=8690021)
[2026-06-08T08:45:39] Detecting strandedness (reverse)
[2026-06-08T08:45:39] Assigning strands to alignments 
[2026-06-08T08:45:42] Annotating alignments 
[2026-06-08T08:46:28] Filtering duplicates (remaining=9937530)
[2026-06-08T08:46:39] 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=9284213)
[2026-06-08T08:46:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9284213)
[2026-06-08T08:46:44] Filtering viral contigs with expression lower than the top 5 (remaining=9284213)
[2026-06-08T08:46:51] Filtering viral contigs with less than 5% coverage (remaining=9284213)
[2026-06-08T08:46:54] Estimating fragment length (mate gap mean=-84.4196, mate gap stddev=27.3182, read length mean=129.301)
[2026-06-08T08:46:54] Filtering read-through fragments with a distance <=10000bp (remaining=8898187)
[2026-06-08T08:46:57] Filtering inconsistently clipped mates (remaining=8750834)
[2026-06-08T08:47:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8586636)
[2026-06-08T08:47:06] Filtering fragments with small insert size (remaining=8585409)
[2026-06-08T08:47:09] Filtering alignments with long gaps (remaining=8585409)
[2026-06-08T08:47:12] Filtering fragments with both mates in the same gene (remaining=8584149)
[2026-06-08T08:47:15] Filtering fusions arising from hairpin structures (remaining=8192518)
[2026-06-08T08:47:18] Filtering reads with a mismatch p-value <=0.01 (remaining=4263841)
[2026-06-08T08:47:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=2169511)
[2026-06-08T08:48:00] Finding fusions and counting supporting reads (total=1881513)
[2026-06-08T08:48:25] Merging adjacent fusion breakpoints (remaining=1872166)
[2026-06-08T08:48:28] Filtering multi-mapping fusions by alignment score and read support (remaining=1110245)
[2026-06-08T08:49:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1108692)
[2026-06-08T08:49:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=921362)
[2026-06-08T08:49:29] Filtering fusions with <2 supporting reads (remaining=40912)
[2026-06-08T08:49:30] Filtering fusions with an e-value >=0.3 (remaining=6121)
[2026-06-08T08:49:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6207)
[2026-06-08T08:49:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6139)
[2026-06-08T08:49:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6139)
[2026-06-08T08:49:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5974)
[2026-06-08T08:49:48] Searching for fusions with spliced split reads (remaining=6010)
[2026-06-08T08:49:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=4214)
[2026-06-08T08:49:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4156)
[2026-06-08T08:49:58] Searching for fusions with >=4 spliced events (remaining=5233)
[2026-06-08T08:50:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2022)
[2026-06-08T08:50:17] Filtering fusions with anchors <=23nt (remaining=1761)
[2026-06-08T08:50:18] Filtering end-to-end fusions with low support (remaining=1727)
[2026-06-08T08:50:19] Filtering fusions with no coverage around the breakpoints (remaining=1696)
[2026-06-08T08:50:20] Indexing gene sequences 
[2026-06-08T08:50:27] Filtering genes with >=30% identity (remaining=474)
[2026-06-08T08:50:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=224)
[2026-06-08T08:50:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=184)
[2026-06-08T08:50:44] Searching for additional isoforms (remaining=239)
[2026-06-08T08:50:46] Assigning confidence scores to events 
[2026-06-08T08:50:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:52] Writing fusions to file '1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:50:55] Writing discarded fusions to file '1173_KQG_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:55] Freeing resources
[2026-06-08T08:52:21] Done (elapsed time=00:15:48, CPU time=00:15:47, peak memory=18.4gb)