[2026-06-08T08:27:22] Launching Arriba 2.4.0
[2026-06-08T08:27:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:38] Reading chimeric alignments from '1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=19601507)
[2026-06-08T08:33:50] Marking multi-mapping alignments (marked=14149941)
[2026-06-08T08:33:57] Detecting strandedness (no)
[2026-06-08T08:33:57] Annotating alignments 
[2026-06-08T08:34:52] Filtering duplicates (remaining=7780555)
[2026-06-08T08:35:01] 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=7008639)
[2026-06-08T08:35:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7008639)
[2026-06-08T08:35:08] Filtering viral contigs with expression lower than the top 5 (remaining=7008639)
[2026-06-08T08:35:15] Filtering viral contigs with less than 5% coverage (remaining=7008639)
[2026-06-08T08:35:18] Estimating fragment length (mate gap mean=-74.5694, mate gap stddev=26.5926, read length mean=112.28)
[2026-06-08T08:35:18] Filtering read-through fragments with a distance <=10000bp (remaining=6821657)
[2026-06-08T08:35:21] Filtering inconsistently clipped mates (remaining=6649810)
[2026-06-08T08:35:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6489186)
[2026-06-08T08:35:29] Filtering fragments with small insert size (remaining=6485189)
[2026-06-08T08:35:33] Filtering alignments with long gaps (remaining=6485189)
[2026-06-08T08:35:36] Filtering fragments with both mates in the same gene (remaining=6483437)
[2026-06-08T08:35:39] Filtering fusions arising from hairpin structures (remaining=6093020)
[2026-06-08T08:35:42] Filtering reads with a mismatch p-value <=0.01 (remaining=2439873)
[2026-06-08T08:35:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=813810)
[2026-06-08T08:36:09] Finding fusions and counting supporting reads (total=731405)
[2026-06-08T08:36:30] Merging adjacent fusion breakpoints (remaining=723429)
[2026-06-08T08:36:31] Filtering multi-mapping fusions by alignment score and read support (remaining=359863)
[2026-06-08T08:37:16] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=358542)
[2026-06-08T08:37:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=256258)
[2026-06-08T08:37:26] Filtering fusions with <2 supporting reads (remaining=14070)
[2026-06-08T08:37:26] Filtering fusions with an e-value >=0.3 (remaining=2814)
[2026-06-08T08:37:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2918)
[2026-06-08T08:37:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2777)
[2026-06-08T08:37:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2777)
[2026-06-08T08:37:35] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2773)
[2026-06-08T08:37:42] Searching for fusions with spliced split reads (remaining=2812)
[2026-06-08T08:37:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=2101)
[2026-06-08T08:37:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2076)
[2026-06-08T08:37:51] Searching for fusions with >=4 spliced events (remaining=2366)
[2026-06-08T08:37:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=971)
[2026-06-08T08:38:06] Filtering fusions with anchors <=23nt (remaining=840)
[2026-06-08T08:38:07] Filtering end-to-end fusions with low support (remaining=808)
[2026-06-08T08:38:07] Filtering fusions with no coverage around the breakpoints (remaining=779)
[2026-06-08T08:38:08] Indexing gene sequences 
[2026-06-08T08:38:12] Filtering genes with >=30% identity (remaining=260)
[2026-06-08T08:38:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=104)
[2026-06-08T08:38:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=95)
[2026-06-08T08:38:17] Searching for additional isoforms (remaining=119)
[2026-06-08T08:38:19] Assigning confidence scores to events 
[2026-06-08T08:38:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:38:23] Writing fusions to file '1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:38:24] Writing discarded fusions to file '1173_RQT_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:51] Freeing resources
[2026-06-08T08:39:16] Done (elapsed time=00:11:54, CPU time=00:11:53, peak memory=23.6gb)