[2026-06-08T07:59:10] Launching Arriba 2.4.0
[2026-06-08T07:59:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:59:27] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:59:32] Reading chimeric alignments from '1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=6496237)
[2026-06-08T08:04:38] Marking multi-mapping alignments (marked=4312378)
[2026-06-08T08:04:41] Detecting strandedness (reverse)
[2026-06-08T08:04:41] Assigning strands to alignments 
[2026-06-08T08:04:42] Annotating alignments 
[2026-06-08T08:05:09] Filtering duplicates (remaining=5316647)
[2026-06-08T08:05:18] 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=4705864)
[2026-06-08T08:05:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4705864)
[2026-06-08T08:05:20] Filtering viral contigs with expression lower than the top 5 (remaining=4705864)
[2026-06-08T08:05:24] Filtering viral contigs with less than 5% coverage (remaining=4705864)
[2026-06-08T08:05:26] Estimating fragment length (mate gap mean=-82.3365, mate gap stddev=27.272, read length mean=124.611)
[2026-06-08T08:05:26] Filtering read-through fragments with a distance <=10000bp (remaining=4546095)
[2026-06-08T08:05:27] Filtering inconsistently clipped mates (remaining=4497178)
[2026-06-08T08:05:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4414303)
[2026-06-08T08:05:32] Filtering fragments with small insert size (remaining=4413736)
[2026-06-08T08:05:33] Filtering alignments with long gaps (remaining=4413736)
[2026-06-08T08:05:35] Filtering fragments with both mates in the same gene (remaining=4412870)
[2026-06-08T08:05:37] Filtering fusions arising from hairpin structures (remaining=4287452)
[2026-06-08T08:05:38] Filtering reads with a mismatch p-value <=0.01 (remaining=2250144)
[2026-06-08T08:05:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=1182153)
[2026-06-08T08:05:58] Finding fusions and counting supporting reads (total=1093266)
[2026-06-08T08:06:13] Merging adjacent fusion breakpoints (remaining=1089771)
[2026-06-08T08:06:15] Filtering multi-mapping fusions by alignment score and read support (remaining=624290)
[2026-06-08T08:06:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:06:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=623515)
[2026-06-08T08:06:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=546016)
[2026-06-08T08:06:47] Filtering fusions with <2 supporting reads (remaining=19012)
[2026-06-08T08:06:48] Filtering fusions with an e-value >=0.3 (remaining=3132)
[2026-06-08T08:06:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3190)
[2026-06-08T08:06:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3151)
[2026-06-08T08:06:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3151)
[2026-06-08T08:06:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3100)
[2026-06-08T08:06:57] Searching for fusions with spliced split reads (remaining=3169)
[2026-06-08T08:07:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=2373)
[2026-06-08T08:07:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2345)
[2026-06-08T08:07:03] Searching for fusions with >=4 spliced events (remaining=2686)
[2026-06-08T08:07:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=859)
[2026-06-08T08:07:20] Filtering fusions with anchors <=23nt (remaining=713)
[2026-06-08T08:07:20] Filtering end-to-end fusions with low support (remaining=701)
[2026-06-08T08:07:21] Filtering fusions with no coverage around the breakpoints (remaining=683)
[2026-06-08T08:07:21] Indexing gene sequences 
[2026-06-08T08:07:25] Filtering genes with >=30% identity (remaining=220)
[2026-06-08T08:07:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=149)
[2026-06-08T08:07:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=143)
[2026-06-08T08:07:33] Searching for additional isoforms (remaining=176)
[2026-06-08T08:07:34] Assigning confidence scores to events 
[2026-06-08T08:07:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:07:37] Writing fusions to file '1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:07:39] Writing discarded fusions to file '1173_KQG_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:08:10] Freeing resources
[2026-06-08T08:08:22] Done (elapsed time=00:09:12, CPU time=00:09:11, peak memory=11.1gb)