[2026-06-08T08:17:10] Launching Arriba 2.4.0
[2026-06-08T08:17:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:25] Reading chimeric alignments from '1173_RQT_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=13125337)
[2026-06-08T08:22:18] Marking multi-mapping alignments (marked=9469805)
[2026-06-08T08:22:22] Detecting strandedness (reverse)
[2026-06-08T08:22:22] Assigning strands to alignments 
[2026-06-08T08:22:25] Annotating alignments 
[2026-06-08T08:23:07] Filtering duplicates (remaining=4604023)
[2026-06-08T08:23:14] 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=4137352)
[2026-06-08T08:23:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4137352)
[2026-06-08T08:23:19] Filtering viral contigs with expression lower than the top 5 (remaining=4137352)
[2026-06-08T08:23:24] Filtering viral contigs with less than 5% coverage (remaining=4137352)
[2026-06-08T08:23:27] Estimating fragment length (mate gap mean=-76.652, mate gap stddev=27.5243, read length mean=113.301)
[2026-06-08T08:23:27] Filtering read-through fragments with a distance <=10000bp (remaining=4020612)
[2026-06-08T08:23:30] Filtering inconsistently clipped mates (remaining=3914802)
[2026-06-08T08:23:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3811543)
[2026-06-08T08:23:36] Filtering fragments with small insert size (remaining=3809405)
[2026-06-08T08:23:38] Filtering alignments with long gaps (remaining=3809405)
[2026-06-08T08:23:41] Filtering fragments with both mates in the same gene (remaining=3808418)
[2026-06-08T08:23:43] Filtering fusions arising from hairpin structures (remaining=3577555)
[2026-06-08T08:23:46] Filtering reads with a mismatch p-value <=0.01 (remaining=1366794)
[2026-06-08T08:23:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=420416)
[2026-06-08T08:24:04] Finding fusions and counting supporting reads (total=374220)
[2026-06-08T08:24:21] Merging adjacent fusion breakpoints (remaining=371009)
[2026-06-08T08:24:23] Filtering multi-mapping fusions by alignment score and read support (remaining=187651)
[2026-06-08T08:25:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:25:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=186714)
[2026-06-08T08:25:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=124009)
[2026-06-08T08:25:07] Filtering fusions with <2 supporting reads (remaining=7963)
[2026-06-08T08:25:07] Filtering fusions with an e-value >=0.3 (remaining=1772)
[2026-06-08T08:25:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1831)
[2026-06-08T08:25:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1751)
[2026-06-08T08:25:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1751)
[2026-06-08T08:25:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1747)
[2026-06-08T08:25:18] Searching for fusions with spliced split reads (remaining=1847)
[2026-06-08T08:25:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=1411)
[2026-06-08T08:25:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1394)
[2026-06-08T08:25:25] Searching for fusions with >=4 spliced events (remaining=1496)
[2026-06-08T08:25:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=538)
[2026-06-08T08:25:38] Filtering fusions with anchors <=23nt (remaining=471)
[2026-06-08T08:25:38] Filtering end-to-end fusions with low support (remaining=438)
[2026-06-08T08:25:39] Filtering fusions with no coverage around the breakpoints (remaining=421)
[2026-06-08T08:25:39] Indexing gene sequences 
[2026-06-08T08:25:42] Filtering genes with >=30% identity (remaining=150)
[2026-06-08T08:25:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=59)
[2026-06-08T08:25:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=52)
[2026-06-08T08:25:45] Searching for additional isoforms (remaining=65)
[2026-06-08T08:25:46] Assigning confidence scores to events 
[2026-06-08T08:25:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:25:49] Writing fusions to file '1173_RQT_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:25:49] Writing discarded fusions to file '1173_RQT_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:26:10] Freeing resources
[2026-06-08T08:26:28] Done (elapsed time=00:09:18, CPU time=00:09:17, peak memory=17.1gb)