[2026-06-08T08:03:18] Launching Arriba 2.4.0
[2026-06-08T08:03:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:03:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:03:37] Reading chimeric alignments from '1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=7613271)
[2026-06-08T08:08:49] Marking multi-mapping alignments (marked=5091293)
[2026-06-08T08:08:52] Detecting strandedness (reverse)
[2026-06-08T08:08:52] Assigning strands to alignments 
[2026-06-08T08:08:54] Annotating alignments 
[2026-06-08T08:09:19] Filtering duplicates (remaining=5293151)
[2026-06-08T08:09:24] 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=5003382)
[2026-06-08T08:09:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5003382)
[2026-06-08T08:09:27] Filtering viral contigs with expression lower than the top 5 (remaining=5003382)
[2026-06-08T08:09:30] Filtering viral contigs with less than 5% coverage (remaining=5003382)
[2026-06-08T08:09:32] Estimating fragment length (mate gap mean=-77.4746, mate gap stddev=25.8002, read length mean=115.109)
[2026-06-08T08:09:32] Filtering read-through fragments with a distance <=10000bp (remaining=4833593)
[2026-06-08T08:09:34] Filtering inconsistently clipped mates (remaining=4766192)
[2026-06-08T08:09:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4654548)
[2026-06-08T08:09:38] Filtering fragments with small insert size (remaining=4653717)
[2026-06-08T08:09:40] Filtering alignments with long gaps (remaining=4653717)
[2026-06-08T08:09:41] Filtering fragments with both mates in the same gene (remaining=4652807)
[2026-06-08T08:09:43] Filtering fusions arising from hairpin structures (remaining=4497075)
[2026-06-08T08:09:45] Filtering reads with a mismatch p-value <=0.01 (remaining=2246475)
[2026-06-08T08:09:55] Filtering reads with low entropy (k-mer content >=60%) (remaining=933202)
[2026-06-08T08:10:04] Finding fusions and counting supporting reads (total=830846)
[2026-06-08T08:10:17] Merging adjacent fusion breakpoints (remaining=827197)
[2026-06-08T08:10:19] Filtering multi-mapping fusions by alignment score and read support (remaining=455638)
[2026-06-08T08:10:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:10:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=454829)
[2026-06-08T08:10:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=393648)
[2026-06-08T08:10:50] Filtering fusions with <2 supporting reads (remaining=18406)
[2026-06-08T08:10:50] Filtering fusions with an e-value >=0.3 (remaining=3476)
[2026-06-08T08:10:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3513)
[2026-06-08T08:10:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3473)
[2026-06-08T08:10:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3473)
[2026-06-08T08:10:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3466)
[2026-06-08T08:11:00] Searching for fusions with spliced split reads (remaining=3521)
[2026-06-08T08:11:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=2644)
[2026-06-08T08:11:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2613)
[2026-06-08T08:11:06] Searching for fusions with >=4 spliced events (remaining=2937)
[2026-06-08T08:11:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1129)
[2026-06-08T08:11:22] Filtering fusions with anchors <=23nt (remaining=931)
[2026-06-08T08:11:22] Filtering end-to-end fusions with low support (remaining=909)
[2026-06-08T08:11:23] Filtering fusions with no coverage around the breakpoints (remaining=866)
[2026-06-08T08:11:24] Indexing gene sequences 
[2026-06-08T08:11:29] Filtering genes with >=30% identity (remaining=348)
[2026-06-08T08:11:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=214)
[2026-06-08T08:11:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-06-08T08:11:36] Searching for additional isoforms (remaining=253)
[2026-06-08T08:11:37] Assigning confidence scores to events 
[2026-06-08T08:11:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:11:40] Writing fusions to file '1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:11:42] Writing discarded fusions to file '1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:12:10] Freeing resources
[2026-06-08T08:12:22] Done (elapsed time=00:09:04, CPU time=00:09:04, peak memory=11.9gb)