[2026-06-08T08:19:19] Launching Arriba 2.4.0
[2026-06-08T08:19:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:27] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:31] Reading chimeric alignments from '1173_NBF_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=9991541)
[2026-06-08T08:24:45] Marking multi-mapping alignments (marked=6960426)
[2026-06-08T08:24:49] Detecting strandedness (reverse)
[2026-06-08T08:24:49] Assigning strands to alignments 
[2026-06-08T08:24:51] Annotating alignments 
[2026-06-08T08:25:25] Filtering duplicates (remaining=7183319)
[2026-06-08T08:25:32] 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=6473850)
[2026-06-08T08:25:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6473850)
[2026-06-08T08:25:36] Filtering viral contigs with expression lower than the top 5 (remaining=6473850)
[2026-06-08T08:25:41] Filtering viral contigs with less than 5% coverage (remaining=6473850)
[2026-06-08T08:25:43] Estimating fragment length (mate gap mean=-80.0528, mate gap stddev=26.9683, read length mean=117.854)
[2026-06-08T08:25:43] Filtering read-through fragments with a distance <=10000bp (remaining=6265379)
[2026-06-08T08:25:45] Filtering inconsistently clipped mates (remaining=6207863)
[2026-06-08T08:25:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6080846)
[2026-06-08T08:25:51] Filtering fragments with small insert size (remaining=6080086)
[2026-06-08T08:25:54] Filtering alignments with long gaps (remaining=6080085)
[2026-06-08T08:25:56] Filtering fragments with both mates in the same gene (remaining=6078955)
[2026-06-08T08:25:58] Filtering fusions arising from hairpin structures (remaining=5961115)
[2026-06-08T08:26:00] Filtering reads with a mismatch p-value <=0.01 (remaining=2844416)
[2026-06-08T08:26:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=1258475)
[2026-06-08T08:26:24] Finding fusions and counting supporting reads (total=1121913)
[2026-06-08T08:26:43] Merging adjacent fusion breakpoints (remaining=1117560)
[2026-06-08T08:26:46] Filtering multi-mapping fusions by alignment score and read support (remaining=582182)
[2026-06-08T08:27:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=581496)
[2026-06-08T08:27:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=516436)
[2026-06-08T08:27:29] Filtering fusions with <2 supporting reads (remaining=19799)
[2026-06-08T08:27:30] Filtering fusions with an e-value >=0.3 (remaining=3571)
[2026-06-08T08:27:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3623)
[2026-06-08T08:27:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3588)
[2026-06-08T08:27:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3588)
[2026-06-08T08:27:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3568)
[2026-06-08T08:27:44] Searching for fusions with spliced split reads (remaining=3636)
[2026-06-08T08:27:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=2709)
[2026-06-08T08:27:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2659)
[2026-06-08T08:27:52] Searching for fusions with >=4 spliced events (remaining=2967)
[2026-06-08T08:27:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1188)
[2026-06-08T08:28:07] Filtering fusions with anchors <=23nt (remaining=923)
[2026-06-08T08:28:08] Filtering end-to-end fusions with low support (remaining=893)
[2026-06-08T08:28:09] Filtering fusions with no coverage around the breakpoints (remaining=847)
[2026-06-08T08:28:10] Indexing gene sequences 
[2026-06-08T08:28:15] Filtering genes with >=30% identity (remaining=318)
[2026-06-08T08:28:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-06-08T08:28:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=145)
[2026-06-08T08:28:21] Searching for additional isoforms (remaining=175)
[2026-06-08T08:28:23] Assigning confidence scores to events 
[2026-06-08T08:28:27] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:28:27] Writing fusions to file '1173_NBF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:28:28] Writing discarded fusions to file '1173_NBF_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:06] Freeing resources
[2026-06-08T08:29:22] Done (elapsed time=00:10:03, CPU time=00:10:02, peak memory=14.6gb)