[2026-06-08T08:18:22] Launching Arriba 2.4.0
[2026-06-08T08:18:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:18:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:18:35] Reading chimeric alignments from '1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=11778792)
[2026-06-08T08:24:04] Marking multi-mapping alignments (marked=8356074)
[2026-06-08T08:24:08] Detecting strandedness (reverse)
[2026-06-08T08:24:08] Assigning strands to alignments 
[2026-06-08T08:24:11] Annotating alignments 
[2026-06-08T08:24:50] Filtering duplicates (remaining=7684312)
[2026-06-08T08:24:59] 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=6892625)
[2026-06-08T08:25:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6892625)
[2026-06-08T08:25:03] Filtering viral contigs with expression lower than the top 5 (remaining=6892625)
[2026-06-08T08:25:09] Filtering viral contigs with less than 5% coverage (remaining=6892625)
[2026-06-08T08:25:11] Estimating fragment length (mate gap mean=-77.6826, mate gap stddev=26.6398, read length mean=116.743)
[2026-06-08T08:25:11] Filtering read-through fragments with a distance <=10000bp (remaining=6714151)
[2026-06-08T08:25:14] Filtering inconsistently clipped mates (remaining=6612597)
[2026-06-08T08:25:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6486951)
[2026-06-08T08:25:20] Filtering fragments with small insert size (remaining=6485916)
[2026-06-08T08:25:22] Filtering alignments with long gaps (remaining=6485916)
[2026-06-08T08:25:25] Filtering fragments with both mates in the same gene (remaining=6484767)
[2026-06-08T08:25:27] Filtering fusions arising from hairpin structures (remaining=6262292)
[2026-06-08T08:25:30] Filtering reads with a mismatch p-value <=0.01 (remaining=2905590)
[2026-06-08T08:25:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=1178396)
[2026-06-08T08:25:56] Finding fusions and counting supporting reads (total=1104572)
[2026-06-08T08:26:17] Merging adjacent fusion breakpoints (remaining=1098487)
[2026-06-08T08:26:19] Filtering multi-mapping fusions by alignment score and read support (remaining=569672)
[2026-06-08T08:26:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=568744)
[2026-06-08T08:27:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=492894)
[2026-06-08T08:27:08] Filtering fusions with <2 supporting reads (remaining=13752)
[2026-06-08T08:27:09] Filtering fusions with an e-value >=0.3 (remaining=2717)
[2026-06-08T08:27:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2783)
[2026-06-08T08:27:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2738)
[2026-06-08T08:27:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2738)
[2026-06-08T08:27:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2737)
[2026-06-08T08:27:24] Searching for fusions with spliced split reads (remaining=2797)
[2026-06-08T08:27:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=2083)
[2026-06-08T08:27:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2050)
[2026-06-08T08:27:34] Searching for fusions with >=4 spliced events (remaining=2294)
[2026-06-08T08:27:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=894)
[2026-06-08T08:27:49] Filtering fusions with anchors <=23nt (remaining=669)
[2026-06-08T08:27:50] Filtering end-to-end fusions with low support (remaining=648)
[2026-06-08T08:27:51] Filtering fusions with no coverage around the breakpoints (remaining=630)
[2026-06-08T08:27:52] Indexing gene sequences 
[2026-06-08T08:27:56] Filtering genes with >=30% identity (remaining=211)
[2026-06-08T08:27:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=100)
[2026-06-08T08:28:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=91)
[2026-06-08T08:28:02] Searching for additional isoforms (remaining=112)
[2026-06-08T08:28:04] Assigning confidence scores to events 
[2026-06-08T08:28:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:28:08] Writing fusions to file '1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:28:09] Writing discarded fusions to file '1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:48] Freeing resources
[2026-06-08T08:29:06] Done (elapsed time=00:10:44, CPU time=00:10:43, peak memory=16.2gb)