[2026-06-08T08:09:31] Launching Arriba 2.4.0
[2026-06-08T08:09:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:09:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:09:44] Reading chimeric alignments from '1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=7440329)
[2026-06-08T08:13:38] Marking multi-mapping alignments (marked=4983654)
[2026-06-08T08:13:41] Detecting strandedness (reverse)
[2026-06-08T08:13:41] Assigning strands to alignments 
[2026-06-08T08:13:43] Annotating alignments 
[2026-06-08T08:14:08] Filtering duplicates (remaining=5757662)
[2026-06-08T08:14:14] 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=5390261)
[2026-06-08T08:14:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5390261)
[2026-06-08T08:14:16] Filtering viral contigs with expression lower than the top 5 (remaining=5390261)
[2026-06-08T08:14:20] Filtering viral contigs with less than 5% coverage (remaining=5390261)
[2026-06-08T08:14:22] Estimating fragment length (mate gap mean=-81.2915, mate gap stddev=27.1539, read length mean=124.283)
[2026-06-08T08:14:22] Filtering read-through fragments with a distance <=10000bp (remaining=5151141)
[2026-06-08T08:14:23] Filtering inconsistently clipped mates (remaining=5070592)
[2026-06-08T08:14:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4982771)
[2026-06-08T08:14:28] Filtering fragments with small insert size (remaining=4982093)
[2026-06-08T08:14:29] Filtering alignments with long gaps (remaining=4982093)
[2026-06-08T08:14:31] Filtering fragments with both mates in the same gene (remaining=4981329)
[2026-06-08T08:14:32] Filtering fusions arising from hairpin structures (remaining=4774942)
[2026-06-08T08:14:35] Filtering reads with a mismatch p-value <=0.01 (remaining=2402622)
[2026-06-08T08:14:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=1094062)
[2026-06-08T08:14:55] Finding fusions and counting supporting reads (total=1016764)
[2026-06-08T08:15:09] Merging adjacent fusion breakpoints (remaining=1011909)
[2026-06-08T08:15:10] Filtering multi-mapping fusions by alignment score and read support (remaining=564070)
[2026-06-08T08:15:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:15:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=563365)
[2026-06-08T08:15:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=455411)
[2026-06-08T08:15:47] Filtering fusions with <2 supporting reads (remaining=15487)
[2026-06-08T08:15:48] Filtering fusions with an e-value >=0.3 (remaining=2941)
[2026-06-08T08:15:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3016)
[2026-06-08T08:15:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2981)
[2026-06-08T08:15:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2981)
[2026-06-08T08:15:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2948)
[2026-06-08T08:16:02] Searching for fusions with spliced split reads (remaining=3009)
[2026-06-08T08:16:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=2255)
[2026-06-08T08:16:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2228)
[2026-06-08T08:16:09] Searching for fusions with >=4 spliced events (remaining=2546)
[2026-06-08T08:16:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1000)
[2026-06-08T08:16:23] Filtering fusions with anchors <=23nt (remaining=804)
[2026-06-08T08:16:23] Filtering end-to-end fusions with low support (remaining=788)
[2026-06-08T08:16:24] Filtering fusions with no coverage around the breakpoints (remaining=768)
[2026-06-08T08:16:25] Indexing gene sequences 
[2026-06-08T08:16:28] Filtering genes with >=30% identity (remaining=285)
[2026-06-08T08:16:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=143)
[2026-06-08T08:16:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=143)
[2026-06-08T08:16:34] Searching for additional isoforms (remaining=168)
[2026-06-08T08:16:35] Assigning confidence scores to events 
[2026-06-08T08:16:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:16:38] Writing fusions to file '1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:16:40] Writing discarded fusions to file '1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:17:09] Freeing resources
[2026-06-08T08:17:23] Done (elapsed time=00:07:52, CPU time=00:07:50, peak memory=11.8gb)