[2026-06-08T08:02:13] Launching Arriba 2.4.0
[2026-06-08T08:02:13] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:02:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:02:35] Reading chimeric alignments from '1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=11033339)
[2026-06-08T08:07:44] Marking multi-mapping alignments (marked=7890846)
[2026-06-08T08:07:48] Detecting strandedness (reverse)
[2026-06-08T08:07:48] Assigning strands to alignments 
[2026-06-08T08:07:50] Annotating alignments 
[2026-06-08T08:08:24] Filtering duplicates (remaining=5055258)
[2026-06-08T08:08:30] 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=4778235)
[2026-06-08T08:08:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4778235)
[2026-06-08T08:08:34] Filtering viral contigs with expression lower than the top 5 (remaining=4778235)
[2026-06-08T08:08:39] Filtering viral contigs with less than 5% coverage (remaining=4778235)
[2026-06-08T08:08:41] Estimating fragment length (mate gap mean=-75.3155, mate gap stddev=25.345, read length mean=114.392)
[2026-06-08T08:08:42] Filtering read-through fragments with a distance <=10000bp (remaining=4601690)
[2026-06-08T08:08:44] Filtering inconsistently clipped mates (remaining=4494427)
[2026-06-08T08:08:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4415242)
[2026-06-08T08:08:49] Filtering fragments with small insert size (remaining=4413788)
[2026-06-08T08:08:51] Filtering alignments with long gaps (remaining=4413788)
[2026-06-08T08:08:54] Filtering fragments with both mates in the same gene (remaining=4412906)
[2026-06-08T08:08:56] Filtering fusions arising from hairpin structures (remaining=4181244)
[2026-06-08T08:08:58] Filtering reads with a mismatch p-value <=0.01 (remaining=1763389)
[2026-06-08T08:09:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=620830)
[2026-06-08T08:09:17] Finding fusions and counting supporting reads (total=572735)
[2026-06-08T08:09:33] Merging adjacent fusion breakpoints (remaining=568541)
[2026-06-08T08:09:34] Filtering multi-mapping fusions by alignment score and read support (remaining=293633)
[2026-06-08T08:10:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:10:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=292985)
[2026-06-08T08:10:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=222371)
[2026-06-08T08:10:12] Filtering fusions with <2 supporting reads (remaining=8611)
[2026-06-08T08:10:13] Filtering fusions with an e-value >=0.3 (remaining=2013)
[2026-06-08T08:10:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2132)
[2026-06-08T08:10:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2073)
[2026-06-08T08:10:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2073)
[2026-06-08T08:10:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2073)
[2026-06-08T08:10:23] Searching for fusions with spliced split reads (remaining=2201)
[2026-06-08T08:10:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=1623)
[2026-06-08T08:10:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1597)
[2026-06-08T08:10:30] Searching for fusions with >=4 spliced events (remaining=1827)
[2026-06-08T08:10:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=859)
[2026-06-08T08:10:45] Filtering fusions with anchors <=23nt (remaining=770)
[2026-06-08T08:10:46] Filtering end-to-end fusions with low support (remaining=743)
[2026-06-08T08:10:46] Filtering fusions with no coverage around the breakpoints (remaining=721)
[2026-06-08T08:10:47] Indexing gene sequences 
[2026-06-08T08:10:52] Filtering genes with >=30% identity (remaining=242)
[2026-06-08T08:10:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=121)
[2026-06-08T08:10:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=118)
[2026-06-08T08:10:57] Searching for additional isoforms (remaining=126)
[2026-06-08T08:10:59] Assigning confidence scores to events 
[2026-06-08T08:11:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:11:02] Writing fusions to file '1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:11:03] Writing discarded fusions to file '1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:11:29] Freeing resources
[2026-06-08T08:11:47] Done (elapsed time=00:09:34, CPU time=00:09:32, peak memory=15.1gb)