[2026-06-08T08:30:32] Launching Arriba 2.4.0
[2026-06-08T08:30:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:45] Reading chimeric alignments from '1173_HRO_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=15929254)
[2026-06-08T08:37:33] Marking multi-mapping alignments (marked=11280038)
[2026-06-08T08:37:38] Detecting strandedness (reverse)
[2026-06-08T08:37:38] Assigning strands to alignments 
[2026-06-08T08:37:41] Annotating alignments 
[2026-06-08T08:38:26] Filtering duplicates (remaining=8304979)
[2026-06-08T08:38:35] 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=7332987)
[2026-06-08T08:38:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7332987)
[2026-06-08T08:38:41] Filtering viral contigs with expression lower than the top 5 (remaining=7332987)
[2026-06-08T08:38:47] Filtering viral contigs with less than 5% coverage (remaining=7332987)
[2026-06-08T08:38:50] Estimating fragment length (mate gap mean=-77.1033, mate gap stddev=27.677, read length mean=113.801)
[2026-06-08T08:38:50] Filtering read-through fragments with a distance <=10000bp (remaining=7046588)
[2026-06-08T08:38:53] Filtering inconsistently clipped mates (remaining=6925397)
[2026-06-08T08:38:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6726394)
[2026-06-08T08:39:01] Filtering fragments with small insert size (remaining=6724759)
[2026-06-08T08:39:04] Filtering alignments with long gaps (remaining=6724758)
[2026-06-08T08:39:06] Filtering fragments with both mates in the same gene (remaining=6723129)
[2026-06-08T08:39:09] Filtering fusions arising from hairpin structures (remaining=6465374)
[2026-06-08T08:39:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2712328)
[2026-06-08T08:39:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=1078835)
[2026-06-08T08:39:39] Finding fusions and counting supporting reads (total=957462)
[2026-06-08T08:40:01] Merging adjacent fusion breakpoints (remaining=950027)
[2026-06-08T08:40:03] Filtering multi-mapping fusions by alignment score and read support (remaining=481261)
[2026-06-08T08:40:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=480269)
[2026-06-08T08:40:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=378826)
[2026-06-08T08:41:01] Filtering fusions with <2 supporting reads (remaining=19122)
[2026-06-08T08:41:02] Filtering fusions with an e-value >=0.3 (remaining=3502)
[2026-06-08T08:41:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3590)
[2026-06-08T08:41:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3529)
[2026-06-08T08:41:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3529)
[2026-06-08T08:41:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3512)
[2026-06-08T08:41:19] Searching for fusions with spliced split reads (remaining=3606)
[2026-06-08T08:41:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=2668)
[2026-06-08T08:41:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2626)
[2026-06-08T08:41:30] Searching for fusions with >=4 spliced events (remaining=2991)
[2026-06-08T08:41:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1150)
[2026-06-08T08:41:45] Filtering fusions with anchors <=23nt (remaining=921)
[2026-06-08T08:41:46] Filtering end-to-end fusions with low support (remaining=898)
[2026-06-08T08:41:47] Filtering fusions with no coverage around the breakpoints (remaining=887)
[2026-06-08T08:41:48] Indexing gene sequences 
[2026-06-08T08:41:52] Filtering genes with >=30% identity (remaining=282)
[2026-06-08T08:41:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=136)
[2026-06-08T08:41:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=136)
[2026-06-08T08:41:59] Searching for additional isoforms (remaining=155)
[2026-06-08T08:42:01] Assigning confidence scores to events 
[2026-06-08T08:42:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:05] Writing fusions to file '1173_HRO_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:07] Writing discarded fusions to file '1173_HRO_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:42] Freeing resources
[2026-06-08T08:43:05] Done (elapsed time=00:12:33, CPU time=00:12:31, peak memory=20.2gb)