[2026-06-08T08:39:31] Launching Arriba 2.4.0
[2026-06-08T08:39:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:48] Reading chimeric alignments from '1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=12920157)
[2026-06-08T08:47:27] Marking multi-mapping alignments (marked=8886172)
[2026-06-08T08:47:32] Detecting strandedness (reverse)
[2026-06-08T08:47:32] Assigning strands to alignments 
[2026-06-08T08:47:34] Annotating alignments 
[2026-06-08T08:48:17] Filtering duplicates (remaining=7331965)
[2026-06-08T08:48:26] 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=6899611)
[2026-06-08T08:48:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6899611)
[2026-06-08T08:48:31] Filtering viral contigs with expression lower than the top 5 (remaining=6899611)
[2026-06-08T08:48:38] Filtering viral contigs with less than 5% coverage (remaining=6899611)
[2026-06-08T08:48:41] Estimating fragment length (mate gap mean=-78.1738, mate gap stddev=26.3079, read length mean=115.814)
[2026-06-08T08:48:41] Filtering read-through fragments with a distance <=10000bp (remaining=6647328)
[2026-06-08T08:48:44] Filtering inconsistently clipped mates (remaining=6534168)
[2026-06-08T08:48:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6417787)
[2026-06-08T08:48:52] Filtering fragments with small insert size (remaining=6416502)
[2026-06-08T08:48:55] Filtering alignments with long gaps (remaining=6416502)
[2026-06-08T08:48:58] Filtering fragments with both mates in the same gene (remaining=6415022)
[2026-06-08T08:49:01] Filtering fusions arising from hairpin structures (remaining=6145188)
[2026-06-08T08:49:04] Filtering reads with a mismatch p-value <=0.01 (remaining=2627863)
[2026-06-08T08:49:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=988625)
[2026-06-08T08:49:37] Finding fusions and counting supporting reads (total=855018)
[2026-06-08T08:49:59] Merging adjacent fusion breakpoints (remaining=847694)
[2026-06-08T08:50:01] Filtering multi-mapping fusions by alignment score and read support (remaining=467758)
[2026-06-08T08:50:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=467034)
[2026-06-08T08:50:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=363074)
[2026-06-08T08:50:52] Filtering fusions with <2 supporting reads (remaining=19265)
[2026-06-08T08:50:52] Filtering fusions with an e-value >=0.3 (remaining=3743)
[2026-06-08T08:50:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3808)
[2026-06-08T08:50:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3734)
[2026-06-08T08:50:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3734)
[2026-06-08T08:51:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3732)
[2026-06-08T08:51:07] Searching for fusions with spliced split reads (remaining=3788)
[2026-06-08T08:51:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=2712)
[2026-06-08T08:51:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2692)
[2026-06-08T08:51:16] Searching for fusions with >=4 spliced events (remaining=3191)
[2026-06-08T08:51:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1594)
[2026-06-08T08:51:37] Filtering fusions with anchors <=23nt (remaining=1322)
[2026-06-08T08:51:38] Filtering end-to-end fusions with low support (remaining=1284)
[2026-06-08T08:51:39] Filtering fusions with no coverage around the breakpoints (remaining=1250)
[2026-06-08T08:51:39] Indexing gene sequences 
[2026-06-08T08:51:47] Filtering genes with >=30% identity (remaining=409)
[2026-06-08T08:51:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=162)
[2026-06-08T08:51:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=144)
[2026-06-08T08:51:57] Searching for additional isoforms (remaining=162)
[2026-06-08T08:51:59] Assigning confidence scores to events 
[2026-06-08T08:52:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:04] Writing fusions to file '1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:52:06] Writing discarded fusions to file '1173_RPC_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:52] Freeing resources
[2026-06-08T08:53:21] Done (elapsed time=00:13:50, CPU time=00:13:49, peak memory=17.1gb)