[2026-06-08T08:26:27] Launching Arriba 2.4.0
[2026-06-08T08:26:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:46] Reading chimeric alignments from '1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=22934085)
[2026-06-08T08:35:21] Marking multi-mapping alignments (marked=17354307)
[2026-06-08T08:35:30] Detecting strandedness (reverse)
[2026-06-08T08:35:30] Assigning strands to alignments 
[2026-06-08T08:35:35] Annotating alignments 
[2026-06-08T08:36:53] Filtering duplicates (remaining=18145370)
[2026-06-08T08:37:12] 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=13076865)
[2026-06-08T08:37:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=13076865)
[2026-06-08T08:37:21] Filtering viral contigs with expression lower than the top 5 (remaining=13076865)
[2026-06-08T08:37:32] Filtering viral contigs with less than 5% coverage (remaining=13076865)
[2026-06-08T08:37:37] Estimating fragment length (mate gap mean=-82.9183, mate gap stddev=27.6827, read length mean=125.901)
[2026-06-08T08:37:37] Filtering read-through fragments with a distance <=10000bp (remaining=12882710)
[2026-06-08T08:37:42] Filtering inconsistently clipped mates (remaining=12822751)
[2026-06-08T08:37:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=12600912)
[2026-06-08T08:37:58] Filtering fragments with small insert size (remaining=12600071)
[2026-06-08T08:38:02] Filtering alignments with long gaps (remaining=12600071)
[2026-06-08T08:38:08] Filtering fragments with both mates in the same gene (remaining=12598585)
[2026-06-08T08:38:12] Filtering fusions arising from hairpin structures (remaining=12483162)
[2026-06-08T08:38:18] Filtering reads with a mismatch p-value <=0.01 (remaining=6638490)
[2026-06-08T08:38:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=4529487)
[2026-06-08T08:39:16] Finding fusions and counting supporting reads (total=4479557)
[2026-06-08T08:40:04] Merging adjacent fusion breakpoints (remaining=4475067)
[2026-06-08T08:40:11] Filtering multi-mapping fusions by alignment score and read support (remaining=1784619)
[2026-06-08T08:41:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1782922)
[2026-06-08T08:41:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1680738)
[2026-06-08T08:41:45] Filtering fusions with <2 supporting reads (remaining=31832)
[2026-06-08T08:41:48] Filtering fusions with an e-value >=0.3 (remaining=4207)
[2026-06-08T08:41:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4236)
[2026-06-08T08:41:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4206)
[2026-06-08T08:42:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4206)
[2026-06-08T08:42:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3956)
[2026-06-08T08:42:21] Searching for fusions with spliced split reads (remaining=4020)
[2026-06-08T08:42:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=2735)
[2026-06-08T08:42:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2707)
[2026-06-08T08:42:42] Searching for fusions with >=4 spliced events (remaining=3317)
[2026-06-08T08:42:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1378)
[2026-06-08T08:43:03] Filtering fusions with anchors <=23nt (remaining=1085)
[2026-06-08T08:43:05] Filtering end-to-end fusions with low support (remaining=1077)
[2026-06-08T08:43:07] Filtering fusions with no coverage around the breakpoints (remaining=1063)
[2026-06-08T08:43:10] Indexing gene sequences 
[2026-06-08T08:43:15] Filtering genes with >=30% identity (remaining=350)
[2026-06-08T08:43:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=215)
[2026-06-08T08:43:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-06-08T08:43:31] Searching for additional isoforms (remaining=233)
[2026-06-08T08:43:35] Assigning confidence scores to events 
[2026-06-08T08:43:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:45] Writing fusions to file '1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:49] Writing discarded fusions to file '1173_JXL_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:16] Freeing resources
[2026-06-08T08:45:56] Done (elapsed time=00:19:29, CPU time=00:19:27, peak memory=30.4gb)