[2026-06-08T08:37:31] Launching Arriba 2.4.0
[2026-06-08T08:37:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:49] Reading chimeric alignments from '1173_GXL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=14124327)
[2026-06-08T08:44:43] Marking multi-mapping alignments (marked=9761805)
[2026-06-08T08:44:48] Detecting strandedness (reverse)
[2026-06-08T08:44:48] Assigning strands to alignments 
[2026-06-08T08:44:51] Annotating alignments 
[2026-06-08T08:45:29] Filtering duplicates (remaining=7540165)
[2026-06-08T08:45:37] 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=6962527)
[2026-06-08T08:45:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6962527)
[2026-06-08T08:45:42] Filtering viral contigs with expression lower than the top 5 (remaining=6962527)
[2026-06-08T08:45:48] Filtering viral contigs with less than 5% coverage (remaining=6962527)
[2026-06-08T08:45:50] Estimating fragment length (mate gap mean=-79.6776, mate gap stddev=27.6406, read length mean=117.815)
[2026-06-08T08:45:50] Filtering read-through fragments with a distance <=10000bp (remaining=6748940)
[2026-06-08T08:45:53] Filtering inconsistently clipped mates (remaining=6614815)
[2026-06-08T08:45:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6466691)
[2026-06-08T08:46:00] Filtering fragments with small insert size (remaining=6465168)
[2026-06-08T08:46:03] Filtering alignments with long gaps (remaining=6465168)
[2026-06-08T08:46:05] Filtering fragments with both mates in the same gene (remaining=6463665)
[2026-06-08T08:46:08] Filtering fusions arising from hairpin structures (remaining=6126042)
[2026-06-08T08:46:11] Filtering reads with a mismatch p-value <=0.01 (remaining=2734925)
[2026-06-08T08:46:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=990241)
[2026-06-08T08:46:37] Finding fusions and counting supporting reads (total=839662)
[2026-06-08T08:46:56] Merging adjacent fusion breakpoints (remaining=830719)
[2026-06-08T08:46:58] Filtering multi-mapping fusions by alignment score and read support (remaining=461693)
[2026-06-08T08:47:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=460689)
[2026-06-08T08:47:45] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=345750)
[2026-06-08T08:47:46] Filtering fusions with <2 supporting reads (remaining=19553)
[2026-06-08T08:47:46] Filtering fusions with an e-value >=0.3 (remaining=4069)
[2026-06-08T08:47:47] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4144)
[2026-06-08T08:47:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4062)
[2026-06-08T08:47:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4062)
[2026-06-08T08:47:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4047)
[2026-06-08T08:48:00] Searching for fusions with spliced split reads (remaining=4111)
[2026-06-08T08:48:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=2983)
[2026-06-08T08:48:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2942)
[2026-06-08T08:48:08] Searching for fusions with >=4 spliced events (remaining=3239)
[2026-06-08T08:48:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1120)
[2026-06-08T08:48:23] Filtering fusions with anchors <=23nt (remaining=912)
[2026-06-08T08:48:24] Filtering end-to-end fusions with low support (remaining=875)
[2026-06-08T08:48:25] Filtering fusions with no coverage around the breakpoints (remaining=847)
[2026-06-08T08:48:26] Indexing gene sequences 
[2026-06-08T08:48:30] Filtering genes with >=30% identity (remaining=313)
[2026-06-08T08:48:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=168)
[2026-06-08T08:48:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=155)
[2026-06-08T08:48:38] Searching for additional isoforms (remaining=189)
[2026-06-08T08:48:39] Assigning confidence scores to events 
[2026-06-08T08:48:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:43] Writing fusions to file '1173_GXL_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:44] Writing discarded fusions to file '1173_GXL_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:17] Freeing resources
[2026-06-08T08:49:37] Done (elapsed time=00:12:06, CPU time=00:12:05, peak memory=18.4gb)