[2026-06-08T08:03:06] Launching Arriba 2.4.0
[2026-06-08T08:03:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:03:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:03:29] Reading chimeric alignments from '1173_M4Y_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=15130091)
[2026-06-08T08:09:07] Marking multi-mapping alignments (marked=11797282)
[2026-06-08T08:09:13] Detecting strandedness (reverse)
[2026-06-08T08:09:13] Assigning strands to alignments 
[2026-06-08T08:09:16] Annotating alignments 
[2026-06-08T08:10:03] Filtering duplicates (remaining=4893573)
[2026-06-08T08:10:11] 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=4148101)
[2026-06-08T08:10:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4148101)
[2026-06-08T08:10:16] Filtering viral contigs with expression lower than the top 5 (remaining=4148101)
[2026-06-08T08:10:22] Filtering viral contigs with less than 5% coverage (remaining=4148101)
[2026-06-08T08:10:25] Estimating fragment length (mate gap mean=-67.3477, mate gap stddev=25.8605, read length mean=105.377)
[2026-06-08T08:10:25] Filtering read-through fragments with a distance <=10000bp (remaining=4065477)
[2026-06-08T08:10:28] Filtering inconsistently clipped mates (remaining=3950643)
[2026-06-08T08:10:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3845869)
[2026-06-08T08:10:35] Filtering fragments with small insert size (remaining=3839705)
[2026-06-08T08:10:38] Filtering alignments with long gaps (remaining=3839705)
[2026-06-08T08:10:41] Filtering fragments with both mates in the same gene (remaining=3838375)
[2026-06-08T08:10:44] Filtering fusions arising from hairpin structures (remaining=3597627)
[2026-06-08T08:10:47] Filtering reads with a mismatch p-value <=0.01 (remaining=1328598)
[2026-06-08T08:10:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=374721)
[2026-06-08T08:11:06] Finding fusions and counting supporting reads (total=344572)
[2026-06-08T08:11:24] Merging adjacent fusion breakpoints (remaining=340709)
[2026-06-08T08:11:25] Filtering multi-mapping fusions by alignment score and read support (remaining=148379)
[2026-06-08T08:12:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:12:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=147174)
[2026-06-08T08:12:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=103483)
[2026-06-08T08:12:12] Filtering fusions with <2 supporting reads (remaining=4520)
[2026-06-08T08:12:13] Filtering fusions with an e-value >=0.3 (remaining=1184)
[2026-06-08T08:12:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1338)
[2026-06-08T08:12:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1251)
[2026-06-08T08:12:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1251)
[2026-06-08T08:12:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1247)
[2026-06-08T08:12:24] Searching for fusions with spliced split reads (remaining=1274)
[2026-06-08T08:12:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=973)
[2026-06-08T08:12:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=967)
[2026-06-08T08:12:31] Searching for fusions with >=4 spliced events (remaining=993)
[2026-06-08T08:12:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=333)
[2026-06-08T08:12:46] Filtering fusions with anchors <=23nt (remaining=278)
[2026-06-08T08:12:46] Filtering end-to-end fusions with low support (remaining=265)
[2026-06-08T08:12:47] Filtering fusions with no coverage around the breakpoints (remaining=254)
[2026-06-08T08:12:47] Indexing gene sequences 
[2026-06-08T08:12:49] Filtering genes with >=30% identity (remaining=105)
[2026-06-08T08:12:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=53)
[2026-06-08T08:12:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=53)
[2026-06-08T08:12:52] Searching for additional isoforms (remaining=54)
[2026-06-08T08:12:53] Assigning confidence scores to events 
[2026-06-08T08:12:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:12:56] Writing fusions to file '1173_M4Y_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:12:57] Writing discarded fusions to file '1173_M4Y_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:13:21] Freeing resources
[2026-06-08T08:13:42] Done (elapsed time=00:10:36, CPU time=00:10:35, peak memory=18.9gb)