[2026-06-08T08:07:26] Launching Arriba 2.4.0
[2026-06-08T08:07:26] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:07:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:07:45] Reading chimeric alignments from '1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=9549683)
[2026-06-08T08:12:18] Marking multi-mapping alignments (marked=6686950)
[2026-06-08T08:12:22] Detecting strandedness (reverse)
[2026-06-08T08:12:22] Assigning strands to alignments 
[2026-06-08T08:12:24] Annotating alignments 
[2026-06-08T08:12:51] Filtering duplicates (remaining=4752957)
[2026-06-08T08:12:56] 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=4400862)
[2026-06-08T08:12:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4400862)
[2026-06-08T08:13:00] Filtering viral contigs with expression lower than the top 5 (remaining=4400862)
[2026-06-08T08:13:04] Filtering viral contigs with less than 5% coverage (remaining=4400862)
[2026-06-08T08:13:06] Estimating fragment length (mate gap mean=-77.9903, mate gap stddev=27.2325, read length mean=116.351)
[2026-06-08T08:13:06] Filtering read-through fragments with a distance <=10000bp (remaining=4260234)
[2026-06-08T08:13:08] Filtering inconsistently clipped mates (remaining=4128902)
[2026-06-08T08:13:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4047727)
[2026-06-08T08:13:13] Filtering fragments with small insert size (remaining=4046280)
[2026-06-08T08:13:14] Filtering alignments with long gaps (remaining=4046280)
[2026-06-08T08:13:16] Filtering fragments with both mates in the same gene (remaining=4045485)
[2026-06-08T08:13:18] Filtering fusions arising from hairpin structures (remaining=3729453)
[2026-06-08T08:13:20] Filtering reads with a mismatch p-value <=0.01 (remaining=1693256)
[2026-06-08T08:13:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=616323)
[2026-06-08T08:13:39] Finding fusions and counting supporting reads (total=528506)
[2026-06-08T08:13:52] Merging adjacent fusion breakpoints (remaining=523735)
[2026-06-08T08:13:53] Filtering multi-mapping fusions by alignment score and read support (remaining=279382)
[2026-06-08T08:14:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:14:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=278422)
[2026-06-08T08:14:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=189170)
[2026-06-08T08:14:24] Filtering fusions with <2 supporting reads (remaining=11397)
[2026-06-08T08:14:25] Filtering fusions with an e-value >=0.3 (remaining=2574)
[2026-06-08T08:14:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2714)
[2026-06-08T08:14:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2618)
[2026-06-08T08:14:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2618)
[2026-06-08T08:14:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2581)
[2026-06-08T08:14:34] Searching for fusions with spliced split reads (remaining=2629)
[2026-06-08T08:14:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=1996)
[2026-06-08T08:14:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1976)
[2026-06-08T08:14:40] Searching for fusions with >=4 spliced events (remaining=2165)
[2026-06-08T08:14:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=721)
[2026-06-08T08:14:56] Filtering fusions with anchors <=23nt (remaining=622)
[2026-06-08T08:14:56] Filtering end-to-end fusions with low support (remaining=603)
[2026-06-08T08:14:57] Filtering fusions with no coverage around the breakpoints (remaining=586)
[2026-06-08T08:14:57] Indexing gene sequences 
[2026-06-08T08:15:01] Filtering genes with >=30% identity (remaining=201)
[2026-06-08T08:15:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=112)
[2026-06-08T08:15:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=105)
[2026-06-08T08:15:05] Searching for additional isoforms (remaining=117)
[2026-06-08T08:15:06] Assigning confidence scores to events 
[2026-06-08T08:15:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:15:09] Writing fusions to file '1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:15:10] Writing discarded fusions to file '1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:15:34] Freeing resources
[2026-06-08T08:15:50] Done (elapsed time=00:08:24, CPU time=00:08:24, peak memory=13.7gb)