[2026-06-08T08:37:27] Launching Arriba 2.4.0
[2026-06-08T08:37:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:41] Reading chimeric alignments from '1173_T46_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=19696351)
[2026-06-08T08:46:10] Marking multi-mapping alignments (marked=13769295)
[2026-06-08T08:46:22] Detecting strandedness (reverse)
[2026-06-08T08:46:22] Assigning strands to alignments 
[2026-06-08T08:46:28] Annotating alignments 
[2026-06-08T08:48:16] Filtering duplicates (remaining=7921987)
[2026-06-08T08:48:33] 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=7404918)
[2026-06-08T08:48:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7404918)
[2026-06-08T08:48:45] Filtering viral contigs with expression lower than the top 5 (remaining=7404918)
[2026-06-08T08:48:57] Filtering viral contigs with less than 5% coverage (remaining=7404918)
[2026-06-08T08:49:03] Estimating fragment length (mate gap mean=-83.2515, mate gap stddev=27.4506, read length mean=117.971)
[2026-06-08T08:49:03] Filtering read-through fragments with a distance <=10000bp (remaining=7290246)
[2026-06-08T08:49:09] Filtering inconsistently clipped mates (remaining=7180565)
[2026-06-08T08:49:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7039658)
[2026-06-08T08:49:25] Filtering fragments with small insert size (remaining=7037317)
[2026-06-08T08:49:31] Filtering alignments with long gaps (remaining=7037316)
[2026-06-08T08:49:37] Filtering fragments with both mates in the same gene (remaining=7036252)
[2026-06-08T08:49:43] Filtering fusions arising from hairpin structures (remaining=6764542)
[2026-06-08T08:49:49] Filtering reads with a mismatch p-value <=0.01 (remaining=2431086)
[2026-06-08T08:50:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=1081255)
[2026-06-08T08:50:30] Finding fusions and counting supporting reads (total=999512)
[2026-06-08T08:51:18] Merging adjacent fusion breakpoints (remaining=994429)
[2026-06-08T08:51:22] Filtering multi-mapping fusions by alignment score and read support (remaining=581975)
[2026-06-08T08:53:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=581327)
[2026-06-08T08:53:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=502499)
[2026-06-08T08:53:30] Filtering fusions with <2 supporting reads (remaining=19393)
[2026-06-08T08:53:32] Filtering fusions with an e-value >=0.3 (remaining=2404)
[2026-06-08T08:53:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2454)
[2026-06-08T08:53:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2420)
[2026-06-08T08:53:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2420)
[2026-06-08T08:53:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2410)
[2026-06-08T08:54:03] Searching for fusions with spliced split reads (remaining=2462)
[2026-06-08T08:54:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=1993)
[2026-06-08T08:54:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1987)
[2026-06-08T08:54:22] Searching for fusions with >=4 spliced events (remaining=2224)
[2026-06-08T08:54:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=999)
[2026-06-08T08:54:43] Filtering fusions with anchors <=23nt (remaining=841)
[2026-06-08T08:54:45] Filtering end-to-end fusions with low support (remaining=687)
[2026-06-08T08:54:47] Filtering fusions with no coverage around the breakpoints (remaining=602)
[2026-06-08T08:54:49] Indexing gene sequences 
[2026-06-08T08:54:57] Filtering genes with >=30% identity (remaining=264)
[2026-06-08T08:55:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=166)
[2026-06-08T08:55:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=162)
[2026-06-08T08:55:08] Searching for additional isoforms (remaining=187)
[2026-06-08T08:55:11] Assigning confidence scores to events 
[2026-06-08T08:55:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:19] Writing fusions to file '1173_T46_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:55:21] Writing discarded fusions to file '1173_T46_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:38] Freeing resources
[2026-06-08T08:57:40] Done (elapsed time=00:20:13, CPU time=00:20:12, peak memory=24.3gb)