[2026-06-08T08:43:33] Launching Arriba 2.4.0
[2026-06-08T08:43:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:46] Reading chimeric alignments from '1173_SK8_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=17483386)
[2026-06-08T08:51:19] Marking multi-mapping alignments (marked=12713777)
[2026-06-08T08:51:26] Detecting strandedness (reverse)
[2026-06-08T08:51:26] Assigning strands to alignments 
[2026-06-08T08:51:29] Annotating alignments 
[2026-06-08T08:52:29] Filtering duplicates (remaining=13353099)
[2026-06-08T08:52:45] 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=10680258)
[2026-06-08T08:52:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10680258)
[2026-06-08T08:52:52] Filtering viral contigs with expression lower than the top 5 (remaining=10680258)
[2026-06-08T08:53:00] Filtering viral contigs with less than 5% coverage (remaining=10680258)
[2026-06-08T08:53:04] Estimating fragment length (mate gap mean=-81.6024, mate gap stddev=27.9379, read length mean=121.958)
[2026-06-08T08:53:04] Filtering read-through fragments with a distance <=10000bp (remaining=10420265)
[2026-06-08T08:53:08] Filtering inconsistently clipped mates (remaining=10306537)
[2026-06-08T08:53:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=10090651)
[2026-06-08T08:53:19] Filtering fragments with small insert size (remaining=10089512)
[2026-06-08T08:53:23] Filtering alignments with long gaps (remaining=10089511)
[2026-06-08T08:53:27] Filtering fragments with both mates in the same gene (remaining=10087836)
[2026-06-08T08:53:30] Filtering fusions arising from hairpin structures (remaining=9882643)
[2026-06-08T08:53:34] Filtering reads with a mismatch p-value <=0.01 (remaining=4854757)
[2026-06-08T08:53:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=2680017)
[2026-06-08T08:54:18] Finding fusions and counting supporting reads (total=2638213)
[2026-06-08T08:54:52] Merging adjacent fusion breakpoints (remaining=2630348)
[2026-06-08T08:54:57] Filtering multi-mapping fusions by alignment score and read support (remaining=1206439)
[2026-06-08T08:55:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1204863)
[2026-06-08T08:56:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1089750)
[2026-06-08T08:56:16] Filtering fusions with <2 supporting reads (remaining=32015)
[2026-06-08T08:56:18] Filtering fusions with an e-value >=0.3 (remaining=5193)
[2026-06-08T08:56:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5238)
[2026-06-08T08:56:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5174)
[2026-06-08T08:56:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5200)
[2026-06-08T08:56:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5050)
[2026-06-08T08:56:44] Searching for fusions with spliced split reads (remaining=5090)
[2026-06-08T08:56:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=3658)
[2026-06-08T08:56:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3607)
[2026-06-08T08:57:00] Searching for fusions with >=4 spliced events (remaining=4180)
[2026-06-08T08:57:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1712)
[2026-06-08T08:57:21] Filtering fusions with anchors <=23nt (remaining=1261)
[2026-06-08T08:57:23] Filtering end-to-end fusions with low support (remaining=1241)
[2026-06-08T08:57:24] Filtering fusions with no coverage around the breakpoints (remaining=1225)
[2026-06-08T08:57:26] Indexing gene sequences 
[2026-06-08T08:57:33] Filtering genes with >=30% identity (remaining=557)
[2026-06-08T08:57:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=364)
[2026-06-08T08:57:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=278)
[2026-06-08T08:57:50] Searching for additional isoforms (remaining=390)
[2026-06-08T08:57:54] Assigning confidence scores to events 
[2026-06-08T08:58:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:02] Writing fusions to file '1173_SK8_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:06] Writing discarded fusions to file '1173_SK8_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:13] Freeing resources
[2026-06-08T08:59:42] Done (elapsed time=00:16:09, CPU time=00:16:07, peak memory=23.3gb)