[2026-06-08T07:57:04] Launching Arriba 2.4.0
[2026-06-08T07:57:04] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:57:21] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:57:26] Reading chimeric alignments from '1173_RDM_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=10032677)
[2026-06-08T08:02:41] Marking multi-mapping alignments (marked=7429044)
[2026-06-08T08:02:45] Detecting strandedness (reverse)
[2026-06-08T08:02:45] Assigning strands to alignments 
[2026-06-08T08:02:47] Annotating alignments 
[2026-06-08T08:03:19] Filtering duplicates (remaining=3508027)
[2026-06-08T08:03:24] 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=3087451)
[2026-06-08T08:03:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3087451)
[2026-06-08T08:03:28] Filtering viral contigs with expression lower than the top 5 (remaining=3087451)
[2026-06-08T08:03:32] Filtering viral contigs with less than 5% coverage (remaining=3087451)
[2026-06-08T08:03:34] Estimating fragment length (mate gap mean=-73.8163, mate gap stddev=27.336, read length mean=109.275)
[2026-06-08T08:03:35] Filtering read-through fragments with a distance <=10000bp (remaining=2993281)
[2026-06-08T08:03:37] Filtering inconsistently clipped mates (remaining=2893295)
[2026-06-08T08:03:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2795459)
[2026-06-08T08:03:41] Filtering fragments with small insert size (remaining=2793584)
[2026-06-08T08:03:43] Filtering alignments with long gaps (remaining=2793584)
[2026-06-08T08:03:45] Filtering fragments with both mates in the same gene (remaining=2792906)
[2026-06-08T08:03:47] Filtering fusions arising from hairpin structures (remaining=2582909)
[2026-06-08T08:03:50] Filtering reads with a mismatch p-value <=0.01 (remaining=945415)
[2026-06-08T08:03:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=280767)
[2026-06-08T08:04:04] Finding fusions and counting supporting reads (total=254298)
[2026-06-08T08:04:16] Merging adjacent fusion breakpoints (remaining=251843)
[2026-06-08T08:04:17] Filtering multi-mapping fusions by alignment score and read support (remaining=124430)
[2026-06-08T08:04:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:04:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=123579)
[2026-06-08T08:04:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=78956)
[2026-06-08T08:04:49] Filtering fusions with <2 supporting reads (remaining=4640)
[2026-06-08T08:04:49] Filtering fusions with an e-value >=0.3 (remaining=1295)
[2026-06-08T08:04:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1376)
[2026-06-08T08:04:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1314)
[2026-06-08T08:04:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1314)
[2026-06-08T08:04:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1302)
[2026-06-08T08:04:57] Searching for fusions with spliced split reads (remaining=1363)
[2026-06-08T08:05:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=1063)
[2026-06-08T08:05:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1056)
[2026-06-08T08:05:02] Searching for fusions with >=4 spliced events (remaining=1098)
[2026-06-08T08:05:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=348)
[2026-06-08T08:05:23] Filtering fusions with anchors <=23nt (remaining=301)
[2026-06-08T08:05:23] Filtering end-to-end fusions with low support (remaining=287)
[2026-06-08T08:05:23] Filtering fusions with no coverage around the breakpoints (remaining=270)
[2026-06-08T08:05:24] Indexing gene sequences 
[2026-06-08T08:05:26] Filtering genes with >=30% identity (remaining=123)
[2026-06-08T08:05:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=79)
[2026-06-08T08:05:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-06-08T08:05:28] Searching for additional isoforms (remaining=84)
[2026-06-08T08:05:29] Assigning confidence scores to events 
[2026-06-08T08:05:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:05:30] Writing fusions to file '1173_RDM_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:05:31] Writing discarded fusions to file '1173_RDM_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:05:48] Freeing resources
[2026-06-08T08:06:01] Done (elapsed time=00:08:57, CPU time=00:08:56, peak memory=14.1gb)