[2026-06-08T08:20:34] Launching Arriba 2.4.0
[2026-06-08T08:20:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:51] Reading chimeric alignments from '1173_SK8_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=10697418)
[2026-06-08T08:26:09] Marking multi-mapping alignments (marked=7132111)
[2026-06-08T08:26:13] Detecting strandedness (reverse)
[2026-06-08T08:26:13] Assigning strands to alignments 
[2026-06-08T08:26:15] Annotating alignments 
[2026-06-08T08:26:46] Filtering duplicates (remaining=8020964)
[2026-06-08T08:26:54] 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=7324339)
[2026-06-08T08:26:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7324339)
[2026-06-08T08:26:58] Filtering viral contigs with expression lower than the top 5 (remaining=7324339)
[2026-06-08T08:27:03] Filtering viral contigs with less than 5% coverage (remaining=7324339)
[2026-06-08T08:27:05] Estimating fragment length (mate gap mean=-84.6037, mate gap stddev=28.0494, read length mean=129.231)
[2026-06-08T08:27:05] Filtering read-through fragments with a distance <=10000bp (remaining=7055058)
[2026-06-08T08:27:07] Filtering inconsistently clipped mates (remaining=6945419)
[2026-06-08T08:27:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6825212)
[2026-06-08T08:27:13] Filtering fragments with small insert size (remaining=6824457)
[2026-06-08T08:27:15] Filtering alignments with long gaps (remaining=6824456)
[2026-06-08T08:27:17] Filtering fragments with both mates in the same gene (remaining=6823404)
[2026-06-08T08:27:19] Filtering fusions arising from hairpin structures (remaining=6527085)
[2026-06-08T08:27:22] Filtering reads with a mismatch p-value <=0.01 (remaining=3348813)
[2026-06-08T08:27:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=1570932)
[2026-06-08T08:27:49] Finding fusions and counting supporting reads (total=1464823)
[2026-06-08T08:28:07] Merging adjacent fusion breakpoints (remaining=1457690)
[2026-06-08T08:28:10] Filtering multi-mapping fusions by alignment score and read support (remaining=811011)
[2026-06-08T08:28:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=809658)
[2026-06-08T08:28:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=668119)
[2026-06-08T08:28:50] Filtering fusions with <2 supporting reads (remaining=26349)
[2026-06-08T08:28:51] Filtering fusions with an e-value >=0.3 (remaining=4907)
[2026-06-08T08:28:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4986)
[2026-06-08T08:28:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4924)
[2026-06-08T08:28:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4976)
[2026-06-08T08:28:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4796)
[2026-06-08T08:29:04] Searching for fusions with spliced split reads (remaining=4919)
[2026-06-08T08:29:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=3571)
[2026-06-08T08:29:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3524)
[2026-06-08T08:29:12] Searching for fusions with >=4 spliced events (remaining=4063)
[2026-06-08T08:29:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1584)
[2026-06-08T08:29:30] Filtering fusions with anchors <=23nt (remaining=1203)
[2026-06-08T08:29:31] Filtering end-to-end fusions with low support (remaining=1183)
[2026-06-08T08:29:32] Filtering fusions with no coverage around the breakpoints (remaining=1155)
[2026-06-08T08:29:33] Indexing gene sequences 
[2026-06-08T08:29:38] Filtering genes with >=30% identity (remaining=501)
[2026-06-08T08:29:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=356)
[2026-06-08T08:29:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=273)
[2026-06-08T08:29:51] Searching for additional isoforms (remaining=375)
[2026-06-08T08:29:53] Assigning confidence scores to events 
[2026-06-08T08:29:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:57] Writing fusions to file '1173_SK8_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:29:59] Writing discarded fusions to file '1173_SK8_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:32] Freeing resources
[2026-06-08T08:30:49] Done (elapsed time=00:10:15, CPU time=00:10:14, peak memory=15.5gb)