[2026-06-08T08:22:20] Launching Arriba 2.4.0
[2026-06-08T08:22:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:22:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:22:33] Reading chimeric alignments from '1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=12738826)
[2026-06-08T08:28:14] Marking multi-mapping alignments (marked=8746496)
[2026-06-08T08:28:19] Detecting strandedness (reverse)
[2026-06-08T08:28:19] Assigning strands to alignments 
[2026-06-08T08:28:21] Annotating alignments 
[2026-06-08T08:29:01] Filtering duplicates (remaining=8467647)
[2026-06-08T08:29:10] 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=7819632)
[2026-06-08T08:29:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7819632)
[2026-06-08T08:29:15] Filtering viral contigs with expression lower than the top 5 (remaining=7819632)
[2026-06-08T08:29:20] Filtering viral contigs with less than 5% coverage (remaining=7819632)
[2026-06-08T08:29:23] Estimating fragment length (mate gap mean=-80.2877, mate gap stddev=26.7917, read length mean=119.996)
[2026-06-08T08:29:23] Filtering read-through fragments with a distance <=10000bp (remaining=7478953)
[2026-06-08T08:29:26] Filtering inconsistently clipped mates (remaining=7354094)
[2026-06-08T08:29:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7224832)
[2026-06-08T08:29:33] Filtering fragments with small insert size (remaining=7223518)
[2026-06-08T08:29:36] Filtering alignments with long gaps (remaining=7223518)
[2026-06-08T08:29:38] Filtering fragments with both mates in the same gene (remaining=7222296)
[2026-06-08T08:29:41] Filtering fusions arising from hairpin structures (remaining=6915477)
[2026-06-08T08:29:44] Filtering reads with a mismatch p-value <=0.01 (remaining=3246909)
[2026-06-08T08:30:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=1422000)
[2026-06-08T08:30:15] Finding fusions and counting supporting reads (total=1260483)
[2026-06-08T08:30:37] Merging adjacent fusion breakpoints (remaining=1251736)
[2026-06-08T08:30:40] Filtering multi-mapping fusions by alignment score and read support (remaining=663255)
[2026-06-08T08:31:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:31:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=661963)
[2026-06-08T08:31:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=519689)
[2026-06-08T08:31:32] Filtering fusions with <2 supporting reads (remaining=23469)
[2026-06-08T08:31:33] Filtering fusions with an e-value >=0.3 (remaining=4486)
[2026-06-08T08:31:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4561)
[2026-06-08T08:31:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4493)
[2026-06-08T08:31:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4500)
[2026-06-08T08:31:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4462)
[2026-06-08T08:31:49] Searching for fusions with spliced split reads (remaining=4538)
[2026-06-08T08:31:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=3232)
[2026-06-08T08:31:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3195)
[2026-06-08T08:32:00] Searching for fusions with >=4 spliced events (remaining=3880)
[2026-06-08T08:32:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1784)
[2026-06-08T08:32:15] Filtering fusions with anchors <=23nt (remaining=1555)
[2026-06-08T08:32:16] Filtering end-to-end fusions with low support (remaining=1508)
[2026-06-08T08:32:17] Filtering fusions with no coverage around the breakpoints (remaining=1473)
[2026-06-08T08:32:18] Indexing gene sequences 
[2026-06-08T08:32:26] Filtering genes with >=30% identity (remaining=567)
[2026-06-08T08:32:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=336)
[2026-06-08T08:32:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=243)
[2026-06-08T08:32:41] Searching for additional isoforms (remaining=309)
[2026-06-08T08:32:43] Assigning confidence scores to events 
[2026-06-08T08:32:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:48] Writing fusions to file '1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:32:51] Writing discarded fusions to file '1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:32] Freeing resources
[2026-06-08T08:33:52] Done (elapsed time=00:11:32, CPU time=00:11:31, peak memory=17.3gb)