[2026-06-08T08:17:19] Launching Arriba 2.4.0
[2026-06-08T08:17:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:33] Reading chimeric alignments from '1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=12407046)
[2026-06-08T08:23:06] Marking multi-mapping alignments (marked=8729163)
[2026-06-08T08:23:11] Detecting strandedness (reverse)
[2026-06-08T08:23:11] Assigning strands to alignments 
[2026-06-08T08:23:14] Annotating alignments 
[2026-06-08T08:23:53] Filtering duplicates (remaining=8673193)
[2026-06-08T08:24:03] 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=7879394)
[2026-06-08T08:24:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7879394)
[2026-06-08T08:24:08] Filtering viral contigs with expression lower than the top 5 (remaining=7879394)
[2026-06-08T08:24:14] Filtering viral contigs with less than 5% coverage (remaining=7879394)
[2026-06-08T08:24:16] Estimating fragment length (mate gap mean=-83.1377, mate gap stddev=27.0823, read length mean=125.955)
[2026-06-08T08:24:16] Filtering read-through fragments with a distance <=10000bp (remaining=7471924)
[2026-06-08T08:24:19] Filtering inconsistently clipped mates (remaining=7332373)
[2026-06-08T08:24:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7201217)
[2026-06-08T08:24:27] Filtering fragments with small insert size (remaining=7200063)
[2026-06-08T08:24:29] Filtering alignments with long gaps (remaining=7200063)
[2026-06-08T08:24:32] Filtering fragments with both mates in the same gene (remaining=7198985)
[2026-06-08T08:24:35] Filtering fusions arising from hairpin structures (remaining=6784662)
[2026-06-08T08:24:38] Filtering reads with a mismatch p-value <=0.01 (remaining=3452853)
[2026-06-08T08:24:55] Filtering reads with low entropy (k-mer content >=60%) (remaining=1752448)
[2026-06-08T08:25:09] Finding fusions and counting supporting reads (total=1596471)
[2026-06-08T08:25:31] Merging adjacent fusion breakpoints (remaining=1585795)
[2026-06-08T08:25:34] Filtering multi-mapping fusions by alignment score and read support (remaining=807980)
[2026-06-08T08:26:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:26:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=806776)
[2026-06-08T08:26:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=652522)
[2026-06-08T08:26:27] Filtering fusions with <2 supporting reads (remaining=21837)
[2026-06-08T08:26:28] Filtering fusions with an e-value >=0.3 (remaining=3552)
[2026-06-08T08:26:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3656)
[2026-06-08T08:26:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3578)
[2026-06-08T08:26:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3578)
[2026-06-08T08:26:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3499)
[2026-06-08T08:26:45] Searching for fusions with spliced split reads (remaining=3575)
[2026-06-08T08:26:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=2554)
[2026-06-08T08:26:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2524)
[2026-06-08T08:26:55] Searching for fusions with >=4 spliced events (remaining=3080)
[2026-06-08T08:26:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1373)
[2026-06-08T08:27:10] Filtering fusions with anchors <=23nt (remaining=1115)
[2026-06-08T08:27:12] Filtering end-to-end fusions with low support (remaining=1095)
[2026-06-08T08:27:13] Filtering fusions with no coverage around the breakpoints (remaining=1079)
[2026-06-08T08:27:14] Indexing gene sequences 
[2026-06-08T08:27:18] Filtering genes with >=30% identity (remaining=331)
[2026-06-08T08:27:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=166)
[2026-06-08T08:27:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=137)
[2026-06-08T08:27:26] Searching for additional isoforms (remaining=163)
[2026-06-08T08:27:28] Assigning confidence scores to events 
[2026-06-08T08:27:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:32] Writing fusions to file '1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:27:34] Writing discarded fusions to file '1173_DSO_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:17] Freeing resources
[2026-06-08T08:28:36] Done (elapsed time=00:11:17, CPU time=00:11:16, peak memory=17.2gb)