[2026-06-08T08:23:27] Launching Arriba 2.4.0
[2026-06-08T08:23:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:46] Reading chimeric alignments from '1173_SDP_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=13671673)
[2026-06-08T08:31:59] Marking multi-mapping alignments (marked=9630231)
[2026-06-08T08:32:04] Detecting strandedness (reverse)
[2026-06-08T08:32:04] Assigning strands to alignments 
[2026-06-08T08:32:07] Annotating alignments 
[2026-06-08T08:32:53] Filtering duplicates (remaining=6937863)
[2026-06-08T08:33:02] 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=6183299)
[2026-06-08T08:33:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6183299)
[2026-06-08T08:33:07] Filtering viral contigs with expression lower than the top 5 (remaining=6183299)
[2026-06-08T08:33:14] Filtering viral contigs with less than 5% coverage (remaining=6183299)
[2026-06-08T08:33:17] Estimating fragment length (mate gap mean=-76.151, mate gap stddev=26.3437, read length mean=112.237)
[2026-06-08T08:33:17] Filtering read-through fragments with a distance <=10000bp (remaining=5997283)
[2026-06-08T08:33:20] Filtering inconsistently clipped mates (remaining=5884379)
[2026-06-08T08:33:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5740613)
[2026-06-08T08:33:28] Filtering fragments with small insert size (remaining=5739123)
[2026-06-08T08:33:30] Filtering alignments with long gaps (remaining=5739122)
[2026-06-08T08:33:33] Filtering fragments with both mates in the same gene (remaining=5737649)
[2026-06-08T08:33:36] Filtering fusions arising from hairpin structures (remaining=5490828)
[2026-06-08T08:33:39] Filtering reads with a mismatch p-value <=0.01 (remaining=2295659)
[2026-06-08T08:33:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=857495)
[2026-06-08T08:34:04] Finding fusions and counting supporting reads (total=776490)
[2026-06-08T08:34:25] Merging adjacent fusion breakpoints (remaining=770454)
[2026-06-08T08:34:27] Filtering multi-mapping fusions by alignment score and read support (remaining=407217)
[2026-06-08T08:35:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=406348)
[2026-06-08T08:35:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=323517)
[2026-06-08T08:35:18] Filtering fusions with <2 supporting reads (remaining=13529)
[2026-06-08T08:35:19] Filtering fusions with an e-value >=0.3 (remaining=2749)
[2026-06-08T08:35:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2808)
[2026-06-08T08:35:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2722)
[2026-06-08T08:35:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2723)
[2026-06-08T08:35:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2723)
[2026-06-08T08:35:33] Searching for fusions with spliced split reads (remaining=2766)
[2026-06-08T08:35:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=2069)
[2026-06-08T08:35:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2043)
[2026-06-08T08:35:42] Searching for fusions with >=4 spliced events (remaining=2307)
[2026-06-08T08:35:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=923)
[2026-06-08T08:36:05] Filtering fusions with anchors <=23nt (remaining=746)
[2026-06-08T08:36:06] Filtering end-to-end fusions with low support (remaining=724)
[2026-06-08T08:36:07] Filtering fusions with no coverage around the breakpoints (remaining=710)
[2026-06-08T08:36:07] Indexing gene sequences 
[2026-06-08T08:36:12] Filtering genes with >=30% identity (remaining=253)
[2026-06-08T08:36:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=140)
[2026-06-08T08:36:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-08T08:36:19] Searching for additional isoforms (remaining=133)
[2026-06-08T08:36:21] Assigning confidence scores to events 
[2026-06-08T08:36:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:25] Writing fusions to file '1173_SDP_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:26] Writing discarded fusions to file '1173_SDP_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:10] Freeing resources
[2026-06-08T08:37:34] Done (elapsed time=00:14:07, CPU time=00:14:06, peak memory=18gb)