[2026-05-28T00:03:43] Launching Arriba 2.4.0
[2026-05-28T00:03:43] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:52] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:03:56] Reading chimeric alignments from '659_buD-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3591098)
[2026-05-28T00:06:17] Marking multi-mapping alignments (marked=2230148)
[2026-05-28T00:06:18] Detecting strandedness (reverse)
[2026-05-28T00:06:18] Assigning strands to alignments 
[2026-05-28T00:06:19] Annotating alignments 
[2026-05-28T00:06:33] Filtering duplicates (remaining=2228056)
[2026-05-28T00:06:36] 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=2147516)
[2026-05-28T00:06:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2147516)
[2026-05-28T00:06:38] Filtering viral contigs with expression lower than the top 5 (remaining=2147516)
[2026-05-28T00:06:40] Filtering viral contigs with less than 5% coverage (remaining=2147516)
[2026-05-28T00:06:41] Estimating fragment length (mate gap mean=-85.7809, mate gap stddev=28.4059, read length mean=130.044)
[2026-05-28T00:06:41] Filtering read-through fragments with a distance <=10000bp (remaining=1992864)
[2026-05-28T00:06:42] Filtering inconsistently clipped mates (remaining=1960465)
[2026-05-28T00:06:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1911179)
[2026-05-28T00:06:45] Filtering fragments with small insert size (remaining=1910877)
[2026-05-28T00:06:45] Filtering alignments with long gaps (remaining=1910876)
[2026-05-28T00:06:46] Filtering fragments with both mates in the same gene (remaining=1910466)
[2026-05-28T00:06:47] Filtering fusions arising from hairpin structures (remaining=1812900)
[2026-05-28T00:06:48] Filtering reads with a mismatch p-value <=0.01 (remaining=817177)
[2026-05-28T00:06:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=370312)
[2026-05-28T00:06:57] Finding fusions and counting supporting reads (total=313178)
[2026-05-28T00:07:05] Merging adjacent fusion breakpoints (remaining=310582)
[2026-05-28T00:07:06] Filtering multi-mapping fusions by alignment score and read support (remaining=195718)
[2026-05-28T00:07:19] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=194772)
[2026-05-28T00:07:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=96159)
[2026-05-28T00:07:22] Filtering fusions with <2 supporting reads (remaining=12913)
[2026-05-28T00:07:23] Filtering fusions with an e-value >=0.3 (remaining=3935)
[2026-05-28T00:07:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3968)
[2026-05-28T00:07:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3939)
[2026-05-28T00:07:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3939)
[2026-05-28T00:07:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3317)
[2026-05-28T00:07:28] Searching for fusions with spliced split reads (remaining=3364)
[2026-05-28T00:07:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=2391)
[2026-05-28T00:07:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2361)
[2026-05-28T00:07:31] Searching for fusions with >=4 spliced events (remaining=2573)
[2026-05-28T00:07:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=820)
[2026-05-28T00:07:44] Filtering fusions with anchors <=23nt (remaining=672)
[2026-05-28T00:07:44] Filtering end-to-end fusions with low support (remaining=649)
[2026-05-28T00:07:45] Filtering fusions with no coverage around the breakpoints (remaining=630)
[2026-05-28T00:07:45] Indexing gene sequences 
[2026-05-28T00:07:49] Filtering genes with >=30% identity (remaining=260)
[2026-05-28T00:07:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-05-28T00:07:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=143)
[2026-05-28T00:07:52] Searching for additional isoforms (remaining=161)
[2026-05-28T00:07:52] Assigning confidence scores to events 
[2026-05-28T00:07:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:54] Writing fusions to file '659_buD-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:07:55] Writing discarded fusions to file '659_buD-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:09] Freeing resources
[2026-05-28T00:08:16] Done (elapsed time=00:04:33, CPU time=00:04:31, peak memory=7.88gb)