[2026-05-28T00:05:43] Launching Arriba 2.4.0
[2026-05-28T00:05:43] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:06:02] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:06:09] Reading chimeric alignments from '659_c95-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3283323)
[2026-05-28T00:09:49] Marking multi-mapping alignments (marked=2066762)
[2026-05-28T00:09:50] Detecting strandedness (reverse)
[2026-05-28T00:09:50] Assigning strands to alignments 
[2026-05-28T00:09:51] Annotating alignments 
[2026-05-28T00:10:05] Filtering duplicates (remaining=2220672)
[2026-05-28T00:10:08] 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=2137510)
[2026-05-28T00:10:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2137510)
[2026-05-28T00:10:09] Filtering viral contigs with expression lower than the top 5 (remaining=2137510)
[2026-05-28T00:10:11] Filtering viral contigs with less than 5% coverage (remaining=2137510)
[2026-05-28T00:10:12] Estimating fragment length (mate gap mean=-86.8377, mate gap stddev=29.9826, read length mean=134.446)
[2026-05-28T00:10:12] Filtering read-through fragments with a distance <=10000bp (remaining=1976617)
[2026-05-28T00:10:13] Filtering inconsistently clipped mates (remaining=1942407)
[2026-05-28T00:10:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1891442)
[2026-05-28T00:10:15] Filtering fragments with small insert size (remaining=1891204)
[2026-05-28T00:10:15] Filtering alignments with long gaps (remaining=1891204)
[2026-05-28T00:10:16] Filtering fragments with both mates in the same gene (remaining=1890848)
[2026-05-28T00:10:17] Filtering fusions arising from hairpin structures (remaining=1767301)
[2026-05-28T00:10:18] Filtering reads with a mismatch p-value <=0.01 (remaining=837911)
[2026-05-28T00:10:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=400623)
[2026-05-28T00:10:27] Finding fusions and counting supporting reads (total=328166)
[2026-05-28T00:10:33] Merging adjacent fusion breakpoints (remaining=324634)
[2026-05-28T00:10:34] Filtering multi-mapping fusions by alignment score and read support (remaining=203208)
[2026-05-28T00:10:45] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:10:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=201639)
[2026-05-28T00:10:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=98674)
[2026-05-28T00:10:49] Filtering fusions with <2 supporting reads (remaining=15042)
[2026-05-28T00:10:49] Filtering fusions with an e-value >=0.3 (remaining=5682)
[2026-05-28T00:10:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5745)
[2026-05-28T00:10:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5675)
[2026-05-28T00:10:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5675)
[2026-05-28T00:10:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3607)
[2026-05-28T00:10:53] Searching for fusions with spliced split reads (remaining=3670)
[2026-05-28T00:10:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=2487)
[2026-05-28T00:10:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2451)
[2026-05-28T00:10:55] Searching for fusions with >=4 spliced events (remaining=2740)
[2026-05-28T00:10:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=905)
[2026-05-28T00:11:16] Filtering fusions with anchors <=23nt (remaining=695)
[2026-05-28T00:11:16] Filtering end-to-end fusions with low support (remaining=672)
[2026-05-28T00:11:16] Filtering fusions with no coverage around the breakpoints (remaining=650)
[2026-05-28T00:11:17] Indexing gene sequences 
[2026-05-28T00:11:20] Filtering genes with >=30% identity (remaining=301)
[2026-05-28T00:11:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-05-28T00:11:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=158)
[2026-05-28T00:11:24] Searching for additional isoforms (remaining=212)
[2026-05-28T00:11:25] Assigning confidence scores to events 
[2026-05-28T00:11:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:11:26] Writing fusions to file '659_c95-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:11:28] Writing discarded fusions to file '659_c95-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:11:41] Freeing resources
[2026-05-28T00:11:48] Done (elapsed time=00:06:05, CPU time=00:06:03, peak memory=7.65gb)