[2026-06-08T08:12:02] Launching Arriba 2.4.0
[2026-06-08T08:12:02] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:12:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:12:15] Reading chimeric alignments from '659_bGc-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=7080023)
[2026-06-08T08:16:24] Marking multi-mapping alignments (marked=4506652)
[2026-06-08T08:16:27] Detecting strandedness (reverse)
[2026-06-08T08:16:27] Assigning strands to alignments 
[2026-06-08T08:16:28] Annotating alignments 
[2026-06-08T08:16:54] Filtering duplicates (remaining=2402593)
[2026-06-08T08:16:58] 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=2267591)
[2026-06-08T08:16:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2267591)
[2026-06-08T08:17:00] Filtering viral contigs with expression lower than the top 5 (remaining=2267591)
[2026-06-08T08:17:03] Filtering viral contigs with less than 5% coverage (remaining=2267591)
[2026-06-08T08:17:05] Estimating fragment length (mate gap mean=-86.3765, mate gap stddev=28.0123, read length mean=128.117)
[2026-06-08T08:17:05] Filtering read-through fragments with a distance <=10000bp (remaining=2159836)
[2026-06-08T08:17:06] Filtering inconsistently clipped mates (remaining=2121928)
[2026-06-08T08:17:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2034120)
[2026-06-08T08:17:10] Filtering fragments with small insert size (remaining=2033669)
[2026-06-08T08:17:12] Filtering alignments with long gaps (remaining=2033669)
[2026-06-08T08:17:13] Filtering fragments with both mates in the same gene (remaining=2033136)
[2026-06-08T08:17:14] Filtering fusions arising from hairpin structures (remaining=1951334)
[2026-06-08T08:17:16] Filtering reads with a mismatch p-value <=0.01 (remaining=764294)
[2026-06-08T08:17:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=271134)
[2026-06-08T08:17:26] Finding fusions and counting supporting reads (total=245207)
[2026-06-08T08:17:36] Merging adjacent fusion breakpoints (remaining=243373)
[2026-06-08T08:17:37] Filtering multi-mapping fusions by alignment score and read support (remaining=145230)
[2026-06-08T08:18:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:18:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=144316)
[2026-06-08T08:18:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=78601)
[2026-06-08T08:18:06] Filtering fusions with <2 supporting reads (remaining=7464)
[2026-06-08T08:18:06] Filtering fusions with an e-value >=0.3 (remaining=2035)
[2026-06-08T08:18:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2056)
[2026-06-08T08:18:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2021)
[2026-06-08T08:18:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2021)
[2026-06-08T08:18:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1902)
[2026-06-08T08:18:12] Searching for fusions with spliced split reads (remaining=2015)
[2026-06-08T08:18:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=1521)
[2026-06-08T08:18:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1506)
[2026-06-08T08:18:16] Searching for fusions with >=4 spliced events (remaining=1598)
[2026-06-08T08:18:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=433)
[2026-06-08T08:18:28] Filtering fusions with anchors <=23nt (remaining=366)
[2026-06-08T08:18:28] Filtering end-to-end fusions with low support (remaining=355)
[2026-06-08T08:18:28] Filtering fusions with no coverage around the breakpoints (remaining=344)
[2026-06-08T08:18:28] Indexing gene sequences 
[2026-06-08T08:18:30] Filtering genes with >=30% identity (remaining=160)
[2026-06-08T08:18:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=88)
[2026-06-08T08:18:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=87)
[2026-06-08T08:18:33] Searching for additional isoforms (remaining=96)
[2026-06-08T08:18:33] Assigning confidence scores to events 
[2026-06-08T08:18:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:18:35] Writing fusions to file '659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:18:35] Writing discarded fusions to file '659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:48] Freeing resources
[2026-06-08T08:19:01] Done (elapsed time=00:06:59, CPU time=00:06:57, peak memory=11.2gb)