[2026-05-28T00:00:40] Launching Arriba 2.4.0
[2026-05-28T00:00:40] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:00:53] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:00:58] Reading chimeric alignments from '659_Mt-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=4038261)
[2026-05-28T00:03:58] Marking multi-mapping alignments (marked=2649104)
[2026-05-28T00:04:00] Detecting strandedness (reverse)
[2026-05-28T00:04:00] Assigning strands to alignments 
[2026-05-28T00:04:01] Annotating alignments 
[2026-05-28T00:04:19] Filtering duplicates (remaining=1323055)
[2026-05-28T00:04:22] 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=1228363)
[2026-05-28T00:04:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1228363)
[2026-05-28T00:04:24] Filtering viral contigs with expression lower than the top 5 (remaining=1228363)
[2026-05-28T00:04:26] Filtering viral contigs with less than 5% coverage (remaining=1228363)
[2026-05-28T00:04:27] Estimating fragment length (mate gap mean=-85.5899, mate gap stddev=28.4277, read length mean=128.288)
[2026-05-28T00:04:27] Filtering read-through fragments with a distance <=10000bp (remaining=1167534)
[2026-05-28T00:04:28] Filtering inconsistently clipped mates (remaining=1142618)
[2026-05-28T00:04:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1087014)
[2026-05-28T00:04:31] Filtering fragments with small insert size (remaining=1086820)
[2026-05-28T00:04:32] Filtering alignments with long gaps (remaining=1086820)
[2026-05-28T00:04:33] Filtering fragments with both mates in the same gene (remaining=1086560)
[2026-05-28T00:04:34] Filtering fusions arising from hairpin structures (remaining=1033044)
[2026-05-28T00:04:35] Filtering reads with a mismatch p-value <=0.01 (remaining=433693)
[2026-05-28T00:04:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=162973)
[2026-05-28T00:04:42] Finding fusions and counting supporting reads (total=137544)
[2026-05-28T00:04:49] Merging adjacent fusion breakpoints (remaining=136644)
[2026-05-28T00:04:50] Filtering multi-mapping fusions by alignment score and read support (remaining=73582)
[2026-05-28T00:05:07] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:05:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=73062)
[2026-05-28T00:05:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=44364)
[2026-05-28T00:05:10] Filtering fusions with <2 supporting reads (remaining=4706)
[2026-05-28T00:05:10] Filtering fusions with an e-value >=0.3 (remaining=1157)
[2026-05-28T00:05:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1177)
[2026-05-28T00:05:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1137)
[2026-05-28T00:05:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1137)
[2026-05-28T00:05:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1079)
[2026-05-28T00:05:14] Searching for fusions with spliced split reads (remaining=1189)
[2026-05-28T00:05:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=924)
[2026-05-28T00:05:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=915)
[2026-05-28T00:05:17] Searching for fusions with >=4 spliced events (remaining=998)
[2026-05-28T00:05:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=250)
[2026-05-28T00:05:34] Filtering fusions with anchors <=23nt (remaining=216)
[2026-05-28T00:05:35] Filtering end-to-end fusions with low support (remaining=208)
[2026-05-28T00:05:35] Filtering fusions with no coverage around the breakpoints (remaining=200)
[2026-05-28T00:05:35] Indexing gene sequences 
[2026-05-28T00:05:37] Filtering genes with >=30% identity (remaining=60)
[2026-05-28T00:05:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=31)
[2026-05-28T00:05:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=31)
[2026-05-28T00:05:38] Searching for additional isoforms (remaining=38)
[2026-05-28T00:05:38] Assigning confidence scores to events 
[2026-05-28T00:05:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:05:40] Writing fusions to file '659_Mt-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:05:40] Writing discarded fusions to file '659_Mt-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:05:49] Freeing resources
[2026-05-28T00:06:01] Done (elapsed time=00:05:21, CPU time=00:05:19, peak memory=8.2gb)