[2026-06-08T08:40:19] Launching Arriba 2.4.0
[2026-06-08T08:40:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:31] Reading chimeric alignments from '659_bGW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10758058)
[2026-06-08T08:47:15] Marking multi-mapping alignments (marked=6855083)
[2026-06-08T08:47:20] Detecting strandedness (reverse)
[2026-06-08T08:47:20] Assigning strands to alignments 
[2026-06-08T08:47:22] Annotating alignments 
[2026-06-08T08:48:02] Filtering duplicates (remaining=4121212)
[2026-06-08T08:48:08] 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=3855874)
[2026-06-08T08:48:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3855874)
[2026-06-08T08:48:13] Filtering viral contigs with expression lower than the top 5 (remaining=3855874)
[2026-06-08T08:48:18] Filtering viral contigs with less than 5% coverage (remaining=3855874)
[2026-06-08T08:48:20] Estimating fragment length (mate gap mean=-88.0637, mate gap stddev=28.4177, read length mean=130.885)
[2026-06-08T08:48:20] Filtering read-through fragments with a distance <=10000bp (remaining=3622846)
[2026-06-08T08:48:23] Filtering inconsistently clipped mates (remaining=3564554)
[2026-06-08T08:48:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3462209)
[2026-06-08T08:48:29] Filtering fragments with small insert size (remaining=3461501)
[2026-06-08T08:48:31] Filtering alignments with long gaps (remaining=3461501)
[2026-06-08T08:48:33] Filtering fragments with both mates in the same gene (remaining=3460812)
[2026-06-08T08:48:36] Filtering fusions arising from hairpin structures (remaining=3286604)
[2026-06-08T08:48:38] Filtering reads with a mismatch p-value <=0.01 (remaining=1358349)
[2026-06-08T08:48:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=570005)
[2026-06-08T08:48:56] Finding fusions and counting supporting reads (total=467966)
[2026-06-08T08:49:12] Merging adjacent fusion breakpoints (remaining=462961)
[2026-06-08T08:49:13] Filtering multi-mapping fusions by alignment score and read support (remaining=292122)
[2026-06-08T08:49:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=290671)
[2026-06-08T08:49:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=144232)
[2026-06-08T08:49:52] Filtering fusions with <2 supporting reads (remaining=19570)
[2026-06-08T08:49:52] Filtering fusions with an e-value >=0.3 (remaining=5868)
[2026-06-08T08:49:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5905)
[2026-06-08T08:49:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5844)
[2026-06-08T08:49:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5844)
[2026-06-08T08:49:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3919)
[2026-06-08T08:50:02] Searching for fusions with spliced split reads (remaining=3961)
[2026-06-08T08:50:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=2799)
[2026-06-08T08:50:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2782)
[2026-06-08T08:50:08] Searching for fusions with >=4 spliced events (remaining=3149)
[2026-06-08T08:50:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1113)
[2026-06-08T08:50:21] Filtering fusions with anchors <=23nt (remaining=883)
[2026-06-08T08:50:22] Filtering end-to-end fusions with low support (remaining=831)
[2026-06-08T08:50:22] Filtering fusions with no coverage around the breakpoints (remaining=803)
[2026-06-08T08:50:23] Indexing gene sequences 
[2026-06-08T08:50:27] Filtering genes with >=30% identity (remaining=307)
[2026-06-08T08:50:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=158)
[2026-06-08T08:50:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T08:50:31] Searching for additional isoforms (remaining=163)
[2026-06-08T08:50:32] Assigning confidence scores to events 
[2026-06-08T08:50:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:35] Writing fusions to file '659_bGW-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:36] Writing discarded fusions to file '659_bGW-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:57] Freeing resources
[2026-06-08T08:51:14] Done (elapsed time=00:10:55, CPU time=00:10:53, peak memory=15.4gb)