[2026-06-08T08:16:12] Launching Arriba 2.4.0
[2026-06-08T08:16:12] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:24] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:16:28] Reading chimeric alignments from '659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=8265193)
[2026-06-08T08:20:54] Marking multi-mapping alignments (marked=5143799)
[2026-06-08T08:20:57] Detecting strandedness (reverse)
[2026-06-08T08:20:57] Assigning strands to alignments 
[2026-06-08T08:20:58] Annotating alignments 
[2026-06-08T08:21:21] Filtering duplicates (remaining=4067728)
[2026-06-08T08:21:26] 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=3969026)
[2026-06-08T08:21:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3969026)
[2026-06-08T08:21:28] Filtering viral contigs with expression lower than the top 5 (remaining=3969026)
[2026-06-08T08:21:31] Filtering viral contigs with less than 5% coverage (remaining=3969026)
[2026-06-08T08:21:33] Estimating fragment length (mate gap mean=-90.5328, mate gap stddev=26.0484, read length mean=132.371)
[2026-06-08T08:21:33] Filtering read-through fragments with a distance <=10000bp (remaining=3719904)
[2026-06-08T08:21:35] Filtering inconsistently clipped mates (remaining=3650765)
[2026-06-08T08:21:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3510908)
[2026-06-08T08:21:39] Filtering fragments with small insert size (remaining=3510370)
[2026-06-08T08:21:40] Filtering alignments with long gaps (remaining=3510369)
[2026-06-08T08:21:42] Filtering fragments with both mates in the same gene (remaining=3509816)
[2026-06-08T08:21:43] Filtering fusions arising from hairpin structures (remaining=3305264)
[2026-06-08T08:21:45] Filtering reads with a mismatch p-value <=0.01 (remaining=1617206)
[2026-06-08T08:21:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=632864)
[2026-06-08T08:22:01] Finding fusions and counting supporting reads (total=530178)
[2026-06-08T08:22:12] Merging adjacent fusion breakpoints (remaining=525796)
[2026-06-08T08:22:13] Filtering multi-mapping fusions by alignment score and read support (remaining=298754)
[2026-06-08T08:22:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:22:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=297594)
[2026-06-08T08:22:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=168640)
[2026-06-08T08:22:41] Filtering fusions with <2 supporting reads (remaining=19009)
[2026-06-08T08:22:41] Filtering fusions with an e-value >=0.3 (remaining=4741)
[2026-06-08T08:22:42] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4778)
[2026-06-08T08:22:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4711)
[2026-06-08T08:22:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4713)
[2026-06-08T08:22:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4598)
[2026-06-08T08:22:49] Searching for fusions with spliced split reads (remaining=4661)
[2026-06-08T08:22:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=3253)
[2026-06-08T08:22:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3221)
[2026-06-08T08:22:54] Searching for fusions with >=4 spliced events (remaining=3639)
[2026-06-08T08:22:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1184)
[2026-06-08T08:23:08] Filtering fusions with anchors <=23nt (remaining=1008)
[2026-06-08T08:23:08] Filtering end-to-end fusions with low support (remaining=970)
[2026-06-08T08:23:09] Filtering fusions with no coverage around the breakpoints (remaining=943)
[2026-06-08T08:23:09] Indexing gene sequences 
[2026-06-08T08:23:14] Filtering genes with >=30% identity (remaining=320)
[2026-06-08T08:23:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=169)
[2026-06-08T08:23:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-06-08T08:23:18] Searching for additional isoforms (remaining=188)
[2026-06-08T08:23:19] Assigning confidence scores to events 
[2026-06-08T08:23:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:23:21] Writing fusions to file '659_6i-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:23:22] Writing discarded fusions to file '659_6i-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:23:40] Freeing resources
[2026-06-08T08:23:54] Done (elapsed time=00:07:42, CPU time=00:07:40, peak memory=12.7gb)