[2026-06-08T08:30:54] Launching Arriba 2.4.0
[2026-06-08T08:30:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:07] Reading chimeric alignments from '659_zO-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8899948)
[2026-06-08T08:37:31] Marking multi-mapping alignments (marked=5606902)
[2026-06-08T08:37:36] Detecting strandedness (reverse)
[2026-06-08T08:37:36] Assigning strands to alignments 
[2026-06-08T08:37:37] Annotating alignments 
[2026-06-08T08:38:11] Filtering duplicates (remaining=5575198)
[2026-06-08T08:38:19] 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=5327639)
[2026-06-08T08:38:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5327639)
[2026-06-08T08:38:25] Filtering viral contigs with expression lower than the top 5 (remaining=5327639)
[2026-06-08T08:38:31] Filtering viral contigs with less than 5% coverage (remaining=5327639)
[2026-06-08T08:38:34] Estimating fragment length (mate gap mean=-88.9031, mate gap stddev=28.7722, read length mean=132.269)
[2026-06-08T08:38:34] Filtering read-through fragments with a distance <=10000bp (remaining=5060198)
[2026-06-08T08:38:37] Filtering inconsistently clipped mates (remaining=4978829)
[2026-06-08T08:38:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4820002)
[2026-06-08T08:38:47] Filtering fragments with small insert size (remaining=4819398)
[2026-06-08T08:38:49] Filtering alignments with long gaps (remaining=4819398)
[2026-06-08T08:38:51] Filtering fragments with both mates in the same gene (remaining=4818363)
[2026-06-08T08:38:53] Filtering fusions arising from hairpin structures (remaining=4547606)
[2026-06-08T08:38:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2363990)
[2026-06-08T08:39:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=910372)
[2026-06-08T08:39:19] Finding fusions and counting supporting reads (total=617393)
[2026-06-08T08:39:34] Merging adjacent fusion breakpoints (remaining=612681)
[2026-06-08T08:39:35] Filtering multi-mapping fusions by alignment score and read support (remaining=382070)
[2026-06-08T08:40:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=379942)
[2026-06-08T08:40:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=223353)
[2026-06-08T08:40:14] Filtering fusions with <2 supporting reads (remaining=28233)
[2026-06-08T08:40:14] Filtering fusions with an e-value >=0.3 (remaining=7369)
[2026-06-08T08:40:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7426)
[2026-06-08T08:40:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7297)
[2026-06-08T08:40:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7302)
[2026-06-08T08:40:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6227)
[2026-06-08T08:40:25] Searching for fusions with spliced split reads (remaining=6247)
[2026-06-08T08:40:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=4168)
[2026-06-08T08:40:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4114)
[2026-06-08T08:40:31] Searching for fusions with >=4 spliced events (remaining=4884)
[2026-06-08T08:40:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1881)
[2026-06-08T08:40:45] Filtering fusions with anchors <=23nt (remaining=1499)
[2026-06-08T08:40:46] Filtering end-to-end fusions with low support (remaining=1456)
[2026-06-08T08:40:46] Filtering fusions with no coverage around the breakpoints (remaining=1408)
[2026-06-08T08:40:47] Indexing gene sequences 
[2026-06-08T08:40:54] Filtering genes with >=30% identity (remaining=609)
[2026-06-08T08:41:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=410)
[2026-06-08T08:41:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=240)
[2026-06-08T08:41:20] Searching for additional isoforms (remaining=320)
[2026-06-08T08:41:21] Assigning confidence scores to events 
[2026-06-08T08:41:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:25] Writing fusions to file '659_zO-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:28] Writing discarded fusions to file '659_zO-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:00] Freeing resources
[2026-06-08T08:42:19] Done (elapsed time=00:11:25, CPU time=00:11:24, peak memory=13.4gb)