[2026-06-08T08:24:52] Launching Arriba 2.4.0
[2026-06-08T08:24:52] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:05] Reading chimeric alignments from '659_bNS-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10937164)
[2026-06-08T08:31:59] Marking multi-mapping alignments (marked=6710909)
[2026-06-08T08:32:03] Detecting strandedness (reverse)
[2026-06-08T08:32:03] Assigning strands to alignments 
[2026-06-08T08:32:05] Annotating alignments 
[2026-06-08T08:32:43] Filtering duplicates (remaining=7673080)
[2026-06-08T08:32:51] 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=7346421)
[2026-06-08T08:32:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7346421)
[2026-06-08T08:32:56] Filtering viral contigs with expression lower than the top 5 (remaining=7346421)
[2026-06-08T08:33:01] Filtering viral contigs with less than 5% coverage (remaining=7346421)
[2026-06-08T08:33:04] Estimating fragment length (mate gap mean=-84.7557, mate gap stddev=29.3802, read length mean=130.974)
[2026-06-08T08:33:04] Filtering read-through fragments with a distance <=10000bp (remaining=6879860)
[2026-06-08T08:33:06] Filtering inconsistently clipped mates (remaining=6771286)
[2026-06-08T08:33:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6569827)
[2026-06-08T08:33:14] Filtering fragments with small insert size (remaining=6568615)
[2026-06-08T08:33:16] Filtering alignments with long gaps (remaining=6568615)
[2026-06-08T08:33:19] Filtering fragments with both mates in the same gene (remaining=6567398)
[2026-06-08T08:33:22] Filtering fusions arising from hairpin structures (remaining=6162503)
[2026-06-08T08:33:25] Filtering reads with a mismatch p-value <=0.01 (remaining=3359524)
[2026-06-08T08:33:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=1414626)
[2026-06-08T08:33:56] Finding fusions and counting supporting reads (total=1010383)
[2026-06-08T08:34:17] Merging adjacent fusion breakpoints (remaining=1000154)
[2026-06-08T08:34:19] Filtering multi-mapping fusions by alignment score and read support (remaining=641295)
[2026-06-08T08:34:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=639447)
[2026-06-08T08:35:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=365849)
[2026-06-08T08:35:09] Filtering fusions with <2 supporting reads (remaining=43844)
[2026-06-08T08:35:10] Filtering fusions with an e-value >=0.3 (remaining=11179)
[2026-06-08T08:35:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11240)
[2026-06-08T08:35:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11157)
[2026-06-08T08:35:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11158)
[2026-06-08T08:35:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8436)
[2026-06-08T08:35:25] Searching for fusions with spliced split reads (remaining=8555)
[2026-06-08T08:35:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=5125)
[2026-06-08T08:35:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5061)
[2026-06-08T08:35:34] Searching for fusions with >=4 spliced events (remaining=6267)
[2026-06-08T08:35:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2179)
[2026-06-08T08:35:50] Filtering fusions with anchors <=23nt (remaining=1734)
[2026-06-08T08:35:51] Filtering end-to-end fusions with low support (remaining=1699)
[2026-06-08T08:35:52] Filtering fusions with no coverage around the breakpoints (remaining=1663)
[2026-06-08T08:35:53] Indexing gene sequences 
[2026-06-08T08:35:59] Filtering genes with >=30% identity (remaining=462)
[2026-06-08T08:36:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=194)
[2026-06-08T08:36:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=187)
[2026-06-08T08:36:12] Searching for additional isoforms (remaining=230)
[2026-06-08T08:36:14] Assigning confidence scores to events 
[2026-06-08T08:36:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:18] Writing fusions to file '659_bNS-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:20] Writing discarded fusions to file '659_bNS-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:57] Freeing resources
[2026-06-08T08:37:18] Done (elapsed time=00:12:26, CPU time=00:12:25, peak memory=15.5gb)