[2026-06-08T08:35:51] Launching Arriba 2.4.0
[2026-06-08T08:35:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:08] Reading chimeric alignments from '659_gK-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10331892)
[2026-06-08T08:43:48] Marking multi-mapping alignments (marked=6629972)
[2026-06-08T08:43:52] Detecting strandedness (reverse)
[2026-06-08T08:43:52] Assigning strands to alignments 
[2026-06-08T08:43:54] Annotating alignments 
[2026-06-08T08:44:24] Filtering duplicates (remaining=7108319)
[2026-06-08T08:44:31] 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=6828835)
[2026-06-08T08:44:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6828835)
[2026-06-08T08:44:35] Filtering viral contigs with expression lower than the top 5 (remaining=6828835)
[2026-06-08T08:44:39] Filtering viral contigs with less than 5% coverage (remaining=6828835)
[2026-06-08T08:44:41] Estimating fragment length (mate gap mean=-86.7493, mate gap stddev=29.3338, read length mean=134.62)
[2026-06-08T08:44:41] Filtering read-through fragments with a distance <=10000bp (remaining=6317730)
[2026-06-08T08:44:43] Filtering inconsistently clipped mates (remaining=6209423)
[2026-06-08T08:44:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6008790)
[2026-06-08T08:44:50] Filtering fragments with small insert size (remaining=6008041)
[2026-06-08T08:44:52] Filtering alignments with long gaps (remaining=6008041)
[2026-06-08T08:44:54] Filtering fragments with both mates in the same gene (remaining=6007022)
[2026-06-08T08:44:57] Filtering fusions arising from hairpin structures (remaining=5562124)
[2026-06-08T08:45:00] Filtering reads with a mismatch p-value <=0.01 (remaining=3004181)
[2026-06-08T08:45:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=1321017)
[2026-06-08T08:45:28] Finding fusions and counting supporting reads (total=902399)
[2026-06-08T08:45:45] Merging adjacent fusion breakpoints (remaining=887130)
[2026-06-08T08:45:47] Filtering multi-mapping fusions by alignment score and read support (remaining=553432)
[2026-06-08T08:46:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=551049)
[2026-06-08T08:46:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=287849)
[2026-06-08T08:46:30] Filtering fusions with <2 supporting reads (remaining=37711)
[2026-06-08T08:46:30] Filtering fusions with an e-value >=0.3 (remaining=11046)
[2026-06-08T08:46:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11100)
[2026-06-08T08:46:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10962)
[2026-06-08T08:46:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10976)
[2026-06-08T08:46:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8113)
[2026-06-08T08:46:42] Searching for fusions with spliced split reads (remaining=8133)
[2026-06-08T08:46:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=4825)
[2026-06-08T08:46:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4786)
[2026-06-08T08:46:49] Searching for fusions with >=4 spliced events (remaining=5738)
[2026-06-08T08:46:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2103)
[2026-06-08T08:47:08] Filtering fusions with anchors <=23nt (remaining=1666)
[2026-06-08T08:47:09] Filtering end-to-end fusions with low support (remaining=1612)
[2026-06-08T08:47:10] Filtering fusions with no coverage around the breakpoints (remaining=1567)
[2026-06-08T08:47:10] Indexing gene sequences 
[2026-06-08T08:47:17] Filtering genes with >=30% identity (remaining=440)
[2026-06-08T08:47:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=175)
[2026-06-08T08:47:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=132)
[2026-06-08T08:47:27] Searching for additional isoforms (remaining=204)
[2026-06-08T08:47:28] Assigning confidence scores to events 
[2026-06-08T08:47:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:32] Writing fusions to file '659_gK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:34] Writing discarded fusions to file '659_gK-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:08] Freeing resources
[2026-06-08T08:48:27] Done (elapsed time=00:12:36, CPU time=00:12:36, peak memory=15.1gb)