[2026-06-08T08:48:30] Launching Arriba 2.4.0
[2026-06-08T08:48:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:44] Reading chimeric alignments from '659_d01-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=10731424)
[2026-06-08T08:55:09] Marking multi-mapping alignments (marked=6603410)
[2026-06-08T08:55:14] Detecting strandedness (reverse)
[2026-06-08T08:55:14] Assigning strands to alignments 
[2026-06-08T08:55:16] Annotating alignments 
[2026-06-08T08:55:53] Filtering duplicates (remaining=6141814)
[2026-06-08T08:56:01] 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=5964011)
[2026-06-08T08:56:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5964011)
[2026-06-08T08:56:06] Filtering viral contigs with expression lower than the top 5 (remaining=5964011)
[2026-06-08T08:56:11] Filtering viral contigs with less than 5% coverage (remaining=5964011)
[2026-06-08T08:56:14] Estimating fragment length (mate gap mean=-90.0574, mate gap stddev=28.7533, read length mean=137.437)
[2026-06-08T08:56:14] Filtering read-through fragments with a distance <=10000bp (remaining=5626493)
[2026-06-08T08:56:16] Filtering inconsistently clipped mates (remaining=5540346)
[2026-06-08T08:56:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5349254)
[2026-06-08T08:56:23] Filtering fragments with small insert size (remaining=5348691)
[2026-06-08T08:56:25] Filtering alignments with long gaps (remaining=5348691)
[2026-06-08T08:56:27] Filtering fragments with both mates in the same gene (remaining=5347765)
[2026-06-08T08:56:30] Filtering fusions arising from hairpin structures (remaining=5035702)
[2026-06-08T08:56:32] Filtering reads with a mismatch p-value <=0.01 (remaining=2612528)
[2026-06-08T08:56:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=880410)
[2026-06-08T08:56:57] Finding fusions and counting supporting reads (total=714031)
[2026-06-08T08:57:15] Merging adjacent fusion breakpoints (remaining=707651)
[2026-06-08T08:57:16] Filtering multi-mapping fusions by alignment score and read support (remaining=430370)
[2026-06-08T08:57:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=427737)
[2026-06-08T08:58:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=237221)
[2026-06-08T08:58:01] Filtering fusions with <2 supporting reads (remaining=27243)
[2026-06-08T08:58:02] Filtering fusions with an e-value >=0.3 (remaining=7947)
[2026-06-08T08:58:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7996)
[2026-06-08T08:58:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7852)
[2026-06-08T08:58:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7852)
[2026-06-08T08:58:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6714)
[2026-06-08T08:58:15] Searching for fusions with spliced split reads (remaining=6720)
[2026-06-08T08:58:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4148)
[2026-06-08T08:58:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4055)
[2026-06-08T08:58:23] Searching for fusions with >=4 spliced events (remaining=4933)
[2026-06-08T08:58:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1771)
[2026-06-08T08:58:38] Filtering fusions with anchors <=23nt (remaining=1456)
[2026-06-08T08:58:39] Filtering end-to-end fusions with low support (remaining=1408)
[2026-06-08T08:58:40] Filtering fusions with no coverage around the breakpoints (remaining=1362)
[2026-06-08T08:58:40] Indexing gene sequences 
[2026-06-08T08:58:46] Filtering genes with >=30% identity (remaining=407)
[2026-06-08T08:58:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=176)
[2026-06-08T08:58:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=158)
[2026-06-08T08:58:53] Searching for additional isoforms (remaining=201)
[2026-06-08T08:58:54] Assigning confidence scores to events 
[2026-06-08T08:58:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:57] Writing fusions to file '659_d01-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:59] Writing discarded fusions to file '659_d01-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:28] Freeing resources
[2026-06-08T08:59:48] Done (elapsed time=00:11:18, CPU time=00:11:16, peak memory=15.2gb)