[2026-06-08T08:51:45] Launching Arriba 2.4.0
[2026-06-08T08:51:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:59] Reading chimeric alignments from '659_ecd-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9292884)
[2026-06-08T08:59:01] Marking multi-mapping alignments (marked=5638861)
[2026-06-08T08:59:06] Detecting strandedness (reverse)
[2026-06-08T08:59:06] Assigning strands to alignments 
[2026-06-08T08:59:08] Annotating alignments 
[2026-06-08T08:59:51] Filtering duplicates (remaining=4852376)
[2026-06-08T09:00:00] 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=4675036)
[2026-06-08T09:00:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4675036)
[2026-06-08T09:00:05] Filtering viral contigs with expression lower than the top 5 (remaining=4675036)
[2026-06-08T09:00:12] Filtering viral contigs with less than 5% coverage (remaining=4675036)
[2026-06-08T09:00:16] Estimating fragment length (mate gap mean=-86.0576, mate gap stddev=31.4314, read length mean=138.255)
[2026-06-08T09:00:16] Filtering read-through fragments with a distance <=10000bp (remaining=4391776)
[2026-06-08T09:00:20] Filtering inconsistently clipped mates (remaining=4332897)
[2026-06-08T09:00:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4183527)
[2026-06-08T09:00:31] Filtering fragments with small insert size (remaining=4183152)
[2026-06-08T09:00:34] Filtering alignments with long gaps (remaining=4183151)
[2026-06-08T09:00:37] Filtering fragments with both mates in the same gene (remaining=4182147)
[2026-06-08T09:00:41] Filtering fusions arising from hairpin structures (remaining=3965093)
[2026-06-08T09:00:46] Filtering reads with a mismatch p-value <=0.01 (remaining=1856017)
[2026-06-08T09:00:59] Filtering reads with low entropy (k-mer content >=60%) (remaining=775962)
[2026-06-08T09:01:08] Finding fusions and counting supporting reads (total=582009)
[2026-06-08T09:01:25] Merging adjacent fusion breakpoints (remaining=577409)
[2026-06-08T09:01:26] Filtering multi-mapping fusions by alignment score and read support (remaining=380069)
[2026-06-08T09:02:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=377061)
[2026-06-08T09:02:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=193603)
[2026-06-08T09:02:21] Filtering fusions with <2 supporting reads (remaining=33567)
[2026-06-08T09:02:22] Filtering fusions with an e-value >=0.3 (remaining=12661)
[2026-06-08T09:02:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12701)
[2026-06-08T09:02:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12555)
[2026-06-08T09:02:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12570)
[2026-06-08T09:02:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7788)
[2026-06-08T09:02:38] Searching for fusions with spliced split reads (remaining=7868)
[2026-06-08T09:02:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=4427)
[2026-06-08T09:02:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4367)
[2026-06-08T09:02:45] Searching for fusions with >=4 spliced events (remaining=5236)
[2026-06-08T09:02:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1846)
[2026-06-08T09:03:01] Filtering fusions with anchors <=23nt (remaining=1531)
[2026-06-08T09:03:01] Filtering end-to-end fusions with low support (remaining=1488)
[2026-06-08T09:03:02] Filtering fusions with no coverage around the breakpoints (remaining=1443)
[2026-06-08T09:03:03] Indexing gene sequences 
[2026-06-08T09:03:10] Filtering genes with >=30% identity (remaining=586)
[2026-06-08T09:03:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=386)
[2026-06-08T09:03:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=301)
[2026-06-08T09:03:21] Searching for additional isoforms (remaining=459)
[2026-06-08T09:03:23] Assigning confidence scores to events 
[2026-06-08T09:03:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:26] Writing fusions to file '659_ecd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:32] Writing discarded fusions to file '659_ecd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:04:03] Freeing resources
[2026-06-08T09:04:22] Done (elapsed time=00:12:37, CPU time=00:12:36, peak memory=13.8gb)