[2026-06-08T08:40:30] Launching Arriba 2.4.0
[2026-06-08T08:40:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:47] Reading chimeric alignments from '659_cAd-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=12962913)
[2026-06-08T08:48:21] Marking multi-mapping alignments (marked=8103052)
[2026-06-08T08:48:27] Detecting strandedness (reverse)
[2026-06-08T08:48:27] Assigning strands to alignments 
[2026-06-08T08:48:30] Annotating alignments 
[2026-06-08T08:49:09] Filtering duplicates (remaining=6078817)
[2026-06-08T08:49:17] 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=5849045)
[2026-06-08T08:49:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5849045)
[2026-06-08T08:49:22] Filtering viral contigs with expression lower than the top 5 (remaining=5849045)
[2026-06-08T08:49:28] Filtering viral contigs with less than 5% coverage (remaining=5849045)
[2026-06-08T08:49:31] Estimating fragment length (mate gap mean=-88.8438, mate gap stddev=27.626, read length mean=132.043)
[2026-06-08T08:49:31] Filtering read-through fragments with a distance <=10000bp (remaining=5494092)
[2026-06-08T08:49:33] Filtering inconsistently clipped mates (remaining=5401753)
[2026-06-08T08:49:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5227433)
[2026-06-08T08:49:41] Filtering fragments with small insert size (remaining=5226613)
[2026-06-08T08:49:43] Filtering alignments with long gaps (remaining=5226612)
[2026-06-08T08:49:46] Filtering fragments with both mates in the same gene (remaining=5225805)
[2026-06-08T08:49:49] Filtering fusions arising from hairpin structures (remaining=4960722)
[2026-06-08T08:49:52] Filtering reads with a mismatch p-value <=0.01 (remaining=2394056)
[2026-06-08T08:50:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=849733)
[2026-06-08T08:50:16] Finding fusions and counting supporting reads (total=681605)
[2026-06-08T08:50:33] Merging adjacent fusion breakpoints (remaining=675541)
[2026-06-08T08:50:35] Filtering multi-mapping fusions by alignment score and read support (remaining=402165)
[2026-06-08T08:51:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=400778)
[2026-06-08T08:51:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=214000)
[2026-06-08T08:51:19] Filtering fusions with <2 supporting reads (remaining=26432)
[2026-06-08T08:51:19] Filtering fusions with an e-value >=0.3 (remaining=6230)
[2026-06-08T08:51:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6265)
[2026-06-08T08:51:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6157)
[2026-06-08T08:51:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6157)
[2026-06-08T08:51:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5744)
[2026-06-08T08:51:31] Searching for fusions with spliced split reads (remaining=5834)
[2026-06-08T08:51:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=3972)
[2026-06-08T08:51:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3944)
[2026-06-08T08:51:38] Searching for fusions with >=4 spliced events (remaining=4586)
[2026-06-08T08:51:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1745)
[2026-06-08T08:51:54] Filtering fusions with anchors <=23nt (remaining=1446)
[2026-06-08T08:51:55] Filtering end-to-end fusions with low support (remaining=1408)
[2026-06-08T08:51:55] Filtering fusions with no coverage around the breakpoints (remaining=1372)
[2026-06-08T08:51:56] Indexing gene sequences 
[2026-06-08T08:52:01] Filtering genes with >=30% identity (remaining=464)
[2026-06-08T08:52:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=180)
[2026-06-08T08:52:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=157)
[2026-06-08T08:52:07] Searching for additional isoforms (remaining=198)
[2026-06-08T08:52:08] Assigning confidence scores to events 
[2026-06-08T08:52:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:11] Writing fusions to file '659_cAd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T08:52:13] Writing discarded fusions to file '659_cAd-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:38] Freeing resources
[2026-06-08T08:52:58] Done (elapsed time=00:12:28, CPU time=00:12:26, peak memory=17.3gb)