[2026-06-08T08:32:49] Launching Arriba 2.4.0
[2026-06-08T08:32:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:01] Reading chimeric alignments from '659_dHy-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10637541)
[2026-06-08T08:39:51] Marking multi-mapping alignments (marked=6776307)
[2026-06-08T08:39:56] Detecting strandedness (reverse)
[2026-06-08T08:39:56] Assigning strands to alignments 
[2026-06-08T08:39:58] Annotating alignments 
[2026-06-08T08:40:35] Filtering duplicates (remaining=6784429)
[2026-06-08T08:40:43] 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=6377083)
[2026-06-08T08:40:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6377083)
[2026-06-08T08:40:47] Filtering viral contigs with expression lower than the top 5 (remaining=6377083)
[2026-06-08T08:40:52] Filtering viral contigs with less than 5% coverage (remaining=6377083)
[2026-06-08T08:40:55] Estimating fragment length (mate gap mean=-86.9471, mate gap stddev=29.2116, read length mean=134.341)
[2026-06-08T08:40:55] Filtering read-through fragments with a distance <=10000bp (remaining=6024892)
[2026-06-08T08:40:57] Filtering inconsistently clipped mates (remaining=5907890)
[2026-06-08T08:40:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5684128)
[2026-06-08T08:41:04] Filtering fragments with small insert size (remaining=5683379)
[2026-06-08T08:41:07] Filtering alignments with long gaps (remaining=5683379)
[2026-06-08T08:41:09] Filtering fragments with both mates in the same gene (remaining=5682272)
[2026-06-08T08:41:12] Filtering fusions arising from hairpin structures (remaining=5240361)
[2026-06-08T08:41:15] Filtering reads with a mismatch p-value <=0.01 (remaining=2871452)
[2026-06-08T08:41:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=1275710)
[2026-06-08T08:41:42] Finding fusions and counting supporting reads (total=818863)
[2026-06-08T08:41:59] Merging adjacent fusion breakpoints (remaining=808529)
[2026-06-08T08:42:00] Filtering multi-mapping fusions by alignment score and read support (remaining=528386)
[2026-06-08T08:42:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=525156)
[2026-06-08T08:42:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=297084)
[2026-06-08T08:42:43] Filtering fusions with <2 supporting reads (remaining=44283)
[2026-06-08T08:42:44] Filtering fusions with an e-value >=0.3 (remaining=11915)
[2026-06-08T08:42:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11984)
[2026-06-08T08:42:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11843)
[2026-06-08T08:42:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11843)
[2026-06-08T08:42:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9512)
[2026-06-08T08:42:55] Searching for fusions with spliced split reads (remaining=9560)
[2026-06-08T08:43:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=5532)
[2026-06-08T08:43:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5463)
[2026-06-08T08:43:02] Searching for fusions with >=4 spliced events (remaining=6709)
[2026-06-08T08:43:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2361)
[2026-06-08T08:43:18] Filtering fusions with anchors <=23nt (remaining=1897)
[2026-06-08T08:43:19] Filtering end-to-end fusions with low support (remaining=1853)
[2026-06-08T08:43:20] Filtering fusions with no coverage around the breakpoints (remaining=1809)
[2026-06-08T08:43:21] Indexing gene sequences 
[2026-06-08T08:43:28] Filtering genes with >=30% identity (remaining=593)
[2026-06-08T08:43:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=363)
[2026-06-08T08:43:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=274)
[2026-06-08T08:43:40] Searching for additional isoforms (remaining=391)
[2026-06-08T08:43:42] Assigning confidence scores to events 
[2026-06-08T08:43:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:45] Writing fusions to file '659_dHy-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:49] Writing discarded fusions to file '659_dHy-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:20] Freeing resources
[2026-06-08T08:44:37] Done (elapsed time=00:11:48, CPU time=00:11:47, peak memory=15.5gb)