[2026-06-08T08:39:51] Launching Arriba 2.4.0
[2026-06-08T08:39:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:03] Reading chimeric alignments from '659_ecd-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10349201)
[2026-06-08T08:46:41] Marking multi-mapping alignments (marked=6404434)
[2026-06-08T08:46:45] Detecting strandedness (reverse)
[2026-06-08T08:46:45] Assigning strands to alignments 
[2026-06-08T08:46:47] Annotating alignments 
[2026-06-08T08:47:22] Filtering duplicates (remaining=7605147)
[2026-06-08T08:47:30] 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=7267440)
[2026-06-08T08:47:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7267440)
[2026-06-08T08:47:34] Filtering viral contigs with expression lower than the top 5 (remaining=7267440)
[2026-06-08T08:47:38] Filtering viral contigs with less than 5% coverage (remaining=7267440)
[2026-06-08T08:47:41] Estimating fragment length (mate gap mean=-84.7591, mate gap stddev=29.9392, read length mean=131.346)
[2026-06-08T08:47:41] Filtering read-through fragments with a distance <=10000bp (remaining=6931742)
[2026-06-08T08:47:43] Filtering inconsistently clipped mates (remaining=6845935)
[2026-06-08T08:47:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6552739)
[2026-06-08T08:47:50] Filtering fragments with small insert size (remaining=6551714)
[2026-06-08T08:47:52] Filtering alignments with long gaps (remaining=6551713)
[2026-06-08T08:47:54] Filtering fragments with both mates in the same gene (remaining=6550258)
[2026-06-08T08:47:56] Filtering fusions arising from hairpin structures (remaining=6235404)
[2026-06-08T08:47:59] Filtering reads with a mismatch p-value <=0.01 (remaining=3341568)
[2026-06-08T08:48:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=1275157)
[2026-06-08T08:48:27] Finding fusions and counting supporting reads (total=869479)
[2026-06-08T08:48:44] Merging adjacent fusion breakpoints (remaining=863370)
[2026-06-08T08:48:46] Filtering multi-mapping fusions by alignment score and read support (remaining=559450)
[2026-06-08T08:49:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=557103)
[2026-06-08T08:49:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=348666)
[2026-06-08T08:49:31] Filtering fusions with <2 supporting reads (remaining=45790)
[2026-06-08T08:49:32] Filtering fusions with an e-value >=0.3 (remaining=12244)
[2026-06-08T08:49:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12296)
[2026-06-08T08:49:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12189)
[2026-06-08T08:49:37] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12218)
[2026-06-08T08:49:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8798)
[2026-06-08T08:49:44] Searching for fusions with spliced split reads (remaining=8864)
[2026-06-08T08:49:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=5093)
[2026-06-08T08:49:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5045)
[2026-06-08T08:49:52] Searching for fusions with >=4 spliced events (remaining=6171)
[2026-06-08T08:49:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2498)
[2026-06-08T08:50:07] Filtering fusions with anchors <=23nt (remaining=1943)
[2026-06-08T08:50:08] Filtering end-to-end fusions with low support (remaining=1892)
[2026-06-08T08:50:09] Filtering fusions with no coverage around the breakpoints (remaining=1850)
[2026-06-08T08:50:09] Indexing gene sequences 
[2026-06-08T08:50:17] Filtering genes with >=30% identity (remaining=749)
[2026-06-08T08:50:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=513)
[2026-06-08T08:50:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=369)
[2026-06-08T08:50:32] Searching for additional isoforms (remaining=595)
[2026-06-08T08:50:33] Assigning confidence scores to events 
[2026-06-08T08:50:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:37] Writing fusions to file '659_ecd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:42] Writing discarded fusions to file '659_ecd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:16] Freeing resources
[2026-06-08T08:51:34] Done (elapsed time=00:11:43, CPU time=00:11:43, peak memory=15gb)