[2026-06-08T08:39:26] Launching Arriba 2.4.0
[2026-06-08T08:39:26] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:43] Reading chimeric alignments from '659_Lx-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=10863901)
[2026-06-08T08:46:21] Marking multi-mapping alignments (marked=6571614)
[2026-06-08T08:46:26] Detecting strandedness (reverse)
[2026-06-08T08:46:26] Assigning strands to alignments 
[2026-06-08T08:46:28] Annotating alignments 
[2026-06-08T08:47:03] Filtering duplicates (remaining=5140022)
[2026-06-08T08:47:10] 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=4936331)
[2026-06-08T08:47:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4936331)
[2026-06-08T08:47:14] Filtering viral contigs with expression lower than the top 5 (remaining=4936331)
[2026-06-08T08:47:19] Filtering viral contigs with less than 5% coverage (remaining=4936331)
[2026-06-08T08:47:22] Estimating fragment length (mate gap mean=-89.9535, mate gap stddev=26.72, read length mean=131.751)
[2026-06-08T08:47:22] Filtering read-through fragments with a distance <=10000bp (remaining=4581655)
[2026-06-08T08:47:24] Filtering inconsistently clipped mates (remaining=4516834)
[2026-06-08T08:47:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4396329)
[2026-06-08T08:47:31] Filtering fragments with small insert size (remaining=4395621)
[2026-06-08T08:47:33] Filtering alignments with long gaps (remaining=4395621)
[2026-06-08T08:47:36] Filtering fragments with both mates in the same gene (remaining=4394899)
[2026-06-08T08:47:38] Filtering fusions arising from hairpin structures (remaining=4206817)
[2026-06-08T08:47:41] Filtering reads with a mismatch p-value <=0.01 (remaining=2023444)
[2026-06-08T08:47:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=793394)
[2026-06-08T08:48:03] Finding fusions and counting supporting reads (total=637150)
[2026-06-08T08:48:18] Merging adjacent fusion breakpoints (remaining=632001)
[2026-06-08T08:48:19] Filtering multi-mapping fusions by alignment score and read support (remaining=392110)
[2026-06-08T08:48:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=390995)
[2026-06-08T08:48:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=204227)
[2026-06-08T08:48:58] Filtering fusions with <2 supporting reads (remaining=25801)
[2026-06-08T08:48:59] Filtering fusions with an e-value >=0.3 (remaining=6230)
[2026-06-08T08:48:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6256)
[2026-06-08T08:49:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6210)
[2026-06-08T08:49:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6210)
[2026-06-08T08:49:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5962)
[2026-06-08T08:49:09] Searching for fusions with spliced split reads (remaining=6037)
[2026-06-08T08:49:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=3912)
[2026-06-08T08:49:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3877)
[2026-06-08T08:49:15] Searching for fusions with >=4 spliced events (remaining=4608)
[2026-06-08T08:49:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1608)
[2026-06-08T08:49:29] Filtering fusions with anchors <=23nt (remaining=1380)
[2026-06-08T08:49:30] Filtering end-to-end fusions with low support (remaining=1341)
[2026-06-08T08:49:30] Filtering fusions with no coverage around the breakpoints (remaining=1309)
[2026-06-08T08:49:31] Indexing gene sequences 
[2026-06-08T08:49:35] Filtering genes with >=30% identity (remaining=384)
[2026-06-08T08:49:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=140)
[2026-06-08T08:49:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=135)
[2026-06-08T08:49:41] Searching for additional isoforms (remaining=155)
[2026-06-08T08:49:42] Assigning confidence scores to events 
[2026-06-08T08:49:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:44] Writing fusions to file '659_Lx-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T08:49:46] Writing discarded fusions to file '659_Lx-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:09] Freeing resources
[2026-06-08T08:50:27] Done (elapsed time=00:11:01, CPU time=00:11:00, peak memory=15.3gb)