[2026-06-08T08:31:51] Launching Arriba 2.4.0
[2026-06-08T08:31:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:04] Reading chimeric alignments from '659_buD-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12020972)
[2026-06-08T08:39:01] Marking multi-mapping alignments (marked=7375974)
[2026-06-08T08:39:06] Detecting strandedness (reverse)
[2026-06-08T08:39:06] Assigning strands to alignments 
[2026-06-08T08:39:09] Annotating alignments 
[2026-06-08T08:39:51] Filtering duplicates (remaining=8662822)
[2026-06-08T08:40:00] 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=8241187)
[2026-06-08T08:40:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8241187)
[2026-06-08T08:40:05] Filtering viral contigs with expression lower than the top 5 (remaining=8241187)
[2026-06-08T08:40:11] Filtering viral contigs with less than 5% coverage (remaining=8241187)
[2026-06-08T08:40:14] Estimating fragment length (mate gap mean=-84.5676, mate gap stddev=28.7576, read length mean=128.412)
[2026-06-08T08:40:14] Filtering read-through fragments with a distance <=10000bp (remaining=7697226)
[2026-06-08T08:40:16] Filtering inconsistently clipped mates (remaining=7554005)
[2026-06-08T08:40:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7372144)
[2026-06-08T08:40:25] Filtering fragments with small insert size (remaining=7370469)
[2026-06-08T08:40:28] Filtering alignments with long gaps (remaining=7370468)
[2026-06-08T08:40:30] Filtering fragments with both mates in the same gene (remaining=7369236)
[2026-06-08T08:40:33] Filtering fusions arising from hairpin structures (remaining=6883249)
[2026-06-08T08:40:37] Filtering reads with a mismatch p-value <=0.01 (remaining=3684938)
[2026-06-08T08:40:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=1638468)
[2026-06-08T08:41:11] Finding fusions and counting supporting reads (total=1240749)
[2026-06-08T08:41:35] Merging adjacent fusion breakpoints (remaining=1226593)
[2026-06-08T08:41:37] Filtering multi-mapping fusions by alignment score and read support (remaining=750375)
[2026-06-08T08:42:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=748217)
[2026-06-08T08:42:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=457196)
[2026-06-08T08:42:33] Filtering fusions with <2 supporting reads (remaining=50001)
[2026-06-08T08:42:34] Filtering fusions with an e-value >=0.3 (remaining=11749)
[2026-06-08T08:42:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11825)
[2026-06-08T08:42:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11682)
[2026-06-08T08:42:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11682)
[2026-06-08T08:42:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9448)
[2026-06-08T08:42:51] Searching for fusions with spliced split reads (remaining=9481)
[2026-06-08T08:42:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=5767)
[2026-06-08T08:43:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5688)
[2026-06-08T08:43:01] Searching for fusions with >=4 spliced events (remaining=7212)
[2026-06-08T08:43:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3064)
[2026-06-08T08:43:18] Filtering fusions with anchors <=23nt (remaining=2522)
[2026-06-08T08:43:19] Filtering end-to-end fusions with low support (remaining=2471)
[2026-06-08T08:43:20] Filtering fusions with no coverage around the breakpoints (remaining=2417)
[2026-06-08T08:43:21] Indexing gene sequences 
[2026-06-08T08:43:29] Filtering genes with >=30% identity (remaining=748)
[2026-06-08T08:43:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=371)
[2026-06-08T08:43:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=284)
[2026-06-08T08:43:44] Searching for additional isoforms (remaining=378)
[2026-06-08T08:43:46] Assigning confidence scores to events 
[2026-06-08T08:43:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:51] Writing fusions to file '659_buD-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:55] Writing discarded fusions to file '659_buD-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:39] Freeing resources
[2026-06-08T08:45:01] Done (elapsed time=00:13:10, CPU time=00:13:09, peak memory=16.9gb)