[2026-06-08T08:28:18] Launching Arriba 2.4.0
[2026-06-08T08:28:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:42] Reading chimeric alignments from '659_6i-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=7630209)
[2026-06-08T08:35:18] Marking multi-mapping alignments (marked=4945256)
[2026-06-08T08:35:21] Detecting strandedness (no)
[2026-06-08T08:35:21] Annotating alignments 
[2026-06-08T08:36:01] Filtering duplicates (remaining=1914152)
[2026-06-08T08:36:07] 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=1814356)
[2026-06-08T08:36:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1814356)
[2026-06-08T08:36:10] Filtering viral contigs with expression lower than the top 5 (remaining=1814356)
[2026-06-08T08:36:14] Filtering viral contigs with less than 5% coverage (remaining=1814356)
[2026-06-08T08:36:16] Estimating fragment length (mate gap mean=-87.9035, mate gap stddev=26.8027, read length mean=126.696)
[2026-06-08T08:36:16] Filtering read-through fragments with a distance <=10000bp (remaining=1723482)
[2026-06-08T08:36:18] Filtering inconsistently clipped mates (remaining=1687255)
[2026-06-08T08:36:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1587514)
[2026-06-08T08:36:22] Filtering fragments with small insert size (remaining=1587174)
[2026-06-08T08:36:23] Filtering alignments with long gaps (remaining=1587174)
[2026-06-08T08:36:25] Filtering fragments with both mates in the same gene (remaining=1586702)
[2026-06-08T08:36:26] Filtering fusions arising from hairpin structures (remaining=1510466)
[2026-06-08T08:36:28] Filtering reads with a mismatch p-value <=0.01 (remaining=576802)
[2026-06-08T08:36:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=246342)
[2026-06-08T08:36:39] Finding fusions and counting supporting reads (total=229650)
[2026-06-08T08:36:50] Merging adjacent fusion breakpoints (remaining=227798)
[2026-06-08T08:36:50] Filtering multi-mapping fusions by alignment score and read support (remaining=117336)
[2026-06-08T08:37:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=116607)
[2026-06-08T08:37:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=69505)
[2026-06-08T08:37:25] Filtering fusions with <2 supporting reads (remaining=6218)
[2026-06-08T08:37:25] Filtering fusions with an e-value >=0.3 (remaining=1664)
[2026-06-08T08:37:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1686)
[2026-06-08T08:37:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1631)
[2026-06-08T08:37:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1631)
[2026-06-08T08:37:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1598)
[2026-06-08T08:37:32] Searching for fusions with spliced split reads (remaining=1710)
[2026-06-08T08:37:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=1333)
[2026-06-08T08:37:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1319)
[2026-06-08T08:37:38] Searching for fusions with >=4 spliced events (remaining=1382)
[2026-06-08T08:37:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=351)
[2026-06-08T08:38:01] Filtering fusions with anchors <=23nt (remaining=285)
[2026-06-08T08:38:01] Filtering end-to-end fusions with low support (remaining=275)
[2026-06-08T08:38:01] Filtering fusions with no coverage around the breakpoints (remaining=266)
[2026-06-08T08:38:01] Indexing gene sequences 
[2026-06-08T08:38:05] Filtering genes with >=30% identity (remaining=103)
[2026-06-08T08:38:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=59)
[2026-06-08T08:38:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=55)
[2026-06-08T08:38:07] Searching for additional isoforms (remaining=67)
[2026-06-08T08:38:07] Assigning confidence scores to events 
[2026-06-08T08:38:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:38:09] Writing fusions to file '659_6i-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:38:09] Writing discarded fusions to file '659_6i-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:28] Freeing resources
[2026-06-08T08:38:46] Done (elapsed time=00:10:28, CPU time=00:10:27, peak memory=12gb)