[2026-06-04T21:12:49] Launching Arriba 2.4.0
[2026-06-04T21:12:49] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:12:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:13:00] Reading chimeric alignments from '659_cIX-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8742353)
[2026-06-04T21:19:25] Marking multi-mapping alignments (marked=5229169)
[2026-06-04T21:19:28] Detecting strandedness (reverse)
[2026-06-04T21:19:28] Assigning strands to alignments 
[2026-06-04T21:19:30] Annotating alignments 
[2026-06-04T21:19:57] Filtering duplicates (remaining=5990029)
[2026-06-04T21:20:03] 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=5749092)
[2026-06-04T21:20:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5749092)
[2026-06-04T21:20:07] Filtering viral contigs with expression lower than the top 5 (remaining=5749092)
[2026-06-04T21:20:11] Filtering viral contigs with less than 5% coverage (remaining=5749092)
[2026-06-04T21:20:13] Estimating fragment length (mate gap mean=-86.8829, mate gap stddev=28.979, read length mean=132.771)
[2026-06-04T21:20:14] Filtering read-through fragments with a distance <=10000bp (remaining=5409651)
[2026-06-04T21:20:15] Filtering inconsistently clipped mates (remaining=5319631)
[2026-06-04T21:20:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5154008)
[2026-06-04T21:20:21] Filtering fragments with small insert size (remaining=5153232)
[2026-06-04T21:20:23] Filtering alignments with long gaps (remaining=5153232)
[2026-06-04T21:20:25] Filtering fragments with both mates in the same gene (remaining=5152110)
[2026-06-04T21:20:27] Filtering fusions arising from hairpin structures (remaining=4842805)
[2026-06-04T21:20:29] Filtering reads with a mismatch p-value <=0.01 (remaining=2564733)
[2026-06-04T21:20:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=1110851)
[2026-06-04T21:20:52] Finding fusions and counting supporting reads (total=779511)
[2026-06-04T21:21:05] Merging adjacent fusion breakpoints (remaining=773696)
[2026-06-04T21:21:07] Filtering multi-mapping fusions by alignment score and read support (remaining=519135)
[2026-06-04T21:21:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:21:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=517216)
[2026-06-04T21:21:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280152)
[2026-06-04T21:21:41] Filtering fusions with <2 supporting reads (remaining=38311)
[2026-06-04T21:21:42] Filtering fusions with an e-value >=0.3 (remaining=9716)
[2026-06-04T21:21:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9765)
[2026-06-04T21:21:46] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9692)
[2026-06-04T21:21:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9692)
[2026-06-04T21:21:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7609)
[2026-06-04T21:21:52] Searching for fusions with spliced split reads (remaining=7631)
[2026-06-04T21:21:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=4852)
[2026-06-04T21:21:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4810)
[2026-06-04T21:21:58] Searching for fusions with >=4 spliced events (remaining=5863)
[2026-06-04T21:22:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2180)
[2026-06-04T21:22:12] Filtering fusions with anchors <=23nt (remaining=1737)
[2026-06-04T21:22:13] Filtering end-to-end fusions with low support (remaining=1693)
[2026-06-04T21:22:13] Filtering fusions with no coverage around the breakpoints (remaining=1645)
[2026-06-04T21:22:14] Indexing gene sequences 
[2026-06-04T21:22:20] Filtering genes with >=30% identity (remaining=534)
[2026-06-04T21:22:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=268)
[2026-06-04T21:22:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=215)
[2026-06-04T21:22:34] Searching for additional isoforms (remaining=284)
[2026-06-04T21:22:35] Assigning confidence scores to events 
[2026-06-04T21:22:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:22:38] Writing fusions to file '659_cIX-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:22:40] Writing discarded fusions to file '659_cIX-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:23:05] Freeing resources
[2026-06-04T21:23:20] Done (elapsed time=00:10:31, CPU time=00:10:30, peak memory=13.4gb)