[2026-06-08T08:29:53] Launching Arriba 2.4.0
[2026-06-08T08:29:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:07] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:12] Reading chimeric alignments from '659_cIX-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8742353)
[2026-06-08T08:38:45] Marking multi-mapping alignments (marked=5229169)
[2026-06-08T08:38:49] Detecting strandedness (reverse)
[2026-06-08T08:38:49] Assigning strands to alignments 
[2026-06-08T08:38:51] Annotating alignments 
[2026-06-08T08:39:27] Filtering duplicates (remaining=5990029)
[2026-06-08T08:39:34] 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)
[2026-06-08T08:39:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5749092)
[2026-06-08T08:39:38] Filtering viral contigs with expression lower than the top 5 (remaining=5749092)
[2026-06-08T08:39:43] Filtering viral contigs with less than 5% coverage (remaining=5749092)
[2026-06-08T08:39:46] Estimating fragment length (mate gap mean=-86.8829, mate gap stddev=28.979, read length mean=132.771)
[2026-06-08T08:39:46] Filtering read-through fragments with a distance <=10000bp (remaining=5409651)
[2026-06-08T08:39:48] Filtering inconsistently clipped mates (remaining=5319631)
[2026-06-08T08:39:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5154008)
[2026-06-08T08:39:55] Filtering fragments with small insert size (remaining=5153232)
[2026-06-08T08:39:57] Filtering alignments with long gaps (remaining=5153232)
[2026-06-08T08:39:59] Filtering fragments with both mates in the same gene (remaining=5152110)
[2026-06-08T08:40:01] Filtering fusions arising from hairpin structures (remaining=4842805)
[2026-06-08T08:40:04] Filtering reads with a mismatch p-value <=0.01 (remaining=2564733)
[2026-06-08T08:40:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=1110851)
[2026-06-08T08:40:30] Finding fusions and counting supporting reads (total=779511)
[2026-06-08T08:40:48] Merging adjacent fusion breakpoints (remaining=773696)
[2026-06-08T08:40:50] Filtering multi-mapping fusions by alignment score and read support (remaining=519135)
[2026-06-08T08:41:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=517216)
[2026-06-08T08:41:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280152)
[2026-06-08T08:41:33] Filtering fusions with <2 supporting reads (remaining=38311)
[2026-06-08T08:41:34] Filtering fusions with an e-value >=0.3 (remaining=9716)
[2026-06-08T08:41:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9765)
[2026-06-08T08:41:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9692)
[2026-06-08T08:41:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9692)
[2026-06-08T08:41:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7609)
[2026-06-08T08:41:46] Searching for fusions with spliced split reads (remaining=7631)
[2026-06-08T08:41:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=4852)
[2026-06-08T08:41:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4810)
[2026-06-08T08:41:53] Searching for fusions with >=4 spliced events (remaining=5863)
[2026-06-08T08:41:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2180)
[2026-06-08T08:42:15] Filtering fusions with anchors <=23nt (remaining=1737)
[2026-06-08T08:42:16] Filtering end-to-end fusions with low support (remaining=1693)
[2026-06-08T08:42:16] Filtering fusions with no coverage around the breakpoints (remaining=1645)
[2026-06-08T08:42:17] Indexing gene sequences 
[2026-06-08T08:42:26] Filtering genes with >=30% identity (remaining=534)
[2026-06-08T08:42:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=268)
[2026-06-08T08:42:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=215)
[2026-06-08T08:42:43] Searching for additional isoforms (remaining=284)
[2026-06-08T08:42:45] Assigning confidence scores to events 
[2026-06-08T08:42:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:49] Writing fusions to file '659_cIX-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:52] Writing discarded fusions to file '659_cIX-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:30] Freeing resources
[2026-06-08T08:43:49] Done (elapsed time=00:13:56, CPU time=00:13:56, peak memory=13.4gb)