[2026-06-08T08:35:25] Launching Arriba 2.4.0
[2026-06-08T08:35:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:38] Reading chimeric alignments from '659_rd-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=9272724)
[2026-06-08T08:41:19] Marking multi-mapping alignments (marked=5250976)
[2026-06-08T08:41:22] Detecting strandedness (reverse)
[2026-06-08T08:41:22] Assigning strands to alignments 
[2026-06-08T08:41:24] Annotating alignments 
[2026-06-08T08:41:55] Filtering duplicates (remaining=6461145)
[2026-06-08T08:42:03] 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=6306489)
[2026-06-08T08:42:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6306489)
[2026-06-08T08:42:06] Filtering viral contigs with expression lower than the top 5 (remaining=6306489)
[2026-06-08T08:42:10] Filtering viral contigs with less than 5% coverage (remaining=6306489)
[2026-06-08T08:42:12] Estimating fragment length (mate gap mean=-86.7707, mate gap stddev=31.3532, read length mean=141.033)
[2026-06-08T08:42:12] Filtering read-through fragments with a distance <=10000bp (remaining=5891243)
[2026-06-08T08:42:14] Filtering inconsistently clipped mates (remaining=5821447)
[2026-06-08T08:42:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5661282)
[2026-06-08T08:42:20] Filtering fragments with small insert size (remaining=5660754)
[2026-06-08T08:42:21] Filtering alignments with long gaps (remaining=5660754)
[2026-06-08T08:42:23] Filtering fragments with both mates in the same gene (remaining=5659781)
[2026-06-08T08:42:25] Filtering fusions arising from hairpin structures (remaining=5359529)
[2026-06-08T08:42:27] Filtering reads with a mismatch p-value <=0.01 (remaining=3010576)
[2026-06-08T08:42:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=1244747)
[2026-06-08T08:42:51] Finding fusions and counting supporting reads (total=818689)
[2026-06-08T08:43:05] Merging adjacent fusion breakpoints (remaining=813904)
[2026-06-08T08:43:07] Filtering multi-mapping fusions by alignment score and read support (remaining=552627)
[2026-06-08T08:43:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=549659)
[2026-06-08T08:43:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=301716)
[2026-06-08T08:43:44] Filtering fusions with <2 supporting reads (remaining=50313)
[2026-06-08T08:43:45] Filtering fusions with an e-value >=0.3 (remaining=16632)
[2026-06-08T08:43:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=16676)
[2026-06-08T08:43:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16608)
[2026-06-08T08:43:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16693)
[2026-06-08T08:43:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10793)
[2026-06-08T08:43:56] Searching for fusions with spliced split reads (remaining=10846)
[2026-06-08T08:44:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=5429)
[2026-06-08T08:44:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5366)
[2026-06-08T08:44:02] Searching for fusions with >=4 spliced events (remaining=6920)
[2026-06-08T08:44:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2296)
[2026-06-08T08:44:17] Filtering fusions with anchors <=23nt (remaining=2005)
[2026-06-08T08:44:17] Filtering end-to-end fusions with low support (remaining=1962)
[2026-06-08T08:44:18] Filtering fusions with no coverage around the breakpoints (remaining=1907)
[2026-06-08T08:44:19] Indexing gene sequences 
[2026-06-08T08:44:26] Filtering genes with >=30% identity (remaining=514)
[2026-06-08T08:44:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=252)
[2026-06-08T08:44:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=225)
[2026-06-08T08:44:46] Searching for additional isoforms (remaining=315)
[2026-06-08T08:44:48] Assigning confidence scores to events 
[2026-06-08T08:44:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:51] Writing fusions to file '659_rd-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:44:54] Writing discarded fusions to file '659_rd-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:20] Freeing resources
[2026-06-08T08:45:37] Done (elapsed time=00:10:12, CPU time=00:10:11, peak memory=13.8gb)