[2026-06-08T09:01:50] Launching Arriba 2.4.0
[2026-06-08T09:01:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:02:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:02:05] Reading chimeric alignments from '659_eHw-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=12418077)
[2026-06-08T09:10:17] Marking multi-mapping alignments (marked=7598202)
[2026-06-08T09:10:23] Detecting strandedness (reverse)
[2026-06-08T09:10:23] Assigning strands to alignments 
[2026-06-08T09:10:25] Annotating alignments 
[2026-06-08T09:11:05] Filtering duplicates (remaining=5923274)
[2026-06-08T09:11:13] 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=5673211)
[2026-06-08T09:11:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5673211)
[2026-06-08T09:11:18] Filtering viral contigs with expression lower than the top 5 (remaining=5673211)
[2026-06-08T09:11:23] Filtering viral contigs with less than 5% coverage (remaining=5673211)
[2026-06-08T09:11:26] Estimating fragment length (mate gap mean=-90.1331, mate gap stddev=28.7627, read length mean=139.361)
[2026-06-08T09:11:26] Filtering read-through fragments with a distance <=10000bp (remaining=5347193)
[2026-06-08T09:11:29] Filtering inconsistently clipped mates (remaining=5253220)
[2026-06-08T09:11:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5090138)
[2026-06-08T09:11:36] Filtering fragments with small insert size (remaining=5089333)
[2026-06-08T09:11:38] Filtering alignments with long gaps (remaining=5089332)
[2026-06-08T09:11:41] Filtering fragments with both mates in the same gene (remaining=5088744)
[2026-06-08T09:11:43] Filtering fusions arising from hairpin structures (remaining=4818408)
[2026-06-08T09:11:46] Filtering reads with a mismatch p-value <=0.01 (remaining=2320239)
[2026-06-08T09:12:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=727401)
[2026-06-08T09:12:11] Finding fusions and counting supporting reads (total=573472)
[2026-06-08T09:12:30] Merging adjacent fusion breakpoints (remaining=567701)
[2026-06-08T09:12:31] Filtering multi-mapping fusions by alignment score and read support (remaining=369354)
[2026-06-08T09:13:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:13:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=366973)
[2026-06-08T09:13:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=190787)
[2026-06-08T09:13:19] Filtering fusions with <2 supporting reads (remaining=25291)
[2026-06-08T09:13:19] Filtering fusions with an e-value >=0.3 (remaining=7931)
[2026-06-08T09:13:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7984)
[2026-06-08T09:13:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7898)
[2026-06-08T09:13:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7898)
[2026-06-08T09:13:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4359)
[2026-06-08T09:13:31] Searching for fusions with spliced split reads (remaining=4446)
[2026-06-08T09:13:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=2972)
[2026-06-08T09:13:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2927)
[2026-06-08T09:13:39] Searching for fusions with >=4 spliced events (remaining=3323)
[2026-06-08T09:13:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1133)
[2026-06-08T09:13:52] Filtering fusions with anchors <=23nt (remaining=889)
[2026-06-08T09:13:53] Filtering end-to-end fusions with low support (remaining=868)
[2026-06-08T09:13:54] Filtering fusions with no coverage around the breakpoints (remaining=837)
[2026-06-08T09:13:54] Indexing gene sequences 
[2026-06-08T09:13:58] Filtering genes with >=30% identity (remaining=321)
[2026-06-08T09:14:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=152)
[2026-06-08T09:14:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=136)
[2026-06-08T09:14:04] Searching for additional isoforms (remaining=170)
[2026-06-08T09:14:06] Assigning confidence scores to events 
[2026-06-08T09:14:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:14:08] Writing fusions to file '659_eHw-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:14:10] Writing discarded fusions to file '659_eHw-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:14:37] Freeing resources
[2026-06-08T09:14:59] Done (elapsed time=00:13:09, CPU time=00:13:07, peak memory=16.7gb)