[2026-06-04T20:50:12] Launching Arriba 2.4.0
[2026-06-04T20:50:12] Loading assembly from 'ref_genome.fa' 
[2026-06-04T20:50:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T20:50:23] Reading chimeric alignments from '659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=8410226)
[2026-06-04T20:53:49] Marking multi-mapping alignments (marked=6135998)
[2026-06-04T20:53:52] Detecting strandedness (reverse)
[2026-06-04T20:53:52] Assigning strands to alignments 
[2026-06-04T20:53:54] Annotating alignments 
[2026-06-04T20:54:16] Filtering duplicates (remaining=2016069)
[2026-06-04T20:54:20] 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=1734091)
[2026-06-04T20:54:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1734091)
[2026-06-04T20:54:22] Filtering viral contigs with expression lower than the top 5 (remaining=1734091)
[2026-06-04T20:54:25] Filtering viral contigs with less than 5% coverage (remaining=1734091)
[2026-06-04T20:54:27] Estimating fragment length (mate gap mean=-81.7277, mate gap stddev=27.8002, read length mean=116.425)
[2026-06-04T20:54:27] Filtering read-through fragments with a distance <=10000bp (remaining=1679830)
[2026-06-04T20:54:29] Filtering inconsistently clipped mates (remaining=1635325)
[2026-06-04T20:54:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1487696)
[2026-06-04T20:54:32] Filtering fragments with small insert size (remaining=1486912)
[2026-06-04T20:54:33] Filtering alignments with long gaps (remaining=1486912)
[2026-06-04T20:54:35] Filtering fragments with both mates in the same gene (remaining=1486366)
[2026-06-04T20:54:36] Filtering fusions arising from hairpin structures (remaining=1396921)
[2026-06-04T20:54:38] Filtering reads with a mismatch p-value <=0.01 (remaining=503471)
[2026-06-04T20:54:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=177123)
[2026-06-04T20:54:45] Finding fusions and counting supporting reads (total=149681)
[2026-06-04T20:54:54] Merging adjacent fusion breakpoints (remaining=148606)
[2026-06-04T20:54:54] Filtering multi-mapping fusions by alignment score and read support (remaining=72726)
[2026-06-04T20:55:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T20:55:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=72081)
[2026-06-04T20:55:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=47235)
[2026-06-04T20:55:17] Filtering fusions with <2 supporting reads (remaining=3400)
[2026-06-04T20:55:17] Filtering fusions with an e-value >=0.3 (remaining=800)
[2026-06-04T20:55:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=811)
[2026-06-04T20:55:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=754)
[2026-06-04T20:55:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=754)
[2026-06-04T20:55:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=750)
[2026-06-04T20:55:23] Searching for fusions with spliced split reads (remaining=785)
[2026-06-04T20:55:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=623)
[2026-06-04T20:55:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=612)
[2026-06-04T20:55:26] Searching for fusions with >=4 spliced events (remaining=639)
[2026-06-04T20:55:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=199)
[2026-06-04T20:55:37] Filtering fusions with anchors <=23nt (remaining=158)
[2026-06-04T20:55:37] Filtering end-to-end fusions with low support (remaining=149)
[2026-06-04T20:55:37] Filtering fusions with no coverage around the breakpoints (remaining=138)
[2026-06-04T20:55:37] Indexing gene sequences 
[2026-06-04T20:55:39] Filtering genes with >=30% identity (remaining=69)
[2026-06-04T20:55:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=30)
[2026-06-04T20:55:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=27)
[2026-06-04T20:55:40] Searching for additional isoforms (remaining=33)
[2026-06-04T20:55:40] Assigning confidence scores to events 
[2026-06-04T20:55:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T20:55:41] Writing fusions to file '659_bMa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T20:55:42] Writing discarded fusions to file '659_bMa-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T20:55:49] Freeing resources
[2026-06-04T20:56:00] Done (elapsed time=00:05:48, CPU time=00:05:48, peak memory=12.7gb)