[2026-06-08T07:48:49] Launching Arriba 2.4.0
[2026-06-08T07:48:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:49:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:49:14] Reading chimeric alignments from '659_dm4-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=4999782)
[2026-06-08T07:53:08] Marking multi-mapping alignments (marked=3578650)
[2026-06-08T07:53:11] Detecting strandedness (reverse)
[2026-06-08T07:53:11] Assigning strands to alignments 
[2026-06-08T07:53:12] Annotating alignments 
[2026-06-08T07:53:35] Filtering duplicates (remaining=1152240)
[2026-06-08T07:53:39] 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=1010047)
[2026-06-08T07:53:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1010047)
[2026-06-08T07:53:41] Filtering viral contigs with expression lower than the top 5 (remaining=1010047)
[2026-06-08T07:53:43] Filtering viral contigs with less than 5% coverage (remaining=1010047)
[2026-06-08T07:53:45] Estimating fragment length (mate gap mean=-82.0731, mate gap stddev=27.1499, read length mean=118.151)
[2026-06-08T07:53:45] Filtering read-through fragments with a distance <=10000bp (remaining=974383)
[2026-06-08T07:53:46] Filtering inconsistently clipped mates (remaining=948680)
[2026-06-08T07:53:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=882947)
[2026-06-08T07:53:49] Filtering fragments with small insert size (remaining=882665)
[2026-06-08T07:53:50] Filtering alignments with long gaps (remaining=882665)
[2026-06-08T07:53:51] Filtering fragments with both mates in the same gene (remaining=882344)
[2026-06-08T07:53:52] Filtering fusions arising from hairpin structures (remaining=839903)
[2026-06-08T07:53:54] Filtering reads with a mismatch p-value <=0.01 (remaining=286671)
[2026-06-08T07:53:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=114130)
[2026-06-08T07:54:01] Finding fusions and counting supporting reads (total=106441)
[2026-06-08T07:54:10] Merging adjacent fusion breakpoints (remaining=105888)
[2026-06-08T07:54:10] Filtering multi-mapping fusions by alignment score and read support (remaining=50430)
[2026-06-08T07:54:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:54:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=49962)
[2026-06-08T07:54:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=33577)
[2026-06-08T07:54:33] Filtering fusions with <2 supporting reads (remaining=2196)
[2026-06-08T07:54:33] Filtering fusions with an e-value >=0.3 (remaining=601)
[2026-06-08T07:54:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=609)
[2026-06-08T07:54:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=567)
[2026-06-08T07:54:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=567)
[2026-06-08T07:54:35] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=556)
[2026-06-08T07:54:38] Searching for fusions with spliced split reads (remaining=597)
[2026-06-08T07:54:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=496)
[2026-06-08T07:54:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=491)
[2026-06-08T07:54:41] Searching for fusions with >=4 spliced events (remaining=512)
[2026-06-08T07:54:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=149)
[2026-06-08T07:55:01] Filtering fusions with anchors <=23nt (remaining=134)
[2026-06-08T07:55:01] Filtering end-to-end fusions with low support (remaining=127)
[2026-06-08T07:55:01] Filtering fusions with no coverage around the breakpoints (remaining=121)
[2026-06-08T07:55:01] Indexing gene sequences 
[2026-06-08T07:55:03] Filtering genes with >=30% identity (remaining=52)
[2026-06-08T07:55:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=33)
[2026-06-08T07:55:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=29)
[2026-06-08T07:55:04] Searching for additional isoforms (remaining=34)
[2026-06-08T07:55:04] Assigning confidence scores to events 
[2026-06-08T07:55:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:55:05] Writing fusions to file '659_dm4-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:55:06] Writing discarded fusions to file '659_dm4-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:55:15] Freeing resources
[2026-06-08T07:55:27] Done (elapsed time=00:06:38, CPU time=00:06:37, peak memory=9.18gb)