[2026-06-08T08:13:03] Launching Arriba 2.4.0
[2026-06-08T08:13:03] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:13:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:13:15] Reading chimeric alignments from '659_dm4-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=7321965)
[2026-06-08T08:16:16] Marking multi-mapping alignments (marked=5059218)
[2026-06-08T08:16:19] Detecting strandedness (reverse)
[2026-06-08T08:16:19] Assigning strands to alignments 
[2026-06-08T08:16:20] Annotating alignments 
[2026-06-08T08:16:44] Filtering duplicates (remaining=2104712)
[2026-06-08T08:16:47] 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=1905351)
[2026-06-08T08:16:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1905351)
[2026-06-08T08:16:50] Filtering viral contigs with expression lower than the top 5 (remaining=1905351)
[2026-06-08T08:16:52] Filtering viral contigs with less than 5% coverage (remaining=1905351)
[2026-06-08T08:16:54] Estimating fragment length (mate gap mean=-87.0631, mate gap stddev=27.079, read length mean=125.376)
[2026-06-08T08:16:54] Filtering read-through fragments with a distance <=10000bp (remaining=1831838)
[2026-06-08T08:16:56] Filtering inconsistently clipped mates (remaining=1794320)
[2026-06-08T08:16:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1676422)
[2026-06-08T08:16:59] Filtering fragments with small insert size (remaining=1675973)
[2026-06-08T08:17:00] Filtering alignments with long gaps (remaining=1675973)
[2026-06-08T08:17:02] Filtering fragments with both mates in the same gene (remaining=1675618)
[2026-06-08T08:17:03] Filtering fusions arising from hairpin structures (remaining=1595740)
[2026-06-08T08:17:05] Filtering reads with a mismatch p-value <=0.01 (remaining=660929)
[2026-06-08T08:17:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=215613)
[2026-06-08T08:17:14] Finding fusions and counting supporting reads (total=192503)
[2026-06-08T08:17:23] Merging adjacent fusion breakpoints (remaining=191405)
[2026-06-08T08:17:23] Filtering multi-mapping fusions by alignment score and read support (remaining=93702)
[2026-06-08T08:17:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:17:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=93025)
[2026-06-08T08:17:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=59943)
[2026-06-08T08:17:50] Filtering fusions with <2 supporting reads (remaining=5138)
[2026-06-08T08:17:50] Filtering fusions with an e-value >=0.3 (remaining=1341)
[2026-06-08T08:17:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1357)
[2026-06-08T08:17:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1281)
[2026-06-08T08:17:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1281)
[2026-06-08T08:17:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1279)
[2026-06-08T08:17:56] Searching for fusions with spliced split reads (remaining=1366)
[2026-06-08T08:17:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=1040)
[2026-06-08T08:17:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1018)
[2026-06-08T08:17:59] Searching for fusions with >=4 spliced events (remaining=1080)
[2026-06-08T08:18:00] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=306)
[2026-06-08T08:18:11] Filtering fusions with anchors <=23nt (remaining=281)
[2026-06-08T08:18:12] Filtering end-to-end fusions with low support (remaining=269)
[2026-06-08T08:18:12] Filtering fusions with no coverage around the breakpoints (remaining=257)
[2026-06-08T08:18:12] Indexing gene sequences 
[2026-06-08T08:18:14] Filtering genes with >=30% identity (remaining=102)
[2026-06-08T08:18:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=57)
[2026-06-08T08:18:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=51)
[2026-06-08T08:18:15] Searching for additional isoforms (remaining=61)
[2026-06-08T08:18:16] Assigning confidence scores to events 
[2026-06-08T08:18:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:18:17] Writing fusions to file '659_dm4-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T08:18:18] Writing discarded fusions to file '659_dm4-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:28] Freeing resources
[2026-06-08T08:18:39] Done (elapsed time=00:05:36, CPU time=00:05:35, peak memory=11.5gb)