[2026-06-08T08:02:29] Launching Arriba 2.4.0
[2026-06-08T08:02:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:02:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:02:50] Reading chimeric alignments from '659_dm4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=7904425)
[2026-06-08T08:08:46] Marking multi-mapping alignments (marked=5534888)
[2026-06-08T08:08:49] Detecting strandedness (reverse)
[2026-06-08T08:08:49] Assigning strands to alignments 
[2026-06-08T08:08:51] Annotating alignments 
[2026-06-08T08:09:16] Filtering duplicates (remaining=2732246)
[2026-06-08T08:09:20] 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=2472673)
[2026-06-08T08:09:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2472673)
[2026-06-08T08:09:23] Filtering viral contigs with expression lower than the top 5 (remaining=2472673)
[2026-06-08T08:09:26] Filtering viral contigs with less than 5% coverage (remaining=2472673)
[2026-06-08T08:09:28] Estimating fragment length (mate gap mean=-83.9333, mate gap stddev=27.0825, read length mean=118.84)
[2026-06-08T08:09:28] Filtering read-through fragments with a distance <=10000bp (remaining=2385208)
[2026-06-08T08:09:30] Filtering inconsistently clipped mates (remaining=2329557)
[2026-06-08T08:09:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2180584)
[2026-06-08T08:09:34] Filtering fragments with small insert size (remaining=2179905)
[2026-06-08T08:09:35] Filtering alignments with long gaps (remaining=2179905)
[2026-06-08T08:09:37] Filtering fragments with both mates in the same gene (remaining=2179305)
[2026-06-08T08:09:38] Filtering fusions arising from hairpin structures (remaining=2056019)
[2026-06-08T08:09:40] Filtering reads with a mismatch p-value <=0.01 (remaining=839838)
[2026-06-08T08:09:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=316679)
[2026-06-08T08:09:53] Finding fusions and counting supporting reads (total=246659)
[2026-06-08T08:10:03] Merging adjacent fusion breakpoints (remaining=244757)
[2026-06-08T08:10:03] Filtering multi-mapping fusions by alignment score and read support (remaining=133745)
[2026-06-08T08:10:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:10:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=132975)
[2026-06-08T08:10:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=85789)
[2026-06-08T08:10:32] Filtering fusions with <2 supporting reads (remaining=9323)
[2026-06-08T08:10:32] Filtering fusions with an e-value >=0.3 (remaining=2169)
[2026-06-08T08:10:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2198)
[2026-06-08T08:10:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2111)
[2026-06-08T08:10:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2112)
[2026-06-08T08:10:35] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2109)
[2026-06-08T08:10:38] Searching for fusions with spliced split reads (remaining=2214)
[2026-06-08T08:10:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=1690)
[2026-06-08T08:10:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1667)
[2026-06-08T08:10:42] Searching for fusions with >=4 spliced events (remaining=1781)
[2026-06-08T08:10:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=539)
[2026-06-08T08:10:57] Filtering fusions with anchors <=23nt (remaining=441)
[2026-06-08T08:10:57] Filtering end-to-end fusions with low support (remaining=415)
[2026-06-08T08:10:57] Filtering fusions with no coverage around the breakpoints (remaining=403)
[2026-06-08T08:10:58] Indexing gene sequences 
[2026-06-08T08:11:00] Filtering genes with >=30% identity (remaining=159)
[2026-06-08T08:11:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=91)
[2026-06-08T08:11:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=85)
[2026-06-08T08:11:03] Searching for additional isoforms (remaining=102)
[2026-06-08T08:11:04] Assigning confidence scores to events 
[2026-06-08T08:11:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:11:06] Writing fusions to file '659_dm4-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:11:06] Writing discarded fusions to file '659_dm4-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:11:22] Freeing resources
[2026-06-08T08:11:34] Done (elapsed time=00:09:05, CPU time=00:09:04, peak memory=12.2gb)