[2026-06-08T08:24:48] Launching Arriba 2.4.0
[2026-06-08T08:24:48] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:00] Reading chimeric alignments from '659_cAd-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10740028)
[2026-06-08T08:31:27] Marking multi-mapping alignments (marked=7007694)
[2026-06-08T08:31:31] Detecting strandedness (reverse)
[2026-06-08T08:31:31] Assigning strands to alignments 
[2026-06-08T08:31:33] Annotating alignments 
[2026-06-08T08:32:07] Filtering duplicates (remaining=6008377)
[2026-06-08T08:32:14] 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=5627043)
[2026-06-08T08:32:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5627043)
[2026-06-08T08:32:18] Filtering viral contigs with expression lower than the top 5 (remaining=5627043)
[2026-06-08T08:32:22] Filtering viral contigs with less than 5% coverage (remaining=5627043)
[2026-06-08T08:32:25] Estimating fragment length (mate gap mean=-86.3491, mate gap stddev=27.9744, read length mean=124.449)
[2026-06-08T08:32:25] Filtering read-through fragments with a distance <=10000bp (remaining=5287041)
[2026-06-08T08:32:27] Filtering inconsistently clipped mates (remaining=5181238)
[2026-06-08T08:32:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5036324)
[2026-06-08T08:32:33] Filtering fragments with small insert size (remaining=5035454)
[2026-06-08T08:32:35] Filtering alignments with long gaps (remaining=5035454)
[2026-06-08T08:32:37] Filtering fragments with both mates in the same gene (remaining=5034476)
[2026-06-08T08:32:39] Filtering fusions arising from hairpin structures (remaining=4731304)
[2026-06-08T08:32:41] Filtering reads with a mismatch p-value <=0.01 (remaining=2272465)
[2026-06-08T08:32:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=979437)
[2026-06-08T08:33:03] Finding fusions and counting supporting reads (total=711851)
[2026-06-08T08:33:19] Merging adjacent fusion breakpoints (remaining=702973)
[2026-06-08T08:33:21] Filtering multi-mapping fusions by alignment score and read support (remaining=430074)
[2026-06-08T08:33:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=428891)
[2026-06-08T08:34:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=240686)
[2026-06-08T08:34:01] Filtering fusions with <2 supporting reads (remaining=29472)
[2026-06-08T08:34:02] Filtering fusions with an e-value >=0.3 (remaining=6709)
[2026-06-08T08:34:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6761)
[2026-06-08T08:34:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6650)
[2026-06-08T08:34:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6652)
[2026-06-08T08:34:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6278)
[2026-06-08T08:34:13] Searching for fusions with spliced split reads (remaining=6370)
[2026-06-08T08:34:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=4346)
[2026-06-08T08:34:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4312)
[2026-06-08T08:34:19] Searching for fusions with >=4 spliced events (remaining=5057)
[2026-06-08T08:34:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1871)
[2026-06-08T08:34:34] Filtering fusions with anchors <=23nt (remaining=1478)
[2026-06-08T08:34:35] Filtering end-to-end fusions with low support (remaining=1446)
[2026-06-08T08:34:36] Filtering fusions with no coverage around the breakpoints (remaining=1407)
[2026-06-08T08:34:36] Indexing gene sequences 
[2026-06-08T08:34:42] Filtering genes with >=30% identity (remaining=463)
[2026-06-08T08:34:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=197)
[2026-06-08T08:34:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=164)
[2026-06-08T08:34:49] Searching for additional isoforms (remaining=215)
[2026-06-08T08:34:50] Assigning confidence scores to events 
[2026-06-08T08:34:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:54] Writing fusions to file '659_cAd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:57] Writing discarded fusions to file '659_cAd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:25] Freeing resources
[2026-06-08T08:35:43] Done (elapsed time=00:10:55, CPU time=00:10:54, peak memory=15.3gb)