[2026-06-04T21:09:39] Launching Arriba 2.4.0
[2026-06-04T21:09:39] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:09:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:09:51] Reading chimeric alignments from '659_cAd-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10740028)
[2026-06-04T21:16:15] Marking multi-mapping alignments (marked=7007694)
[2026-06-04T21:16:19] Detecting strandedness (reverse)
[2026-06-04T21:16:19] Assigning strands to alignments 
[2026-06-04T21:16:21] Annotating alignments 
[2026-06-04T21:16:54] Filtering duplicates (remaining=6008377)
[2026-06-04T21:17:01] 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)
[2026-06-04T21:17:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5627043)
[2026-06-04T21:17:05] Filtering viral contigs with expression lower than the top 5 (remaining=5627043)
[2026-06-04T21:17:10] Filtering viral contigs with less than 5% coverage (remaining=5627043)
[2026-06-04T21:17:12] Estimating fragment length (mate gap mean=-86.3491, mate gap stddev=27.9744, read length mean=124.449)
[2026-06-04T21:17:12] Filtering read-through fragments with a distance <=10000bp (remaining=5287041)
[2026-06-04T21:17:15] Filtering inconsistently clipped mates (remaining=5181238)
[2026-06-04T21:17:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5036324)
[2026-06-04T21:17:21] Filtering fragments with small insert size (remaining=5035454)
[2026-06-04T21:17:23] Filtering alignments with long gaps (remaining=5035454)
[2026-06-04T21:17:25] Filtering fragments with both mates in the same gene (remaining=5034476)
[2026-06-04T21:17:27] Filtering fusions arising from hairpin structures (remaining=4731304)
[2026-06-04T21:17:30] Filtering reads with a mismatch p-value <=0.01 (remaining=2272465)
[2026-06-04T21:17:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=979437)
[2026-06-04T21:17:52] Finding fusions and counting supporting reads (total=711851)
[2026-06-04T21:18:07] Merging adjacent fusion breakpoints (remaining=702973)
[2026-06-04T21:18:08] Filtering multi-mapping fusions by alignment score and read support (remaining=430074)
[2026-06-04T21:18:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:18:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=428891)
[2026-06-04T21:18:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=240686)
[2026-06-04T21:18:47] Filtering fusions with <2 supporting reads (remaining=29472)
[2026-06-04T21:18:48] Filtering fusions with an e-value >=0.3 (remaining=6709)
[2026-06-04T21:18:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6761)
[2026-06-04T21:18:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6650)
[2026-06-04T21:18:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6652)
[2026-06-04T21:18:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6278)
[2026-06-04T21:18:59] Searching for fusions with spliced split reads (remaining=6370)
[2026-06-04T21:19:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=4346)
[2026-06-04T21:19:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4312)
[2026-06-04T21:19:06] Searching for fusions with >=4 spliced events (remaining=5057)
[2026-06-04T21:19:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1871)
[2026-06-04T21:19:21] Filtering fusions with anchors <=23nt (remaining=1478)
[2026-06-04T21:19:21] Filtering end-to-end fusions with low support (remaining=1446)
[2026-06-04T21:19:22] Filtering fusions with no coverage around the breakpoints (remaining=1407)
[2026-06-04T21:19:23] Indexing gene sequences 
[2026-06-04T21:19:29] Filtering genes with >=30% identity (remaining=463)
[2026-06-04T21:19:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=197)
[2026-06-04T21:19:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=164)
[2026-06-04T21:19:35] Searching for additional isoforms (remaining=215)
[2026-06-04T21:19:36] Assigning confidence scores to events 
[2026-06-04T21:19:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:19:39] Writing fusions to file '659_cAd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:19:41] Writing discarded fusions to file '659_cAd-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:20:05] Freeing resources
[2026-06-04T21:20:22] Done (elapsed time=00:10:43, CPU time=00:10:42, peak memory=15.4gb)