[2026-06-08T08:30:51] Launching Arriba 2.4.0
[2026-06-08T08:30:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:03] Reading chimeric alignments from '659_bUs-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9128110)
[2026-06-08T08:37:56] Marking multi-mapping alignments (marked=5128047)
[2026-06-08T08:37:59] Detecting strandedness (reverse)
[2026-06-08T08:37:59] Assigning strands to alignments 
[2026-06-08T08:38:01] Annotating alignments 
[2026-06-08T08:38:32] Filtering duplicates (remaining=6783512)
[2026-06-08T08:38:39] 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=6544260)
[2026-06-08T08:38:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6544260)
[2026-06-08T08:38:43] Filtering viral contigs with expression lower than the top 5 (remaining=6544260)
[2026-06-08T08:38:47] Filtering viral contigs with less than 5% coverage (remaining=6544260)
[2026-06-08T08:38:50] Estimating fragment length (mate gap mean=-84.4486, mate gap stddev=32.5935, read length mean=140.521)
[2026-06-08T08:38:50] Filtering read-through fragments with a distance <=10000bp (remaining=6147682)
[2026-06-08T08:38:52] Filtering inconsistently clipped mates (remaining=6074617)
[2026-06-08T08:38:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5905474)
[2026-06-08T08:38:58] Filtering fragments with small insert size (remaining=5905056)
[2026-06-08T08:39:00] Filtering alignments with long gaps (remaining=5905055)
[2026-06-08T08:39:02] Filtering fragments with both mates in the same gene (remaining=5903391)
[2026-06-08T08:39:04] Filtering fusions arising from hairpin structures (remaining=5600997)
[2026-06-08T08:39:07] Filtering reads with a mismatch p-value <=0.01 (remaining=3267397)
[2026-06-08T08:39:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=1541561)
[2026-06-08T08:39:34] Finding fusions and counting supporting reads (total=916168)
[2026-06-08T08:39:50] Merging adjacent fusion breakpoints (remaining=909436)
[2026-06-08T08:39:51] Filtering multi-mapping fusions by alignment score and read support (remaining=624207)
[2026-06-08T08:40:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=619527)
[2026-06-08T08:40:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=337941)
[2026-06-08T08:40:29] Filtering fusions with <2 supporting reads (remaining=62474)
[2026-06-08T08:40:30] Filtering fusions with an e-value >=0.3 (remaining=23857)
[2026-06-08T08:40:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=23914)
[2026-06-08T08:40:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=23819)
[2026-06-08T08:40:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=23843)
[2026-06-08T08:40:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=14182)
[2026-06-08T08:40:41] Searching for fusions with spliced split reads (remaining=14299)
[2026-06-08T08:40:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=6221)
[2026-06-08T08:40:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=6160)
[2026-06-08T08:40:47] Searching for fusions with >=4 spliced events (remaining=7680)
[2026-06-08T08:40:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2418)
[2026-06-08T08:41:01] Filtering fusions with anchors <=23nt (remaining=1994)
[2026-06-08T08:41:02] Filtering end-to-end fusions with low support (remaining=1950)
[2026-06-08T08:41:03] Filtering fusions with no coverage around the breakpoints (remaining=1910)
[2026-06-08T08:41:03] Indexing gene sequences 
[2026-06-08T08:41:10] Filtering genes with >=30% identity (remaining=572)
[2026-06-08T08:41:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=300)
[2026-06-08T08:41:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=241)
[2026-06-08T08:41:27] Searching for additional isoforms (remaining=342)
[2026-06-08T08:41:28] Assigning confidence scores to events 
[2026-06-08T08:41:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:31] Writing fusions to file '659_bUs-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:34] Writing discarded fusions to file '659_bUs-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:04] Freeing resources
[2026-06-08T08:42:21] Done (elapsed time=00:11:30, CPU time=00:11:28, peak memory=13.8gb)