[2026-06-08T08:39:47] Launching Arriba 2.4.0
[2026-06-08T08:39:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:58] Reading chimeric alignments from '659_wQ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11382975)
[2026-06-08T08:47:16] Marking multi-mapping alignments (marked=7065772)
[2026-06-08T08:47:21] Detecting strandedness (reverse)
[2026-06-08T08:47:21] Assigning strands to alignments 
[2026-06-08T08:47:24] Annotating alignments 
[2026-06-08T08:48:03] Filtering duplicates (remaining=5238904)
[2026-06-08T08:48:10] 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=4938330)
[2026-06-08T08:48:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4938330)
[2026-06-08T08:48:15] Filtering viral contigs with expression lower than the top 5 (remaining=4938330)
[2026-06-08T08:48:21] Filtering viral contigs with less than 5% coverage (remaining=4938330)
[2026-06-08T08:48:24] Estimating fragment length (mate gap mean=-85.2701, mate gap stddev=30.1094, read length mean=132.406)
[2026-06-08T08:48:24] Filtering read-through fragments with a distance <=10000bp (remaining=4747062)
[2026-06-08T08:48:26] Filtering inconsistently clipped mates (remaining=4651261)
[2026-06-08T08:48:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4503534)
[2026-06-08T08:48:34] Filtering fragments with small insert size (remaining=4502252)
[2026-06-08T08:48:36] Filtering alignments with long gaps (remaining=4502252)
[2026-06-08T08:48:39] Filtering fragments with both mates in the same gene (remaining=4501259)
[2026-06-08T08:48:41] Filtering fusions arising from hairpin structures (remaining=4168281)
[2026-06-08T08:48:44] Filtering reads with a mismatch p-value <=0.01 (remaining=1990299)
[2026-06-08T08:48:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=588750)
[2026-06-08T08:49:06] Finding fusions and counting supporting reads (total=423929)
[2026-06-08T08:49:23] Merging adjacent fusion breakpoints (remaining=419808)
[2026-06-08T08:49:25] Filtering multi-mapping fusions by alignment score and read support (remaining=276826)
[2026-06-08T08:50:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=274863)
[2026-06-08T08:50:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=147302)
[2026-06-08T08:50:09] Filtering fusions with <2 supporting reads (remaining=21683)
[2026-06-08T08:50:10] Filtering fusions with an e-value >=0.3 (remaining=6832)
[2026-06-08T08:50:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6887)
[2026-06-08T08:50:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6804)
[2026-06-08T08:50:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6804)
[2026-06-08T08:50:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4634)
[2026-06-08T08:50:21] Searching for fusions with spliced split reads (remaining=4754)
[2026-06-08T08:50:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=3116)
[2026-06-08T08:50:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3067)
[2026-06-08T08:50:28] Searching for fusions with >=4 spliced events (remaining=3449)
[2026-06-08T08:50:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1157)
[2026-06-08T08:50:43] Filtering fusions with anchors <=23nt (remaining=868)
[2026-06-08T08:50:44] Filtering end-to-end fusions with low support (remaining=843)
[2026-06-08T08:50:44] Filtering fusions with no coverage around the breakpoints (remaining=825)
[2026-06-08T08:50:45] Indexing gene sequences 
[2026-06-08T08:50:50] Filtering genes with >=30% identity (remaining=350)
[2026-06-08T08:50:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=227)
[2026-06-08T08:51:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-06-08T08:51:01] Searching for additional isoforms (remaining=257)
[2026-06-08T08:51:02] Assigning confidence scores to events 
[2026-06-08T08:51:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:05] Writing fusions to file '659_wQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:07] Writing discarded fusions to file '659_wQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:31] Freeing resources
[2026-06-08T08:51:51] Done (elapsed time=00:12:04, CPU time=00:12:03, peak memory=15.7gb)