[2026-06-04T20:46:12] Launching Arriba 2.4.0
[2026-06-04T20:46:12] Loading assembly from 'ref_genome.fa' 
[2026-06-04T20:46:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T20:46:23] Reading chimeric alignments from '659_dcz-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=7738391)
[2026-06-04T20:49:45] Marking multi-mapping alignments (marked=5437236)
[2026-06-04T20:49:48] Detecting strandedness (reverse)
[2026-06-04T20:49:48] Assigning strands to alignments 
[2026-06-04T20:49:50] Annotating alignments 
[2026-06-04T20:50:12] Filtering duplicates (remaining=2280041)
[2026-06-04T20:50:15] 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=2100511)
[2026-06-04T20:50:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2100511)
[2026-06-04T20:50:18] Filtering viral contigs with expression lower than the top 5 (remaining=2100511)
[2026-06-04T20:50:21] Filtering viral contigs with less than 5% coverage (remaining=2100511)
[2026-06-04T20:50:22] Estimating fragment length (mate gap mean=-81.6464, mate gap stddev=26.7723, read length mean=116.185)
[2026-06-04T20:50:22] Filtering read-through fragments with a distance <=10000bp (remaining=2031950)
[2026-06-04T20:50:24] Filtering inconsistently clipped mates (remaining=1976481)
[2026-06-04T20:50:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1855529)
[2026-06-04T20:50:27] Filtering fragments with small insert size (remaining=1854489)
[2026-06-04T20:50:29] Filtering alignments with long gaps (remaining=1854489)
[2026-06-04T20:50:30] Filtering fragments with both mates in the same gene (remaining=1853891)
[2026-06-04T20:50:31] Filtering fusions arising from hairpin structures (remaining=1738264)
[2026-06-04T20:50:33] Filtering reads with a mismatch p-value <=0.01 (remaining=634861)
[2026-06-04T20:50:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=234178)
[2026-06-04T20:50:42] Finding fusions and counting supporting reads (total=208433)
[2026-06-04T20:50:51] Merging adjacent fusion breakpoints (remaining=206846)
[2026-06-04T20:50:51] Filtering multi-mapping fusions by alignment score and read support (remaining=104344)
[2026-06-04T20:51:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T20:51:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=103673)
[2026-06-04T20:51:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=68598)
[2026-06-04T20:51:15] Filtering fusions with <2 supporting reads (remaining=5018)
[2026-06-04T20:51:15] Filtering fusions with an e-value >=0.3 (remaining=1275)
[2026-06-04T20:51:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1311)
[2026-06-04T20:51:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1262)
[2026-06-04T20:51:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1266)
[2026-06-04T20:51:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1260)
[2026-06-04T20:51:21] Searching for fusions with spliced split reads (remaining=1342)
[2026-06-04T20:51:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=1062)
[2026-06-04T20:51:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1039)
[2026-06-04T20:51:24] Searching for fusions with >=4 spliced events (remaining=1077)
[2026-06-04T20:51:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=379)
[2026-06-04T20:51:35] Filtering fusions with anchors <=23nt (remaining=324)
[2026-06-04T20:51:35] Filtering end-to-end fusions with low support (remaining=291)
[2026-06-04T20:51:36] Filtering fusions with no coverage around the breakpoints (remaining=283)
[2026-06-04T20:51:36] Indexing gene sequences 
[2026-06-04T20:51:38] Filtering genes with >=30% identity (remaining=138)
[2026-06-04T20:51:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=83)
[2026-06-04T20:51:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=83)
[2026-06-04T20:51:39] Searching for additional isoforms (remaining=94)
[2026-06-04T20:51:40] Assigning confidence scores to events 
[2026-06-04T20:51:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T20:51:41] Writing fusions to file '659_dcz-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T20:51:42] Writing discarded fusions to file '659_dcz-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T20:51:52] Freeing resources
[2026-06-04T20:52:02] Done (elapsed time=00:05:50, CPU time=00:05:49, peak memory=12gb)