[2026-06-04T21:10:47] Launching Arriba 2.4.0
[2026-06-04T21:10:47] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:10:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:10:58] Reading chimeric alignments from '659_cfy-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10768974)
[2026-06-04T21:17:33] Marking multi-mapping alignments (marked=6512184)
[2026-06-04T21:17:37] Detecting strandedness (reverse)
[2026-06-04T21:17:37] Assigning strands to alignments 
[2026-06-04T21:17:39] Annotating alignments 
[2026-06-04T21:18:11] Filtering duplicates (remaining=7698511)
[2026-06-04T21:18:19] 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=7277464)
[2026-06-04T21:18:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7277464)
[2026-06-04T21:18:23] Filtering viral contigs with expression lower than the top 5 (remaining=7277464)
[2026-06-04T21:18:28] Filtering viral contigs with less than 5% coverage (remaining=7277464)
[2026-06-04T21:18:31] Estimating fragment length (mate gap mean=-84.7489, mate gap stddev=28.7597, read length mean=130.943)
[2026-06-04T21:18:31] Filtering read-through fragments with a distance <=10000bp (remaining=6853712)
[2026-06-04T21:18:33] Filtering inconsistently clipped mates (remaining=6747230)
[2026-06-04T21:18:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6558608)
[2026-06-04T21:18:40] Filtering fragments with small insert size (remaining=6557403)
[2026-06-04T21:18:42] Filtering alignments with long gaps (remaining=6557403)
[2026-06-04T21:18:44] Filtering fragments with both mates in the same gene (remaining=6556343)
[2026-06-04T21:18:47] Filtering fusions arising from hairpin structures (remaining=6181904)
[2026-06-04T21:18:49] Filtering reads with a mismatch p-value <=0.01 (remaining=3363715)
[2026-06-04T21:19:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=1312290)
[2026-06-04T21:19:17] Finding fusions and counting supporting reads (total=991846)
[2026-06-04T21:19:34] Merging adjacent fusion breakpoints (remaining=984442)
[2026-06-04T21:19:36] Filtering multi-mapping fusions by alignment score and read support (remaining=637417)
[2026-06-04T21:20:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:20:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=635918)
[2026-06-04T21:20:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=386386)
[2026-06-04T21:20:17] Filtering fusions with <2 supporting reads (remaining=41866)
[2026-06-04T21:20:18] Filtering fusions with an e-value >=0.3 (remaining=10149)
[2026-06-04T21:20:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10205)
[2026-06-04T21:20:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10128)
[2026-06-04T21:20:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10211)
[2026-06-04T21:20:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7580)
[2026-06-04T21:20:32] Searching for fusions with spliced split reads (remaining=7714)
[2026-06-04T21:20:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=4777)
[2026-06-04T21:20:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4731)
[2026-06-04T21:20:40] Searching for fusions with >=4 spliced events (remaining=5838)
[2026-06-04T21:20:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2270)
[2026-06-04T21:20:55] Filtering fusions with anchors <=23nt (remaining=1767)
[2026-06-04T21:20:56] Filtering end-to-end fusions with low support (remaining=1737)
[2026-06-04T21:20:56] Filtering fusions with no coverage around the breakpoints (remaining=1702)
[2026-06-04T21:20:57] Indexing gene sequences 
[2026-06-04T21:21:03] Filtering genes with >=30% identity (remaining=524)
[2026-06-04T21:21:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=230)
[2026-06-04T21:21:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=190)
[2026-06-04T21:21:12] Searching for additional isoforms (remaining=242)
[2026-06-04T21:21:14] Assigning confidence scores to events 
[2026-06-04T21:21:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:21:18] Writing fusions to file '659_cfy-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:21:20] Writing discarded fusions to file '659_cfy-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:21:51] Freeing resources
[2026-06-04T21:22:11] Done (elapsed time=00:11:24, CPU time=00:11:22, peak memory=15.4gb)