[2026-06-04T21:07:40] Launching Arriba 2.4.0
[2026-06-04T21:07:40] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:07:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:07:51] Reading chimeric alignments from '659_ciZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10536974)
[2026-06-04T21:13:47] Marking multi-mapping alignments (marked=6868185)
[2026-06-04T21:13:51] Detecting strandedness (reverse)
[2026-06-04T21:13:51] Assigning strands to alignments 
[2026-06-04T21:13:53] Annotating alignments 
[2026-06-04T21:14:23] Filtering duplicates (remaining=4916214)
[2026-06-04T21:14:28] 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=4604078)
[2026-06-04T21:14:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4604078)
[2026-06-04T21:14:32] Filtering viral contigs with expression lower than the top 5 (remaining=4604078)
[2026-06-04T21:14:36] Filtering viral contigs with less than 5% coverage (remaining=4604078)
[2026-06-04T21:14:38] Estimating fragment length (mate gap mean=-88.4687, mate gap stddev=26.4914, read length mean=127.001)
[2026-06-04T21:14:38] Filtering read-through fragments with a distance <=10000bp (remaining=4295746)
[2026-06-04T21:14:40] Filtering inconsistently clipped mates (remaining=4223834)
[2026-06-04T21:14:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4068980)
[2026-06-04T21:14:46] Filtering fragments with small insert size (remaining=4068284)
[2026-06-04T21:14:48] Filtering alignments with long gaps (remaining=4068284)
[2026-06-04T21:14:50] Filtering fragments with both mates in the same gene (remaining=4067430)
[2026-06-04T21:14:52] Filtering fusions arising from hairpin structures (remaining=3871154)
[2026-06-04T21:14:54] Filtering reads with a mismatch p-value <=0.01 (remaining=1824368)
[2026-06-04T21:15:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=806343)
[2026-06-04T21:15:11] Finding fusions and counting supporting reads (total=609604)
[2026-06-04T21:15:25] Merging adjacent fusion breakpoints (remaining=602497)
[2026-06-04T21:15:26] Filtering multi-mapping fusions by alignment score and read support (remaining=350450)
[2026-06-04T21:15:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:16:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=349413)
[2026-06-04T21:16:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=193323)
[2026-06-04T21:16:01] Filtering fusions with <2 supporting reads (remaining=24545)
[2026-06-04T21:16:02] Filtering fusions with an e-value >=0.3 (remaining=5617)
[2026-06-04T21:16:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5653)
[2026-06-04T21:16:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5545)
[2026-06-04T21:16:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5545)
[2026-06-04T21:16:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5453)
[2026-06-04T21:16:12] Searching for fusions with spliced split reads (remaining=5507)
[2026-06-04T21:16:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=3731)
[2026-06-04T21:16:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3710)
[2026-06-04T21:16:18] Searching for fusions with >=4 spliced events (remaining=4245)
[2026-06-04T21:16:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1530)
[2026-06-04T21:16:33] Filtering fusions with anchors <=23nt (remaining=1203)
[2026-06-04T21:16:34] Filtering end-to-end fusions with low support (remaining=1172)
[2026-06-04T21:16:35] Filtering fusions with no coverage around the breakpoints (remaining=1142)
[2026-06-04T21:16:35] Indexing gene sequences 
[2026-06-04T21:16:41] Filtering genes with >=30% identity (remaining=339)
[2026-06-04T21:16:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=115)
[2026-06-04T21:16:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=98)
[2026-06-04T21:16:45] Searching for additional isoforms (remaining=122)
[2026-06-04T21:16:47] Assigning confidence scores to events 
[2026-06-04T21:16:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:16:50] Writing fusions to file '659_ciZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:16:51] Writing discarded fusions to file '659_ciZ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:17:19] Freeing resources
[2026-06-04T21:17:40] Done (elapsed time=00:10:00, CPU time=00:09:59, peak memory=15.1gb)