[2026-06-08T08:48:32] Launching Arriba 2.4.0
[2026-06-08T08:48:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:46] Reading chimeric alignments from '659_rd-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10049731)
[2026-06-08T08:55:41] Marking multi-mapping alignments (marked=5901263)
[2026-06-08T08:55:45] Detecting strandedness (reverse)
[2026-06-08T08:55:45] Assigning strands to alignments 
[2026-06-08T08:55:48] Annotating alignments 
[2026-06-08T08:56:23] Filtering duplicates (remaining=4873346)
[2026-06-08T08:56:30] 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=4658447)
[2026-06-08T08:56:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4658447)
[2026-06-08T08:56:34] Filtering viral contigs with expression lower than the top 5 (remaining=4658447)
[2026-06-08T08:56:39] Filtering viral contigs with less than 5% coverage (remaining=4658447)
[2026-06-08T08:56:41] Estimating fragment length (mate gap mean=-86.5976, mate gap stddev=30.6716, read length mean=138.123)
[2026-06-08T08:56:41] Filtering read-through fragments with a distance <=10000bp (remaining=4362696)
[2026-06-08T08:56:43] Filtering inconsistently clipped mates (remaining=4305305)
[2026-06-08T08:56:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4148670)
[2026-06-08T08:56:50] Filtering fragments with small insert size (remaining=4148211)
[2026-06-08T08:56:52] Filtering alignments with long gaps (remaining=4148211)
[2026-06-08T08:56:54] Filtering fragments with both mates in the same gene (remaining=4147389)
[2026-06-08T08:56:56] Filtering fusions arising from hairpin structures (remaining=3946039)
[2026-06-08T08:56:58] Filtering reads with a mismatch p-value <=0.01 (remaining=1824438)
[2026-06-08T08:57:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=805519)
[2026-06-08T08:57:19] Finding fusions and counting supporting reads (total=568428)
[2026-06-08T08:57:35] Merging adjacent fusion breakpoints (remaining=563688)
[2026-06-08T08:57:36] Filtering multi-mapping fusions by alignment score and read support (remaining=371810)
[2026-06-08T08:58:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=368900)
[2026-06-08T08:58:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=191597)
[2026-06-08T08:58:16] Filtering fusions with <2 supporting reads (remaining=34212)
[2026-06-08T08:58:17] Filtering fusions with an e-value >=0.3 (remaining=11978)
[2026-06-08T08:58:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12008)
[2026-06-08T08:58:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11943)
[2026-06-08T08:58:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11964)
[2026-06-08T08:58:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7918)
[2026-06-08T08:58:27] Searching for fusions with spliced split reads (remaining=8067)
[2026-06-08T08:58:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=4515)
[2026-06-08T08:58:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4452)
[2026-06-08T08:58:33] Searching for fusions with >=4 spliced events (remaining=5377)
[2026-06-08T08:58:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1616)
[2026-06-08T08:58:47] Filtering fusions with anchors <=23nt (remaining=1359)
[2026-06-08T08:58:48] Filtering end-to-end fusions with low support (remaining=1315)
[2026-06-08T08:58:49] Filtering fusions with no coverage around the breakpoints (remaining=1281)
[2026-06-08T08:58:49] Indexing gene sequences 
[2026-06-08T08:58:55] Filtering genes with >=30% identity (remaining=394)
[2026-06-08T08:58:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=230)
[2026-06-08T08:59:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-06-08T08:59:10] Searching for additional isoforms (remaining=266)
[2026-06-08T08:59:11] Assigning confidence scores to events 
[2026-06-08T08:59:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:13] Writing fusions to file '659_rd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:15] Writing discarded fusions to file '659_rd-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:39] Freeing resources
[2026-06-08T08:59:56] Done (elapsed time=00:11:24, CPU time=00:11:22, peak memory=14.6gb)