[2026-06-08T08:58:33] Launching Arriba 2.4.0
[2026-06-08T08:58:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:46] Reading chimeric alignments from '659_c95-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=11429508)
[2026-06-08T09:06:13] Marking multi-mapping alignments (marked=6983990)
[2026-06-08T09:06:18] Detecting strandedness (reverse)
[2026-06-08T09:06:18] Assigning strands to alignments 
[2026-06-08T09:06:20] Annotating alignments 
[2026-06-08T09:06:59] Filtering duplicates (remaining=7601673)
[2026-06-08T09:07:08] 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=7414102)
[2026-06-08T09:07:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7414102)
[2026-06-08T09:07:12] Filtering viral contigs with expression lower than the top 5 (remaining=7414102)
[2026-06-08T09:07:18] Filtering viral contigs with less than 5% coverage (remaining=7414102)
[2026-06-08T09:07:20] Estimating fragment length (mate gap mean=-88.6961, mate gap stddev=29.703, read length mean=138.945)
[2026-06-08T09:07:20] Filtering read-through fragments with a distance <=10000bp (remaining=6921868)
[2026-06-08T09:07:23] Filtering inconsistently clipped mates (remaining=6826703)
[2026-06-08T09:07:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6632748)
[2026-06-08T09:07:30] Filtering fragments with small insert size (remaining=6632135)
[2026-06-08T09:07:32] Filtering alignments with long gaps (remaining=6632135)
[2026-06-08T09:07:35] Filtering fragments with both mates in the same gene (remaining=6631083)
[2026-06-08T09:07:37] Filtering fusions arising from hairpin structures (remaining=6262424)
[2026-06-08T09:07:40] Filtering reads with a mismatch p-value <=0.01 (remaining=3359678)
[2026-06-08T09:07:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=1327578)
[2026-06-08T09:08:12] Finding fusions and counting supporting reads (total=976980)
[2026-06-08T09:08:31] Merging adjacent fusion breakpoints (remaining=967422)
[2026-06-08T09:08:33] Filtering multi-mapping fusions by alignment score and read support (remaining=607647)
[2026-06-08T09:09:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:09:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=603962)
[2026-06-08T09:09:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=329048)
[2026-06-08T09:09:22] Filtering fusions with <2 supporting reads (remaining=48455)
[2026-06-08T09:09:23] Filtering fusions with an e-value >=0.3 (remaining=15716)
[2026-06-08T09:09:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=15790)
[2026-06-08T09:09:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=15610)
[2026-06-08T09:09:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15612)
[2026-06-08T09:09:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9734)
[2026-06-08T09:09:36] Searching for fusions with spliced split reads (remaining=9806)
[2026-06-08T09:09:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=5461)
[2026-06-08T09:09:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5370)
[2026-06-08T09:09:44] Searching for fusions with >=4 spliced events (remaining=6784)
[2026-06-08T09:09:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2761)
[2026-06-08T09:10:07] Filtering fusions with anchors <=23nt (remaining=2227)
[2026-06-08T09:10:08] Filtering end-to-end fusions with low support (remaining=2164)
[2026-06-08T09:10:09] Filtering fusions with no coverage around the breakpoints (remaining=2111)
[2026-06-08T09:10:09] Indexing gene sequences 
[2026-06-08T09:10:16] Filtering genes with >=30% identity (remaining=657)
[2026-06-08T09:10:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=324)
[2026-06-08T09:10:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=245)
[2026-06-08T09:10:31] Searching for additional isoforms (remaining=375)
[2026-06-08T09:10:32] Assigning confidence scores to events 
[2026-06-08T09:10:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:10:36] Writing fusions to file '659_c95-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:40] Writing discarded fusions to file '659_c95-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:11:16] Freeing resources
[2026-06-08T09:11:39] Done (elapsed time=00:13:06, CPU time=00:13:05, peak memory=16gb)