[2026-06-08T08:50:51] Launching Arriba 2.4.0
[2026-06-08T08:50:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:07] Reading chimeric alignments from '659_cfy-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11860328)
[2026-06-08T08:58:28] Marking multi-mapping alignments (marked=7073440)
[2026-06-08T08:58:32] Detecting strandedness (reverse)
[2026-06-08T08:58:32] Assigning strands to alignments 
[2026-06-08T08:58:35] Annotating alignments 
[2026-06-08T08:59:15] Filtering duplicates (remaining=5781412)
[2026-06-08T08:59:22] 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=5632683)
[2026-06-08T08:59:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5632683)
[2026-06-08T08:59:27] Filtering viral contigs with expression lower than the top 5 (remaining=5632683)
[2026-06-08T08:59:32] Filtering viral contigs with less than 5% coverage (remaining=5632683)
[2026-06-08T08:59:34] Estimating fragment length (mate gap mean=-87.7676, mate gap stddev=29.3685, read length mean=138.685)
[2026-06-08T08:59:34] Filtering read-through fragments with a distance <=10000bp (remaining=5344421)
[2026-06-08T08:59:37] Filtering inconsistently clipped mates (remaining=5287454)
[2026-06-08T08:59:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5116651)
[2026-06-08T08:59:43] Filtering fragments with small insert size (remaining=5116138)
[2026-06-08T08:59:45] Filtering alignments with long gaps (remaining=5116138)
[2026-06-08T08:59:48] Filtering fragments with both mates in the same gene (remaining=5115442)
[2026-06-08T08:59:50] Filtering fusions arising from hairpin structures (remaining=4922959)
[2026-06-08T08:59:53] Filtering reads with a mismatch p-value <=0.01 (remaining=2401485)
[2026-06-08T09:00:19] Filtering reads with low entropy (k-mer content >=60%) (remaining=684372)
[2026-06-08T09:00:31] Finding fusions and counting supporting reads (total=565314)
[2026-06-08T09:00:53] Merging adjacent fusion breakpoints (remaining=560742)
[2026-06-08T09:00:54] Filtering multi-mapping fusions by alignment score and read support (remaining=370570)
[2026-06-08T09:01:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=368996)
[2026-06-08T09:01:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=186264)
[2026-06-08T09:01:50] Filtering fusions with <2 supporting reads (remaining=25923)
[2026-06-08T09:01:51] Filtering fusions with an e-value >=0.3 (remaining=8477)
[2026-06-08T09:01:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8510)
[2026-06-08T09:01:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8441)
[2026-06-08T09:01:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8488)
[2026-06-08T09:01:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5515)
[2026-06-08T09:02:04] Searching for fusions with spliced split reads (remaining=5591)
[2026-06-08T09:02:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=3531)
[2026-06-08T09:02:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3491)
[2026-06-08T09:02:12] Searching for fusions with >=4 spliced events (remaining=4135)
[2026-06-08T09:02:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1462)
[2026-06-08T09:02:27] Filtering fusions with anchors <=23nt (remaining=1187)
[2026-06-08T09:02:27] Filtering end-to-end fusions with low support (remaining=1164)
[2026-06-08T09:02:28] Filtering fusions with no coverage around the breakpoints (remaining=1134)
[2026-06-08T09:02:29] Indexing gene sequences 
[2026-06-08T09:02:34] Filtering genes with >=30% identity (remaining=364)
[2026-06-08T09:02:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=154)
[2026-06-08T09:02:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=144)
[2026-06-08T09:02:39] Searching for additional isoforms (remaining=187)
[2026-06-08T09:02:40] Assigning confidence scores to events 
[2026-06-08T09:02:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:44] Writing fusions to file '659_cfy-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:02:46] Writing discarded fusions to file '659_cfy-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:14] Freeing resources
[2026-06-08T09:03:38] Done (elapsed time=00:12:47, CPU time=00:12:46, peak memory=16gb)