[2026-06-08T07:56:35] Launching Arriba 2.4.0
[2026-06-08T07:56:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:56:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:57:00] Reading chimeric alignments from '659_zC_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam' (total=5648923)
[2026-06-08T08:02:11] Marking multi-mapping alignments (marked=3692914)
[2026-06-08T08:02:14] Detecting strandedness (reverse)
[2026-06-08T08:02:14] Assigning strands to alignments 
[2026-06-08T08:02:16] Annotating alignments 
[2026-06-08T08:02:42] Filtering duplicates (remaining=2902586)
[2026-06-08T08:02:47] 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=2682458)
[2026-06-08T08:02:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2682458)
[2026-06-08T08:02:50] Filtering viral contigs with expression lower than the top 5 (remaining=2682458)
[2026-06-08T08:02:53] Filtering viral contigs with less than 5% coverage (remaining=2682458)
[2026-06-08T08:02:54] Estimating fragment length (mate gap mean=-91.6403, mate gap stddev=27.238, read length mean=131.355)
[2026-06-08T08:02:54] Filtering read-through fragments with a distance <=10000bp (remaining=2486527)
[2026-06-08T08:02:56] Filtering inconsistently clipped mates (remaining=2416634)
[2026-06-08T08:02:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2245616)
[2026-06-08T08:03:00] Filtering fragments with small insert size (remaining=2244791)
[2026-06-08T08:03:02] Filtering alignments with long gaps (remaining=2244790)
[2026-06-08T08:03:03] Filtering fragments with both mates in the same gene (remaining=2244303)
[2026-06-08T08:03:05] Filtering fusions arising from hairpin structures (remaining=2012415)
[2026-06-08T08:03:07] Filtering reads with a mismatch p-value <=0.01 (remaining=790453)
[2026-06-08T08:03:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=539949)
[2026-06-08T08:03:22] Finding fusions and counting supporting reads (total=475106)
[2026-06-08T08:03:34] Merging adjacent fusion breakpoints (remaining=472062)
[2026-06-08T08:03:35] Filtering multi-mapping fusions by alignment score and read support (remaining=270623)
[2026-06-08T08:04:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:04:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=269362)
[2026-06-08T08:04:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=157199)
[2026-06-08T08:04:07] Filtering fusions with <2 supporting reads (remaining=13598)
[2026-06-08T08:04:07] Filtering fusions with an e-value >=0.3 (remaining=3087)
[2026-06-08T08:04:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3136)
[2026-06-08T08:04:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3059)
[2026-06-08T08:04:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3059)
[2026-06-08T08:04:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2979)
[2026-06-08T08:04:16] Searching for fusions with spliced split reads (remaining=3029)
[2026-06-08T08:04:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=2228)
[2026-06-08T08:04:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2199)
[2026-06-08T08:04:21] Searching for fusions with >=4 spliced events (remaining=2619)
[2026-06-08T08:04:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=998)
[2026-06-08T08:04:43] Filtering fusions with anchors <=23nt (remaining=860)
[2026-06-08T08:04:43] Filtering end-to-end fusions with low support (remaining=843)
[2026-06-08T08:04:44] Filtering fusions with no coverage around the breakpoints (remaining=832)
[2026-06-08T08:04:44] Indexing gene sequences 
[2026-06-08T08:04:50] Filtering genes with >=30% identity (remaining=261)
[2026-06-08T08:04:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=151)
[2026-06-08T08:04:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=145)
[2026-06-08T08:04:54] Searching for additional isoforms (remaining=177)
[2026-06-08T08:04:55] Assigning confidence scores to events 
[2026-06-08T08:04:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:04:58] Writing fusions to file '659_zC_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:04:59] Writing discarded fusions to file '659_zC_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:05:24] Freeing resources
[2026-06-08T08:05:40] Done (elapsed time=00:09:05, CPU time=00:09:05, peak memory=10.4gb)