[2026-05-28T00:05:44] Launching Arriba 2.4.0
[2026-05-28T00:05:44] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:52] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:56] Reading chimeric alignments from '659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3515252)
[2026-05-28T00:08:09] Marking multi-mapping alignments (marked=2197535)
[2026-05-28T00:08:10] Detecting strandedness (reverse)
[2026-05-28T00:08:10] Assigning strands to alignments 
[2026-05-28T00:08:11] Annotating alignments 
[2026-05-28T00:08:23] Filtering duplicates (remaining=2105699)
[2026-05-28T00:08:25] 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=1996888)
[2026-05-28T00:08:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1996888)
[2026-05-28T00:08:26] Filtering viral contigs with expression lower than the top 5 (remaining=1996888)
[2026-05-28T00:08:27] Filtering viral contigs with less than 5% coverage (remaining=1996888)
[2026-05-28T00:08:28] Estimating fragment length (mate gap mean=-87.9345, mate gap stddev=30.6662, read length mean=136.473)
[2026-05-28T00:08:29] Filtering read-through fragments with a distance <=10000bp (remaining=1856525)
[2026-05-28T00:08:29] Filtering inconsistently clipped mates (remaining=1828319)
[2026-05-28T00:08:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1772705)
[2026-05-28T00:08:31] Filtering fragments with small insert size (remaining=1772497)
[2026-05-28T00:08:32] Filtering alignments with long gaps (remaining=1772497)
[2026-05-28T00:08:33] Filtering fragments with both mates in the same gene (remaining=1772154)
[2026-05-28T00:08:33] Filtering fusions arising from hairpin structures (remaining=1670713)
[2026-05-28T00:08:34] Filtering reads with a mismatch p-value <=0.01 (remaining=747968)
[2026-05-28T00:08:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=301235)
[2026-05-28T00:08:42] Finding fusions and counting supporting reads (total=260710)
[2026-05-28T00:08:47] Merging adjacent fusion breakpoints (remaining=258525)
[2026-05-28T00:08:48] Filtering multi-mapping fusions by alignment score and read support (remaining=168693)
[2026-05-28T00:08:59] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:09:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=167332)
[2026-05-28T00:09:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=83653)
[2026-05-28T00:09:02] Filtering fusions with <2 supporting reads (remaining=11816)
[2026-05-28T00:09:02] Filtering fusions with an e-value >=0.3 (remaining=5039)
[2026-05-28T00:09:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5076)
[2026-05-28T00:09:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5034)
[2026-05-28T00:09:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5037)
[2026-05-28T00:09:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3151)
[2026-05-28T00:09:06] Searching for fusions with spliced split reads (remaining=3185)
[2026-05-28T00:09:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=2182)
[2026-05-28T00:09:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2150)
[2026-05-28T00:09:09] Searching for fusions with >=4 spliced events (remaining=2274)
[2026-05-28T00:09:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=614)
[2026-05-28T00:09:22] Filtering fusions with anchors <=23nt (remaining=430)
[2026-05-28T00:09:22] Filtering end-to-end fusions with low support (remaining=414)
[2026-05-28T00:09:22] Filtering fusions with no coverage around the breakpoints (remaining=399)
[2026-05-28T00:09:22] Indexing gene sequences 
[2026-05-28T00:09:25] Filtering genes with >=30% identity (remaining=184)
[2026-05-28T00:09:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=133)
[2026-05-28T00:09:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=127)
[2026-05-28T00:09:27] Searching for additional isoforms (remaining=143)
[2026-05-28T00:09:28] Assigning confidence scores to events 
[2026-05-28T00:09:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:09:29] Writing fusions to file '659_ciJ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:09:30] Writing discarded fusions to file '659_ciJ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:41] Freeing resources
[2026-05-28T00:09:47] Done (elapsed time=00:04:03, CPU time=00:04:02, peak memory=7.87gb)