[2026-05-28T00:02:41] Launching Arriba 2.4.0
[2026-05-28T00:02:41] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:02:50] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:02:54] Reading chimeric alignments from '659_cRa-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3075447)
[2026-05-28T00:05:18] Marking multi-mapping alignments (marked=1854877)
[2026-05-28T00:05:19] Detecting strandedness (reverse)
[2026-05-28T00:05:19] Assigning strands to alignments 
[2026-05-28T00:05:20] Annotating alignments 
[2026-05-28T00:05:31] Filtering duplicates (remaining=1836046)
[2026-05-28T00:05:34] 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=1767358)
[2026-05-28T00:05:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1767358)
[2026-05-28T00:05:35] Filtering viral contigs with expression lower than the top 5 (remaining=1767358)
[2026-05-28T00:05:36] Filtering viral contigs with less than 5% coverage (remaining=1767358)
[2026-05-28T00:05:37] Estimating fragment length (mate gap mean=-87.2685, mate gap stddev=29.4771, read length mean=134.941)
[2026-05-28T00:05:37] Filtering read-through fragments with a distance <=10000bp (remaining=1649943)
[2026-05-28T00:05:38] Filtering inconsistently clipped mates (remaining=1617602)
[2026-05-28T00:05:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1574576)
[2026-05-28T00:05:40] Filtering fragments with small insert size (remaining=1574215)
[2026-05-28T00:05:40] Filtering alignments with long gaps (remaining=1574215)
[2026-05-28T00:05:41] Filtering fragments with both mates in the same gene (remaining=1573888)
[2026-05-28T00:05:42] Filtering fusions arising from hairpin structures (remaining=1467533)
[2026-05-28T00:05:43] Filtering reads with a mismatch p-value <=0.01 (remaining=662579)
[2026-05-28T00:05:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=293553)
[2026-05-28T00:05:50] Finding fusions and counting supporting reads (total=238557)
[2026-05-28T00:05:56] Merging adjacent fusion breakpoints (remaining=236272)
[2026-05-28T00:05:56] Filtering multi-mapping fusions by alignment score and read support (remaining=155179)
[2026-05-28T00:06:09] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:06:12] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=153992)
[2026-05-28T00:06:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=74696)
[2026-05-28T00:06:12] Filtering fusions with <2 supporting reads (remaining=11613)
[2026-05-28T00:06:13] Filtering fusions with an e-value >=0.3 (remaining=4046)
[2026-05-28T00:06:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4086)
[2026-05-28T00:06:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4034)
[2026-05-28T00:06:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4034)
[2026-05-28T00:06:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2497)
[2026-05-28T00:06:17] Searching for fusions with spliced split reads (remaining=2544)
[2026-05-28T00:06:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=1840)
[2026-05-28T00:06:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1822)
[2026-05-28T00:06:19] Searching for fusions with >=4 spliced events (remaining=1944)
[2026-05-28T00:06:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=512)
[2026-05-28T00:06:32] Filtering fusions with anchors <=23nt (remaining=386)
[2026-05-28T00:06:32] Filtering end-to-end fusions with low support (remaining=374)
[2026-05-28T00:06:33] Filtering fusions with no coverage around the breakpoints (remaining=363)
[2026-05-28T00:06:33] Indexing gene sequences 
[2026-05-28T00:06:36] Filtering genes with >=30% identity (remaining=156)
[2026-05-28T00:06:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=83)
[2026-05-28T00:06:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=80)
[2026-05-28T00:06:38] Searching for additional isoforms (remaining=95)
[2026-05-28T00:06:39] Assigning confidence scores to events 
[2026-05-28T00:06:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:06:40] Writing fusions to file '659_cRa-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:06:40] Writing discarded fusions to file '659_cRa-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:06:52] Freeing resources
[2026-05-28T00:07:01] Done (elapsed time=00:04:20, CPU time=00:04:18, peak memory=7.3gb)