[2026-06-08T08:52:30] Launching Arriba 2.4.0
[2026-06-08T08:52:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:50] Reading chimeric alignments from '659_cIX-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=10757208)
[2026-06-08T09:01:03] Marking multi-mapping alignments (marked=6391783)
[2026-06-08T09:01:08] Detecting strandedness (reverse)
[2026-06-08T09:01:08] Assigning strands to alignments 
[2026-06-08T09:01:10] Annotating alignments 
[2026-06-08T09:01:45] Filtering duplicates (remaining=5730768)
[2026-06-08T09:01:51] 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=5612018)
[2026-06-08T09:01:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5612018)
[2026-06-08T09:01:56] Filtering viral contigs with expression lower than the top 5 (remaining=5612018)
[2026-06-08T09:02:00] Filtering viral contigs with less than 5% coverage (remaining=5612018)
[2026-06-08T09:02:03] Estimating fragment length (mate gap mean=-89.0059, mate gap stddev=29.2376, read length mean=139.863)
[2026-06-08T09:02:03] Filtering read-through fragments with a distance <=10000bp (remaining=5315084)
[2026-06-08T09:02:05] Filtering inconsistently clipped mates (remaining=5252058)
[2026-06-08T09:02:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5076820)
[2026-06-08T09:02:11] Filtering fragments with small insert size (remaining=5076358)
[2026-06-08T09:02:13] Filtering alignments with long gaps (remaining=5076358)
[2026-06-08T09:02:15] Filtering fragments with both mates in the same gene (remaining=5075540)
[2026-06-08T09:02:17] Filtering fusions arising from hairpin structures (remaining=4835765)
[2026-06-08T09:02:20] Filtering reads with a mismatch p-value <=0.01 (remaining=2444461)
[2026-06-08T09:02:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=784740)
[2026-06-08T09:02:45] Finding fusions and counting supporting reads (total=618408)
[2026-06-08T09:03:01] Merging adjacent fusion breakpoints (remaining=614792)
[2026-06-08T09:03:03] Filtering multi-mapping fusions by alignment score and read support (remaining=404855)
[2026-06-08T09:03:37] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=402372)
[2026-06-08T09:03:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=205365)
[2026-06-08T09:03:45] Filtering fusions with <2 supporting reads (remaining=30617)
[2026-06-08T09:03:45] Filtering fusions with an e-value >=0.3 (remaining=9741)
[2026-06-08T09:03:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9773)
[2026-06-08T09:03:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9686)
[2026-06-08T09:03:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9686)
[2026-06-08T09:03:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6503)
[2026-06-08T09:03:56] Searching for fusions with spliced split reads (remaining=6522)
[2026-06-08T09:04:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=4114)
[2026-06-08T09:04:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4072)
[2026-06-08T09:04:02] Searching for fusions with >=4 spliced events (remaining=4987)
[2026-06-08T09:04:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1782)
[2026-06-08T09:04:18] Filtering fusions with anchors <=23nt (remaining=1493)
[2026-06-08T09:04:19] Filtering end-to-end fusions with low support (remaining=1455)
[2026-06-08T09:04:19] Filtering fusions with no coverage around the breakpoints (remaining=1413)
[2026-06-08T09:04:20] Indexing gene sequences 
[2026-06-08T09:04:27] Filtering genes with >=30% identity (remaining=452)
[2026-06-08T09:04:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=228)
[2026-06-08T09:04:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=186)
[2026-06-08T09:04:40] Searching for additional isoforms (remaining=230)
[2026-06-08T09:04:41] Assigning confidence scores to events 
[2026-06-08T09:04:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:45] Writing fusions to file '659_cIX-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:04:47] Writing discarded fusions to file '659_cIX-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:15] Freeing resources
[2026-06-08T09:05:34] Done (elapsed time=00:13:04, CPU time=00:13:03, peak memory=15.1gb)