[2026-06-08T08:56:32] Launching Arriba 2.4.0
[2026-06-08T08:56:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:56:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:56:45] Reading chimeric alignments from '659_ciJ-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam' (total=11853724)
[2026-06-08T09:04:05] Marking multi-mapping alignments (marked=7155309)
[2026-06-08T09:04:10] Detecting strandedness (reverse)
[2026-06-08T09:04:10] Assigning strands to alignments 
[2026-06-08T09:04:13] Annotating alignments 
[2026-06-08T09:04:58] Filtering duplicates (remaining=6801885)
[2026-06-08T09:05:08] 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=6627580)
[2026-06-08T09:05:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6627580)
[2026-06-08T09:05:13] Filtering viral contigs with expression lower than the top 5 (remaining=6627580)
[2026-06-08T09:05:20] Filtering viral contigs with less than 5% coverage (remaining=6627580)
[2026-06-08T09:05:23] Estimating fragment length (mate gap mean=-89.2359, mate gap stddev=30.6402, read length mean=141.023)
[2026-06-08T09:05:23] Filtering read-through fragments with a distance <=10000bp (remaining=6235128)
[2026-06-08T09:05:26] Filtering inconsistently clipped mates (remaining=6167231)
[2026-06-08T09:05:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5933699)
[2026-06-08T09:05:33] Filtering fragments with small insert size (remaining=5933271)
[2026-06-08T09:05:36] Filtering alignments with long gaps (remaining=5933271)
[2026-06-08T09:05:39] Filtering fragments with both mates in the same gene (remaining=5932275)
[2026-06-08T09:05:42] Filtering fusions arising from hairpin structures (remaining=5656403)
[2026-06-08T09:05:45] Filtering reads with a mismatch p-value <=0.01 (remaining=2901967)
[2026-06-08T09:06:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=926422)
[2026-06-08T09:06:12] Finding fusions and counting supporting reads (total=734801)
[2026-06-08T09:06:33] Merging adjacent fusion breakpoints (remaining=729719)
[2026-06-08T09:06:35] Filtering multi-mapping fusions by alignment score and read support (remaining=473275)
[2026-06-08T09:07:16] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:07:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=469983)
[2026-06-08T09:07:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=249533)
[2026-06-08T09:07:27] Filtering fusions with <2 supporting reads (remaining=37680)
[2026-06-08T09:07:28] Filtering fusions with an e-value >=0.3 (remaining=14788)
[2026-06-08T09:07:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14854)
[2026-06-08T09:07:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14738)
[2026-06-08T09:07:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14743)
[2026-06-08T09:07:35] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8576)
[2026-06-08T09:07:41] Searching for fusions with spliced split reads (remaining=8594)
[2026-06-08T09:07:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=4839)
[2026-06-08T09:07:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4772)
[2026-06-08T09:07:49] Searching for fusions with >=4 spliced events (remaining=5634)
[2026-06-08T09:07:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1916)
[2026-06-08T09:08:08] Filtering fusions with anchors <=23nt (remaining=1445)
[2026-06-08T09:08:09] Filtering end-to-end fusions with low support (remaining=1389)
[2026-06-08T09:08:10] Filtering fusions with no coverage around the breakpoints (remaining=1344)
[2026-06-08T09:08:10] Indexing gene sequences 
[2026-06-08T09:08:16] Filtering genes with >=30% identity (remaining=434)
[2026-06-08T09:08:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=210)
[2026-06-08T09:08:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=180)
[2026-06-08T09:08:25] Searching for additional isoforms (remaining=225)
[2026-06-08T09:08:27] Assigning confidence scores to events 
[2026-06-08T09:08:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:08:30] Writing fusions to file '659_ciJ-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.tsv' 
[2026-06-08T09:08:33] Writing discarded fusions to file '659_ciJ-T1-TRNA-1_A23MVY2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:09:05] Freeing resources
[2026-06-08T09:09:25] Done (elapsed time=00:12:53, CPU time=00:12:51, peak memory=16.3gb)