[2026-06-08T08:54:34] Launching Arriba 2.4.0
[2026-06-08T08:54:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:52] Reading chimeric alignments from 'tih_rna_sample_00665_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11155801)
[2026-06-08T09:02:03] Marking multi-mapping alignments (marked=6894634)
[2026-06-08T09:02:08] Detecting strandedness (reverse)
[2026-06-08T09:02:08] Assigning strands to alignments 
[2026-06-08T09:02:10] Annotating alignments 
[2026-06-08T09:02:42] Filtering duplicates (remaining=7427664)
[2026-06-08T09:02:49] 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=7093793)
[2026-06-08T09:02:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7093793)
[2026-06-08T09:02:53] Filtering viral contigs with expression lower than the top 5 (remaining=7093793)
[2026-06-08T09:02:58] Filtering viral contigs with less than 5% coverage (remaining=7093793)
[2026-06-08T09:03:00] Estimating fragment length (mate gap mean=-87.7484, mate gap stddev=29.3692, read length mean=134.406)
[2026-06-08T09:03:00] Filtering read-through fragments with a distance <=10000bp (remaining=6622880)
[2026-06-08T09:03:02] Filtering inconsistently clipped mates (remaining=6513294)
[2026-06-08T09:03:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6373791)
[2026-06-08T09:03:09] Filtering fragments with small insert size (remaining=6372893)
[2026-06-08T09:03:11] Filtering alignments with long gaps (remaining=6372889)
[2026-06-08T09:03:13] Filtering fragments with both mates in the same gene (remaining=6371875)
[2026-06-08T09:03:15] Filtering fusions arising from hairpin structures (remaining=5995490)
[2026-06-08T09:03:18] Filtering reads with a mismatch p-value <=0.01 (remaining=2966228)
[2026-06-08T09:03:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=1142477)
[2026-06-08T09:03:44] Finding fusions and counting supporting reads (total=820081)
[2026-06-08T09:04:01] Merging adjacent fusion breakpoints (remaining=810494)
[2026-06-08T09:04:02] Filtering multi-mapping fusions by alignment score and read support (remaining=516057)
[2026-06-08T09:04:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=513817)
[2026-06-08T09:04:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=277030)
[2026-06-08T09:04:42] Filtering fusions with <2 supporting reads (remaining=42361)
[2026-06-08T09:04:43] Filtering fusions with an e-value >=0.3 (remaining=11987)
[2026-06-08T09:04:44] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12044)
[2026-06-08T09:04:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11949)
[2026-06-08T09:04:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11949)
[2026-06-08T09:04:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9734)
[2026-06-08T09:04:55] Searching for fusions with spliced split reads (remaining=9767)
[2026-06-08T09:05:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=5743)
[2026-06-08T09:05:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5672)
[2026-06-08T09:05:02] Searching for fusions with >=4 spliced events (remaining=7150)
[2026-06-08T09:05:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3064)
[2026-06-08T09:05:21] Filtering fusions with anchors <=23nt (remaining=2506)
[2026-06-08T09:05:22] Filtering end-to-end fusions with low support (remaining=2442)
[2026-06-08T09:05:22] Filtering fusions with no coverage around the breakpoints (remaining=2404)
[2026-06-08T09:05:23] Indexing gene sequences 
[2026-06-08T09:05:31] Filtering genes with >=30% identity (remaining=955)
[2026-06-08T09:05:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=647)
[2026-06-08T09:05:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=348)
[2026-06-08T09:05:49] Searching for additional isoforms (remaining=526)
[2026-06-08T09:05:51] Assigning confidence scores to events 
[2026-06-08T09:05:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:54] Writing fusions to file 'tih_rna_sample_00665_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:59] Writing discarded fusions to file 'tih_rna_sample_00665_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:29] Freeing resources
[2026-06-08T09:06:47] Done (elapsed time=00:12:13, CPU time=00:12:11, peak memory=15.9gb)