[2026-06-08T08:01:12] Launching Arriba 2.4.0
[2026-06-08T08:01:12] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:01:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:01:35] Reading chimeric alignments from 'tih_rna_sample_00685_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=5626901)
[2026-06-08T08:06:16] Marking multi-mapping alignments (marked=3568131)
[2026-06-08T08:06:18] Detecting strandedness (reverse)
[2026-06-08T08:06:18] Assigning strands to alignments 
[2026-06-08T08:06:19] Annotating alignments 
[2026-06-08T08:06:42] Filtering duplicates (remaining=3804961)
[2026-06-08T08:06:47] 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=3622584)
[2026-06-08T08:06:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3622584)
[2026-06-08T08:06:49] Filtering viral contigs with expression lower than the top 5 (remaining=3622584)
[2026-06-08T08:06:52] Filtering viral contigs with less than 5% coverage (remaining=3622584)
[2026-06-08T08:06:53] Estimating fragment length (mate gap mean=-85.266, mate gap stddev=28.175, read length mean=128.112)
[2026-06-08T08:06:53] Filtering read-through fragments with a distance <=10000bp (remaining=3380475)
[2026-06-08T08:06:54] Filtering inconsistently clipped mates (remaining=3313861)
[2026-06-08T08:06:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3249143)
[2026-06-08T08:06:58] Filtering fragments with small insert size (remaining=3248488)
[2026-06-08T08:06:59] Filtering alignments with long gaps (remaining=3248488)
[2026-06-08T08:07:00] Filtering fragments with both mates in the same gene (remaining=3247312)
[2026-06-08T08:07:01] Filtering fusions arising from hairpin structures (remaining=3041633)
[2026-06-08T08:07:03] Filtering reads with a mismatch p-value <=0.01 (remaining=1486111)
[2026-06-08T08:07:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=534349)
[2026-06-08T08:07:17] Finding fusions and counting supporting reads (total=429170)
[2026-06-08T08:07:27] Merging adjacent fusion breakpoints (remaining=425397)
[2026-06-08T08:07:28] Filtering multi-mapping fusions by alignment score and read support (remaining=262701)
[2026-06-08T08:07:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:07:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=261596)
[2026-06-08T08:07:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=135475)
[2026-06-08T08:07:51] Filtering fusions with <2 supporting reads (remaining=16252)
[2026-06-08T08:07:51] Filtering fusions with an e-value >=0.3 (remaining=4354)
[2026-06-08T08:07:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4409)
[2026-06-08T08:07:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4365)
[2026-06-08T08:07:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4366)
[2026-06-08T08:07:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4008)
[2026-06-08T08:07:58] Searching for fusions with spliced split reads (remaining=4083)
[2026-06-08T08:08:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=2873)
[2026-06-08T08:08:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2834)
[2026-06-08T08:08:02] Searching for fusions with >=4 spliced events (remaining=3227)
[2026-06-08T08:08:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1287)
[2026-06-08T08:08:18] Filtering fusions with anchors <=23nt (remaining=1100)
[2026-06-08T08:08:19] Filtering end-to-end fusions with low support (remaining=1067)
[2026-06-08T08:08:19] Filtering fusions with no coverage around the breakpoints (remaining=1045)
[2026-06-08T08:08:20] Indexing gene sequences 
[2026-06-08T08:08:26] Filtering genes with >=30% identity (remaining=395)
[2026-06-08T08:08:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=231)
[2026-06-08T08:08:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=197)
[2026-06-08T08:08:33] Searching for additional isoforms (remaining=250)
[2026-06-08T08:08:34] Assigning confidence scores to events 
[2026-06-08T08:08:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:08:36] Writing fusions to file 'tih_rna_sample_00685_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:08:38] Writing discarded fusions to file 'tih_rna_sample_00685_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:08:58] Freeing resources
[2026-06-08T08:09:07] Done (elapsed time=00:07:55, CPU time=00:07:54, peak memory=10gb)