[2026-06-08T08:47:42] Launching Arriba 2.4.0
[2026-06-08T08:47:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:54] Reading chimeric alignments from 'tih_rna_sample_00711_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11151929)
[2026-06-08T08:55:36] Marking multi-mapping alignments (marked=6943548)
[2026-06-08T08:55:42] Detecting strandedness (reverse)
[2026-06-08T08:55:42] Assigning strands to alignments 
[2026-06-08T08:55:45] Annotating alignments 
[2026-06-08T08:56:31] Filtering duplicates (remaining=7898281)
[2026-06-08T08:56:40] 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=7630864)
[2026-06-08T08:56:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7630864)
[2026-06-08T08:56:46] Filtering viral contigs with expression lower than the top 5 (remaining=7630864)
[2026-06-08T08:56:53] Filtering viral contigs with less than 5% coverage (remaining=7630864)
[2026-06-08T08:56:56] Estimating fragment length (mate gap mean=-85.2516, mate gap stddev=30.7672, read length mean=136.808)
[2026-06-08T08:56:56] Filtering read-through fragments with a distance <=10000bp (remaining=7091752)
[2026-06-08T08:56:59] Filtering inconsistently clipped mates (remaining=7006570)
[2026-06-08T08:57:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6854248)
[2026-06-08T08:57:07] Filtering fragments with small insert size (remaining=6853560)
[2026-06-08T08:57:10] Filtering alignments with long gaps (remaining=6853560)
[2026-06-08T08:57:13] Filtering fragments with both mates in the same gene (remaining=6852485)
[2026-06-08T08:57:16] Filtering fusions arising from hairpin structures (remaining=6493782)
[2026-06-08T08:57:19] Filtering reads with a mismatch p-value <=0.01 (remaining=3438767)
[2026-06-08T08:57:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=1282974)
[2026-06-08T08:57:51] Finding fusions and counting supporting reads (total=960765)
[2026-06-08T08:58:16] Merging adjacent fusion breakpoints (remaining=951414)
[2026-06-08T08:58:18] Filtering multi-mapping fusions by alignment score and read support (remaining=611219)
[2026-06-08T08:59:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=607926)
[2026-06-08T08:59:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=336033)
[2026-06-08T08:59:14] Filtering fusions with <2 supporting reads (remaining=42148)
[2026-06-08T08:59:15] Filtering fusions with an e-value >=0.3 (remaining=14135)
[2026-06-08T08:59:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14187)
[2026-06-08T08:59:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14049)
[2026-06-08T08:59:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14049)
[2026-06-08T08:59:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9575)
[2026-06-08T08:59:31] Searching for fusions with spliced split reads (remaining=9588)
[2026-06-08T08:59:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=4775)
[2026-06-08T08:59:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4732)
[2026-06-08T08:59:41] Searching for fusions with >=4 spliced events (remaining=6048)
[2026-06-08T08:59:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2582)
[2026-06-08T09:00:03] Filtering fusions with anchors <=23nt (remaining=2085)
[2026-06-08T09:00:04] Filtering end-to-end fusions with low support (remaining=2014)
[2026-06-08T09:00:05] Filtering fusions with no coverage around the breakpoints (remaining=1960)
[2026-06-08T09:00:06] Indexing gene sequences 
[2026-06-08T09:00:14] Filtering genes with >=30% identity (remaining=507)
[2026-06-08T09:00:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=187)
[2026-06-08T09:00:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=150)
[2026-06-08T09:00:23] Searching for additional isoforms (remaining=198)
[2026-06-08T09:00:25] Assigning confidence scores to events 
[2026-06-08T09:00:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:30] Writing fusions to file 'tih_rna_sample_00711_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:32] Writing discarded fusions to file 'tih_rna_sample_00711_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:17] Freeing resources
[2026-06-08T09:01:46] Done (elapsed time=00:14:04, CPU time=00:14:02, peak memory=15.7gb)