[2026-06-08T08:47:38] Launching Arriba 2.4.0
[2026-06-08T08:47:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:57] Reading chimeric alignments from 'tih_rna_sample_00704_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10558023)
[2026-06-08T08:55:34] Marking multi-mapping alignments (marked=6607939)
[2026-06-08T08:55:38] Detecting strandedness (reverse)
[2026-06-08T08:55:38] Assigning strands to alignments 
[2026-06-08T08:55:41] Annotating alignments 
[2026-06-08T08:56:17] Filtering duplicates (remaining=7462027)
[2026-06-08T08:56:25] 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=7136563)
[2026-06-08T08:56:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7136563)
[2026-06-08T08:56:29] Filtering viral contigs with expression lower than the top 5 (remaining=7136563)
[2026-06-08T08:56:34] Filtering viral contigs with less than 5% coverage (remaining=7136563)
[2026-06-08T08:56:37] Estimating fragment length (mate gap mean=-87.3285, mate gap stddev=29.4515, read length mean=134.746)
[2026-06-08T08:56:37] Filtering read-through fragments with a distance <=10000bp (remaining=6737637)
[2026-06-08T08:56:39] Filtering inconsistently clipped mates (remaining=6633263)
[2026-06-08T08:56:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6505215)
[2026-06-08T08:56:46] Filtering fragments with small insert size (remaining=6504673)
[2026-06-08T08:56:48] Filtering alignments with long gaps (remaining=6504673)
[2026-06-08T08:56:51] Filtering fragments with both mates in the same gene (remaining=6502871)
[2026-06-08T08:56:53] Filtering fusions arising from hairpin structures (remaining=6111099)
[2026-06-08T08:56:56] Filtering reads with a mismatch p-value <=0.01 (remaining=3150800)
[2026-06-08T08:57:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=1135139)
[2026-06-08T08:57:25] Finding fusions and counting supporting reads (total=821955)
[2026-06-08T08:57:42] Merging adjacent fusion breakpoints (remaining=812472)
[2026-06-08T08:57:44] Filtering multi-mapping fusions by alignment score and read support (remaining=512676)
[2026-06-08T08:58:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=509664)
[2026-06-08T08:58:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=282577)
[2026-06-08T08:58:29] Filtering fusions with <2 supporting reads (remaining=39851)
[2026-06-08T08:58:30] Filtering fusions with an e-value >=0.3 (remaining=12926)
[2026-06-08T08:58:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12979)
[2026-06-08T08:58:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12858)
[2026-06-08T08:58:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12859)
[2026-06-08T08:58:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9078)
[2026-06-08T08:58:42] Searching for fusions with spliced split reads (remaining=9096)
[2026-06-08T08:58:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=5042)
[2026-06-08T08:58:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4994)
[2026-06-08T08:58:50] Searching for fusions with >=4 spliced events (remaining=6141)
[2026-06-08T08:58:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2649)
[2026-06-08T08:59:06] Filtering fusions with anchors <=23nt (remaining=2149)
[2026-06-08T08:59:07] Filtering end-to-end fusions with low support (remaining=2091)
[2026-06-08T08:59:08] Filtering fusions with no coverage around the breakpoints (remaining=2044)
[2026-06-08T08:59:09] Indexing gene sequences 
[2026-06-08T08:59:16] Filtering genes with >=30% identity (remaining=635)
[2026-06-08T08:59:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=321)
[2026-06-08T08:59:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=231)
[2026-06-08T08:59:26] Searching for additional isoforms (remaining=334)
[2026-06-08T08:59:28] Assigning confidence scores to events 
[2026-06-08T08:59:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:32] Writing fusions to file 'tih_rna_sample_00704_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:35] Writing discarded fusions to file 'tih_rna_sample_00704_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:08] Freeing resources
[2026-06-08T09:00:25] Done (elapsed time=00:12:47, CPU time=00:12:47, peak memory=15.1gb)