[2026-06-08T07:44:20] Launching Arriba 2.4.0
[2026-06-08T07:44:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:44:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:44:47] Reading chimeric alignments from 'tih_rna_sample_00378_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam' (total=9438137)
[2026-06-08T07:52:11] Marking multi-mapping alignments (marked=6641981)
[2026-06-08T07:52:17] Detecting strandedness (reverse)
[2026-06-08T07:52:17] Assigning strands to alignments 
[2026-06-08T07:52:20] Annotating alignments 
[2026-06-08T07:53:15] Filtering duplicates (remaining=5815380)
[2026-06-08T07:53:27] 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=5473568)
[2026-06-08T07:53:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5473568)
[2026-06-08T07:53:33] Filtering viral contigs with expression lower than the top 5 (remaining=5473568)
[2026-06-08T07:53:39] Filtering viral contigs with less than 5% coverage (remaining=5473568)
[2026-06-08T07:53:43] Estimating fragment length (mate gap mean=-82.8656, mate gap stddev=29.3301, read length mean=116.677)
[2026-06-08T07:53:43] Filtering read-through fragments with a distance <=10000bp (remaining=5105786)
[2026-06-08T07:53:46] Filtering inconsistently clipped mates (remaining=5009278)
[2026-06-08T07:53:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4417557)
[2026-06-08T07:53:56] Filtering fragments with small insert size (remaining=4413966)
[2026-06-08T07:53:59] Filtering alignments with long gaps (remaining=4413966)
[2026-06-08T07:54:02] Filtering fragments with both mates in the same gene (remaining=4412355)
[2026-06-08T07:54:05] Filtering fusions arising from hairpin structures (remaining=4158627)
[2026-06-08T07:54:09] Filtering reads with a mismatch p-value <=0.01 (remaining=1425758)
[2026-06-08T07:54:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=1069817)
[2026-06-08T07:54:37] Finding fusions and counting supporting reads (total=911116)
[2026-06-08T07:55:04] Merging adjacent fusion breakpoints (remaining=901281)
[2026-06-08T07:55:07] Filtering multi-mapping fusions by alignment score and read support (remaining=449336)
[2026-06-08T07:56:00] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:56:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=447957)
[2026-06-08T07:56:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=323833)
[2026-06-08T07:56:14] Filtering fusions with <2 supporting reads (remaining=29496)
[2026-06-08T07:56:15] Filtering fusions with an e-value >=0.3 (remaining=5393)
[2026-06-08T07:56:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5431)
[2026-06-08T07:56:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5248)
[2026-06-08T07:56:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5248)
[2026-06-08T07:56:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5213)
[2026-06-08T07:56:32] Searching for fusions with spliced split reads (remaining=5270)
[2026-06-08T07:56:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=3766)
[2026-06-08T07:56:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3735)
[2026-06-08T07:56:42] Searching for fusions with >=4 spliced events (remaining=4362)
[2026-06-08T07:56:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1616)
[2026-06-08T07:57:10] Filtering fusions with anchors <=23nt (remaining=1397)
[2026-06-08T07:57:11] Filtering end-to-end fusions with low support (remaining=1349)
[2026-06-08T07:57:12] Filtering fusions with no coverage around the breakpoints (remaining=1329)
[2026-06-08T07:57:13] Indexing gene sequences 
[2026-06-08T07:57:22] Filtering genes with >=30% identity (remaining=386)
[2026-06-08T07:57:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=119)
[2026-06-08T07:57:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=115)
[2026-06-08T07:57:31] Searching for additional isoforms (remaining=141)
[2026-06-08T07:57:33] Assigning confidence scores to events 
[2026-06-08T07:57:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:57:40] Writing fusions to file 'tih_rna_sample_00378_23H5VFLT4_s24.arriba.fusions.tsv' 
[2026-06-08T07:57:42] Writing discarded fusions to file 'tih_rna_sample_00378_23H5VFLT4_s24.arriba.fusions.discarded.tsv'
[2026-06-08T07:58:37] Freeing resources
[2026-06-08T07:59:09] Done (elapsed time=00:14:49, CPU time=00:14:48, peak memory=14.7gb)