[2026-06-08T08:15:08] Launching Arriba 2.4.0
[2026-06-08T08:15:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:22] Reading chimeric alignments from 'tih_rna_sample_00678_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=8127821)
[2026-06-08T08:18:49] Marking multi-mapping alignments (marked=5666095)
[2026-06-08T08:18:52] Detecting strandedness (reverse)
[2026-06-08T08:18:52] Assigning strands to alignments 
[2026-06-08T08:18:54] Annotating alignments 
[2026-06-08T08:19:21] Filtering duplicates (remaining=3170752)
[2026-06-08T08:19:25] 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=2881693)
[2026-06-08T08:19:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2881693)
[2026-06-08T08:19:28] Filtering viral contigs with expression lower than the top 5 (remaining=2881693)
[2026-06-08T08:19:31] Filtering viral contigs with less than 5% coverage (remaining=2881693)
[2026-06-08T08:19:33] Estimating fragment length (mate gap mean=-81.6392, mate gap stddev=28.3319, read length mean=117.683)
[2026-06-08T08:19:33] Filtering read-through fragments with a distance <=10000bp (remaining=2750280)
[2026-06-08T08:19:35] Filtering inconsistently clipped mates (remaining=2686951)
[2026-06-08T08:19:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2606270)
[2026-06-08T08:19:39] Filtering fragments with small insert size (remaining=2605467)
[2026-06-08T08:19:40] Filtering alignments with long gaps (remaining=2605467)
[2026-06-08T08:19:42] Filtering fragments with both mates in the same gene (remaining=2604871)
[2026-06-08T08:19:43] Filtering fusions arising from hairpin structures (remaining=2445269)
[2026-06-08T08:19:45] Filtering reads with a mismatch p-value <=0.01 (remaining=967249)
[2026-06-08T08:19:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=329467)
[2026-06-08T08:19:57] Finding fusions and counting supporting reads (total=279003)
[2026-06-08T08:20:08] Merging adjacent fusion breakpoints (remaining=276062)
[2026-06-08T08:20:09] Filtering multi-mapping fusions by alignment score and read support (remaining=147163)
[2026-06-08T08:20:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:20:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=146430)
[2026-06-08T08:20:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=84648)
[2026-06-08T08:20:38] Filtering fusions with <2 supporting reads (remaining=8822)
[2026-06-08T08:20:39] Filtering fusions with an e-value >=0.3 (remaining=2282)
[2026-06-08T08:20:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2326)
[2026-06-08T08:20:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2280)
[2026-06-08T08:20:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2280)
[2026-06-08T08:20:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2233)
[2026-06-08T08:20:46] Searching for fusions with spliced split reads (remaining=2358)
[2026-06-08T08:20:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=1718)
[2026-06-08T08:20:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1698)
[2026-06-08T08:20:50] Searching for fusions with >=4 spliced events (remaining=1859)
[2026-06-08T08:20:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=663)
[2026-06-08T08:21:02] Filtering fusions with anchors <=23nt (remaining=559)
[2026-06-08T08:21:03] Filtering end-to-end fusions with low support (remaining=529)
[2026-06-08T08:21:03] Filtering fusions with no coverage around the breakpoints (remaining=519)
[2026-06-08T08:21:03] Indexing gene sequences 
[2026-06-08T08:21:06] Filtering genes with >=30% identity (remaining=162)
[2026-06-08T08:21:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=80)
[2026-06-08T08:21:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=80)
[2026-06-08T08:21:08] Searching for additional isoforms (remaining=87)
[2026-06-08T08:21:09] Assigning confidence scores to events 
[2026-06-08T08:21:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:21:11] Writing fusions to file 'tih_rna_sample_00678_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:21:11] Writing discarded fusions to file 'tih_rna_sample_00678_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:21:27] Freeing resources
[2026-06-08T08:21:38] Done (elapsed time=00:06:30, CPU time=00:06:29, peak memory=12.4gb)