[2026-06-08T08:23:30] Launching Arriba 2.4.0
[2026-06-08T08:23:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:46] Reading chimeric alignments from 'tih_rna_sample_00760_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10324613)
[2026-06-08T08:29:09] Marking multi-mapping alignments (marked=6483748)
[2026-06-08T08:29:13] Detecting strandedness (reverse)
[2026-06-08T08:29:13] Assigning strands to alignments 
[2026-06-08T08:29:15] Annotating alignments 
[2026-06-08T08:29:45] Filtering duplicates (remaining=6424266)
[2026-06-08T08:29:52] 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=6098167)
[2026-06-08T08:29:54] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6098167)
[2026-06-08T08:29:55] Filtering viral contigs with expression lower than the top 5 (remaining=6098167)
[2026-06-08T08:29:59] Filtering viral contigs with less than 5% coverage (remaining=6098167)
[2026-06-08T08:30:01] Estimating fragment length (mate gap mean=-86.5023, mate gap stddev=27.0257, read length mean=127.115)
[2026-06-08T08:30:01] Filtering read-through fragments with a distance <=10000bp (remaining=5669898)
[2026-06-08T08:30:03] Filtering inconsistently clipped mates (remaining=5593288)
[2026-06-08T08:30:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5498148)
[2026-06-08T08:30:09] Filtering fragments with small insert size (remaining=5497400)
[2026-06-08T08:30:10] Filtering alignments with long gaps (remaining=5497400)
[2026-06-08T08:30:12] Filtering fragments with both mates in the same gene (remaining=5496351)
[2026-06-08T08:30:14] Filtering fusions arising from hairpin structures (remaining=5262029)
[2026-06-08T08:30:16] Filtering reads with a mismatch p-value <=0.01 (remaining=2426680)
[2026-06-08T08:30:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=1008768)
[2026-06-08T08:30:37] Finding fusions and counting supporting reads (total=766971)
[2026-06-08T08:30:53] Merging adjacent fusion breakpoints (remaining=760913)
[2026-06-08T08:30:54] Filtering multi-mapping fusions by alignment score and read support (remaining=480932)
[2026-06-08T08:31:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:31:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=479737)
[2026-06-08T08:31:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=270802)
[2026-06-08T08:31:30] Filtering fusions with <2 supporting reads (remaining=34588)
[2026-06-08T08:31:31] Filtering fusions with an e-value >=0.3 (remaining=8185)
[2026-06-08T08:31:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8230)
[2026-06-08T08:31:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8183)
[2026-06-08T08:31:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8183)
[2026-06-08T08:31:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7596)
[2026-06-08T08:31:41] Searching for fusions with spliced split reads (remaining=7671)
[2026-06-08T08:31:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=4924)
[2026-06-08T08:31:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4883)
[2026-06-08T08:31:48] Searching for fusions with >=4 spliced events (remaining=5928)
[2026-06-08T08:31:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2527)
[2026-06-08T08:32:03] Filtering fusions with anchors <=23nt (remaining=2039)
[2026-06-08T08:32:04] Filtering end-to-end fusions with low support (remaining=1944)
[2026-06-08T08:32:04] Filtering fusions with no coverage around the breakpoints (remaining=1903)
[2026-06-08T08:32:05] Indexing gene sequences 
[2026-06-08T08:32:11] Filtering genes with >=30% identity (remaining=550)
[2026-06-08T08:32:14] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=191)
[2026-06-08T08:32:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=182)
[2026-06-08T08:32:21] Searching for additional isoforms (remaining=204)
[2026-06-08T08:32:22] Assigning confidence scores to events 
[2026-06-08T08:32:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:26] Writing fusions to file 'tih_rna_sample_00760_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:32:28] Writing discarded fusions to file 'tih_rna_sample_00760_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:32:56] Freeing resources
[2026-06-08T08:33:11] Done (elapsed time=00:09:41, CPU time=00:09:40, peak memory=15gb)