[2026-06-08T08:38:20] Launching Arriba 2.4.0
[2026-06-08T08:38:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:39] Reading chimeric alignments from 'tih_rna_sample_00467_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=14466215)
[2026-06-08T08:47:06] Marking multi-mapping alignments (marked=10389107)
[2026-06-08T08:47:13] Detecting strandedness (reverse)
[2026-06-08T08:47:13] Assigning strands to alignments 
[2026-06-08T08:47:15] Annotating alignments 
[2026-06-08T08:48:05] Filtering duplicates (remaining=5635927)
[2026-06-08T08:48:27] 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=5061385)
[2026-06-08T08:48:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5061385)
[2026-06-08T08:48:34] Filtering viral contigs with expression lower than the top 5 (remaining=5061385)
[2026-06-08T08:48:41] Filtering viral contigs with less than 5% coverage (remaining=5061385)
[2026-06-08T08:48:44] Estimating fragment length (mate gap mean=-83.186, mate gap stddev=27.9553, read length mean=118.539)
[2026-06-08T08:48:44] Filtering read-through fragments with a distance <=10000bp (remaining=4734425)
[2026-06-08T08:48:48] Filtering inconsistently clipped mates (remaining=4625650)
[2026-06-08T08:48:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4477448)
[2026-06-08T08:48:56] Filtering fragments with small insert size (remaining=4475887)
[2026-06-08T08:48:59] Filtering alignments with long gaps (remaining=4475886)
[2026-06-08T08:49:02] Filtering fragments with both mates in the same gene (remaining=4474923)
[2026-06-08T08:49:05] Filtering fusions arising from hairpin structures (remaining=4210461)
[2026-06-08T08:49:08] Filtering reads with a mismatch p-value <=0.01 (remaining=1596070)
[2026-06-08T08:49:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=730046)
[2026-06-08T08:49:32] Finding fusions and counting supporting reads (total=598368)
[2026-06-08T08:49:51] Merging adjacent fusion breakpoints (remaining=591114)
[2026-06-08T08:49:53] Filtering multi-mapping fusions by alignment score and read support (remaining=325520)
[2026-06-08T08:50:35] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=324014)
[2026-06-08T08:50:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=181274)
[2026-06-08T08:50:42] Filtering fusions with <2 supporting reads (remaining=19271)
[2026-06-08T08:50:43] Filtering fusions with an e-value >=0.3 (remaining=4535)
[2026-06-08T08:50:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4598)
[2026-06-08T08:50:48] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4497)
[2026-06-08T08:50:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4497)
[2026-06-08T08:50:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4289)
[2026-06-08T08:50:56] Searching for fusions with spliced split reads (remaining=4348)
[2026-06-08T08:51:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=2960)
[2026-06-08T08:51:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2938)
[2026-06-08T08:51:03] Searching for fusions with >=4 spliced events (remaining=3503)
[2026-06-08T08:51:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1472)
[2026-06-08T08:51:23] Filtering fusions with anchors <=23nt (remaining=1251)
[2026-06-08T08:51:23] Filtering end-to-end fusions with low support (remaining=1213)
[2026-06-08T08:51:24] Filtering fusions with no coverage around the breakpoints (remaining=1194)
[2026-06-08T08:51:25] Indexing gene sequences 
[2026-06-08T08:51:29] Filtering genes with >=30% identity (remaining=368)
[2026-06-08T08:51:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=167)
[2026-06-08T08:51:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=156)
[2026-06-08T08:51:34] Searching for additional isoforms (remaining=181)
[2026-06-08T08:51:35] Assigning confidence scores to events 
[2026-06-08T08:51:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:38] Writing fusions to file 'tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:51:40] Writing discarded fusions to file 'tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:08] Freeing resources
[2026-06-08T08:52:32] Done (elapsed time=00:14:12, CPU time=00:14:11, peak memory=19.1gb)