[2026-05-28T00:03:44] Launching Arriba 2.4.0
[2026-05-28T00:03:44] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:03:53] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:03:57] Reading chimeric alignments from 'tih_rna_sample_00087_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3269362)
[2026-05-28T00:06:17] Marking multi-mapping alignments (marked=2099442)
[2026-05-28T00:06:19] Detecting strandedness (reverse)
[2026-05-28T00:06:19] Assigning strands to alignments 
[2026-05-28T00:06:19] Annotating alignments 
[2026-05-28T00:06:31] Filtering duplicates (remaining=2563774)
[2026-05-28T00:06:34] 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=2461431)
[2026-05-28T00:06:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2461431)
[2026-05-28T00:06:36] Filtering viral contigs with expression lower than the top 5 (remaining=2461431)
[2026-05-28T00:06:37] Filtering viral contigs with less than 5% coverage (remaining=2461431)
[2026-05-28T00:06:38] Estimating fragment length (mate gap mean=-86.5857, mate gap stddev=29.2283, read length mean=133.126)
[2026-05-28T00:06:38] Filtering read-through fragments with a distance <=10000bp (remaining=2289751)
[2026-05-28T00:06:39] Filtering inconsistently clipped mates (remaining=2246624)
[2026-05-28T00:06:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2192184)
[2026-05-28T00:06:42] Filtering fragments with small insert size (remaining=2191745)
[2026-05-28T00:06:42] Filtering alignments with long gaps (remaining=2191745)
[2026-05-28T00:06:43] Filtering fragments with both mates in the same gene (remaining=2191293)
[2026-05-28T00:06:44] Filtering fusions arising from hairpin structures (remaining=2039911)
[2026-05-28T00:06:45] Filtering reads with a mismatch p-value <=0.01 (remaining=984747)
[2026-05-28T00:06:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=494898)
[2026-05-28T00:06:55] Finding fusions and counting supporting reads (total=388302)
[2026-05-28T00:07:03] Merging adjacent fusion breakpoints (remaining=385048)
[2026-05-28T00:07:03] Filtering multi-mapping fusions by alignment score and read support (remaining=230537)
[2026-05-28T00:07:16] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:07:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=228776)
[2026-05-28T00:07:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=125598)
[2026-05-28T00:07:20] Filtering fusions with <2 supporting reads (remaining=17596)
[2026-05-28T00:07:21] Filtering fusions with an e-value >=0.3 (remaining=5626)
[2026-05-28T00:07:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5666)
[2026-05-28T00:07:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5623)
[2026-05-28T00:07:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5623)
[2026-05-28T00:07:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4591)
[2026-05-28T00:07:25] Searching for fusions with spliced split reads (remaining=4679)
[2026-05-28T00:07:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=3108)
[2026-05-28T00:07:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3067)
[2026-05-28T00:07:28] Searching for fusions with >=4 spliced events (remaining=3400)
[2026-05-28T00:07:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1040)
[2026-05-28T00:07:43] Filtering fusions with anchors <=23nt (remaining=874)
[2026-05-28T00:07:43] Filtering end-to-end fusions with low support (remaining=842)
[2026-05-28T00:07:43] Filtering fusions with no coverage around the breakpoints (remaining=814)
[2026-05-28T00:07:44] Indexing gene sequences 
[2026-05-28T00:07:48] Filtering genes with >=30% identity (remaining=241)
[2026-05-28T00:07:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=135)
[2026-05-28T00:07:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=133)
[2026-05-28T00:07:54] Searching for additional isoforms (remaining=182)
[2026-05-28T00:07:55] Assigning confidence scores to events 
[2026-05-28T00:07:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:57] Writing fusions to file 'tih_rna_sample_00087_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:07:58] Writing discarded fusions to file 'tih_rna_sample_00087_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:17] Freeing resources
[2026-05-28T00:08:24] Done (elapsed time=00:04:40, CPU time=00:04:38, peak memory=7.63gb)