[2026-06-08T08:32:22] Launching Arriba 2.4.0
[2026-06-08T08:32:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:40] Reading chimeric alignments from 'tih_rna_sample_00097_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=11390034)
[2026-06-08T08:40:34] Marking multi-mapping alignments (marked=7387627)
[2026-06-08T08:40:39] Detecting strandedness (no)
[2026-06-08T08:40:39] Annotating alignments 
[2026-06-08T08:41:22] Filtering duplicates (remaining=5158061)
[2026-06-08T08:41:28] 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=4947857)
[2026-06-08T08:41:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4947857)
[2026-06-08T08:41:32] Filtering viral contigs with expression lower than the top 5 (remaining=4947857)
[2026-06-08T08:41:37] Filtering viral contigs with less than 5% coverage (remaining=4947857)
[2026-06-08T08:41:39] Estimating fragment length (mate gap mean=-85.3108, mate gap stddev=26.9255, read length mean=125.113)
[2026-06-08T08:41:39] Filtering read-through fragments with a distance <=10000bp (remaining=4579310)
[2026-06-08T08:41:41] Filtering inconsistently clipped mates (remaining=4504200)
[2026-06-08T08:41:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4396094)
[2026-06-08T08:41:47] Filtering fragments with small insert size (remaining=4395240)
[2026-06-08T08:41:49] Filtering alignments with long gaps (remaining=4395239)
[2026-06-08T08:41:51] Filtering fragments with both mates in the same gene (remaining=4394247)
[2026-06-08T08:41:54] Filtering fusions arising from hairpin structures (remaining=4196399)
[2026-06-08T08:41:56] Filtering reads with a mismatch p-value <=0.01 (remaining=1777216)
[2026-06-08T08:42:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=876832)
[2026-06-08T08:42:17] Finding fusions and counting supporting reads (total=687807)
[2026-06-08T08:42:31] Merging adjacent fusion breakpoints (remaining=675806)
[2026-06-08T08:42:33] Filtering multi-mapping fusions by alignment score and read support (remaining=390751)
[2026-06-08T08:43:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:13] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=389623)
[2026-06-08T08:43:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=208866)
[2026-06-08T08:43:14] Filtering fusions with <2 supporting reads (remaining=28101)
[2026-06-08T08:43:15] Filtering fusions with an e-value >=0.3 (remaining=6600)
[2026-06-08T08:43:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6639)
[2026-06-08T08:43:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6508)
[2026-06-08T08:43:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6508)
[2026-06-08T08:43:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6229)
[2026-06-08T08:43:25] Searching for fusions with spliced split reads (remaining=6281)
[2026-06-08T08:43:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=3861)
[2026-06-08T08:43:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3822)
[2026-06-08T08:43:32] Searching for fusions with >=4 spliced events (remaining=4700)
[2026-06-08T08:43:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2197)
[2026-06-08T08:43:50] Filtering fusions with anchors <=23nt (remaining=1925)
[2026-06-08T08:43:50] Filtering end-to-end fusions with low support (remaining=1891)
[2026-06-08T08:43:51] Filtering fusions with no coverage around the breakpoints (remaining=1846)
[2026-06-08T08:43:52] Indexing gene sequences 
[2026-06-08T08:43:58] Filtering genes with >=30% identity (remaining=577)
[2026-06-08T08:44:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=183)
[2026-06-08T08:44:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=156)
[2026-06-08T08:44:04] Searching for additional isoforms (remaining=203)
[2026-06-08T08:44:05] Assigning confidence scores to events 
[2026-06-08T08:44:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:08] Writing fusions to file 'tih_rna_sample_00097_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:44:10] Writing discarded fusions to file 'tih_rna_sample_00097_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:35] Freeing resources
[2026-06-08T08:44:54] Done (elapsed time=00:12:32, CPU time=00:12:31, peak memory=15.9gb)