[2026-06-08T08:29:09] Launching Arriba 2.4.0
[2026-06-08T08:29:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:21] Reading chimeric alignments from 'tih_rna_sample_00149_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=8119938)
[2026-06-08T08:34:24] Marking multi-mapping alignments (marked=5065229)
[2026-06-08T08:34:28] Detecting strandedness (reverse)
[2026-06-08T08:34:28] Assigning strands to alignments 
[2026-06-08T08:34:30] Annotating alignments 
[2026-06-08T08:34:58] Filtering duplicates (remaining=3291249)
[2026-06-08T08:35:03] 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=3138211)
[2026-06-08T08:35:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3138211)
[2026-06-08T08:35:06] Filtering viral contigs with expression lower than the top 5 (remaining=3138211)
[2026-06-08T08:35:09] Filtering viral contigs with less than 5% coverage (remaining=3138211)
[2026-06-08T08:35:11] Estimating fragment length (mate gap mean=-88.4821, mate gap stddev=27.2975, read length mean=130.547)
[2026-06-08T08:35:11] Filtering read-through fragments with a distance <=10000bp (remaining=2920548)
[2026-06-08T08:35:13] Filtering inconsistently clipped mates (remaining=2871515)
[2026-06-08T08:35:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2774005)
[2026-06-08T08:35:17] Filtering fragments with small insert size (remaining=2773586)
[2026-06-08T08:35:19] Filtering alignments with long gaps (remaining=2773586)
[2026-06-08T08:35:20] Filtering fragments with both mates in the same gene (remaining=2773036)
[2026-06-08T08:35:22] Filtering fusions arising from hairpin structures (remaining=2639429)
[2026-06-08T08:35:24] Filtering reads with a mismatch p-value <=0.01 (remaining=1118963)
[2026-06-08T08:35:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=506289)
[2026-06-08T08:35:39] Finding fusions and counting supporting reads (total=435906)
[2026-06-08T08:35:53] Merging adjacent fusion breakpoints (remaining=432389)
[2026-06-08T08:35:54] Filtering multi-mapping fusions by alignment score and read support (remaining=253687)
[2026-06-08T08:36:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=252456)
[2026-06-08T08:36:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=134381)
[2026-06-08T08:36:27] Filtering fusions with <2 supporting reads (remaining=15823)
[2026-06-08T08:36:27] Filtering fusions with an e-value >=0.3 (remaining=4116)
[2026-06-08T08:36:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4139)
[2026-06-08T08:36:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4077)
[2026-06-08T08:36:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4077)
[2026-06-08T08:36:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3611)
[2026-06-08T08:36:35] Searching for fusions with spliced split reads (remaining=3686)
[2026-06-08T08:36:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=2553)
[2026-06-08T08:36:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2539)
[2026-06-08T08:36:40] Searching for fusions with >=4 spliced events (remaining=2891)
[2026-06-08T08:36:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1072)
[2026-06-08T08:36:53] Filtering fusions with anchors <=23nt (remaining=884)
[2026-06-08T08:36:54] Filtering end-to-end fusions with low support (remaining=863)
[2026-06-08T08:36:54] Filtering fusions with no coverage around the breakpoints (remaining=847)
[2026-06-08T08:36:55] Indexing gene sequences 
[2026-06-08T08:36:58] Filtering genes with >=30% identity (remaining=292)
[2026-06-08T08:37:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=159)
[2026-06-08T08:37:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=123)
[2026-06-08T08:37:03] Searching for additional isoforms (remaining=163)
[2026-06-08T08:37:04] Assigning confidence scores to events 
[2026-06-08T08:37:06] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:06] Writing fusions to file 'tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:37:07] Writing discarded fusions to file 'tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:27] Freeing resources
[2026-06-08T08:37:41] Done (elapsed time=00:08:32, CPU time=00:08:31, peak memory=12.6gb)