[2026-06-08T08:47:24] Launching Arriba 2.4.0
[2026-06-08T08:47:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:39] Reading chimeric alignments from 'tih_rna_sample_00434_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10028942)
[2026-06-08T08:53:51] Marking multi-mapping alignments (marked=6324424)
[2026-06-08T08:53:55] Detecting strandedness (reverse)
[2026-06-08T08:53:55] Assigning strands to alignments 
[2026-06-08T08:53:56] Annotating alignments 
[2026-06-08T08:54:25] Filtering duplicates (remaining=3729901)
[2026-06-08T08:54:29] 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=3561991)
[2026-06-08T08:54:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3561991)
[2026-06-08T08:54:33] Filtering viral contigs with expression lower than the top 5 (remaining=3561991)
[2026-06-08T08:54:36] Filtering viral contigs with less than 5% coverage (remaining=3561991)
[2026-06-08T08:54:38] Estimating fragment length (mate gap mean=-86.2522, mate gap stddev=27.5009, read length mean=128.184)
[2026-06-08T08:54:38] Filtering read-through fragments with a distance <=10000bp (remaining=3347794)
[2026-06-08T08:54:40] Filtering inconsistently clipped mates (remaining=3292838)
[2026-06-08T08:54:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3208498)
[2026-06-08T08:54:45] Filtering fragments with small insert size (remaining=3207976)
[2026-06-08T08:54:46] Filtering alignments with long gaps (remaining=3207976)
[2026-06-08T08:54:48] Filtering fragments with both mates in the same gene (remaining=3207270)
[2026-06-08T08:54:50] Filtering fusions arising from hairpin structures (remaining=3072159)
[2026-06-08T08:54:52] Filtering reads with a mismatch p-value <=0.01 (remaining=1303755)
[2026-06-08T08:55:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=542191)
[2026-06-08T08:55:07] Finding fusions and counting supporting reads (total=449925)
[2026-06-08T08:55:20] Merging adjacent fusion breakpoints (remaining=446077)
[2026-06-08T08:55:21] Filtering multi-mapping fusions by alignment score and read support (remaining=277479)
[2026-06-08T08:55:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:55:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=276121)
[2026-06-08T08:55:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=140819)
[2026-06-08T08:55:55] Filtering fusions with <2 supporting reads (remaining=18697)
[2026-06-08T08:55:55] Filtering fusions with an e-value >=0.3 (remaining=5408)
[2026-06-08T08:55:56] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5441)
[2026-06-08T08:55:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5395)
[2026-06-08T08:55:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5395)
[2026-06-08T08:56:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4486)
[2026-06-08T08:56:03] Searching for fusions with spliced split reads (remaining=4544)
[2026-06-08T08:56:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=3121)
[2026-06-08T08:56:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3082)
[2026-06-08T08:56:08] Searching for fusions with >=4 spliced events (remaining=3459)
[2026-06-08T08:56:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1078)
[2026-06-08T08:56:22] Filtering fusions with anchors <=23nt (remaining=904)
[2026-06-08T08:56:22] Filtering end-to-end fusions with low support (remaining=874)
[2026-06-08T08:56:23] Filtering fusions with no coverage around the breakpoints (remaining=849)
[2026-06-08T08:56:23] Indexing gene sequences 
[2026-06-08T08:56:27] Filtering genes with >=30% identity (remaining=293)
[2026-06-08T08:56:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=142)
[2026-06-08T08:56:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=138)
[2026-06-08T08:56:31] Searching for additional isoforms (remaining=157)
[2026-06-08T08:56:32] Assigning confidence scores to events 
[2026-06-08T08:56:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:56:34] Writing fusions to file 'tih_rna_sample_00434_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:35] Writing discarded fusions to file 'tih_rna_sample_00434_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:54] Freeing resources
[2026-06-08T08:57:10] Done (elapsed time=00:09:46, CPU time=00:09:45, peak memory=14.4gb)