[2026-06-08T08:30:38] Launching Arriba 2.4.0
[2026-06-08T08:30:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:52] Reading chimeric alignments from 'tih_rna_sample_00088_23H5VFLT4_s02.Aligned.sortedByCoord.out.bam' (total=11377887)
[2026-06-08T08:39:06] Marking multi-mapping alignments (marked=7678632)
[2026-06-08T08:39:12] Detecting strandedness (no)
[2026-06-08T08:39:12] Annotating alignments 
[2026-06-08T08:40:11] Filtering duplicates (remaining=6558742)
[2026-06-08T08:40:21] 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=5935145)
[2026-06-08T08:40:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5935145)
[2026-06-08T08:40:27] Filtering viral contigs with expression lower than the top 5 (remaining=5935145)
[2026-06-08T08:40:34] Filtering viral contigs with less than 5% coverage (remaining=5935145)
[2026-06-08T08:40:37] Estimating fragment length (mate gap mean=-86.2046, mate gap stddev=30.177, read length mean=126.208)
[2026-06-08T08:40:37] Filtering read-through fragments with a distance <=10000bp (remaining=5604037)
[2026-06-08T08:40:40] Filtering inconsistently clipped mates (remaining=5460390)
[2026-06-08T08:40:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5064894)
[2026-06-08T08:40:50] Filtering fragments with small insert size (remaining=5062812)
[2026-06-08T08:40:52] Filtering alignments with long gaps (remaining=5062812)
[2026-06-08T08:40:56] Filtering fragments with both mates in the same gene (remaining=5061314)
[2026-06-08T08:40:59] Filtering fusions arising from hairpin structures (remaining=4530533)
[2026-06-08T08:41:03] Filtering reads with a mismatch p-value <=0.01 (remaining=1681917)
[2026-06-08T08:41:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=997927)
[2026-06-08T08:41:30] Finding fusions and counting supporting reads (total=838881)
[2026-06-08T08:41:52] Merging adjacent fusion breakpoints (remaining=828671)
[2026-06-08T08:41:54] Filtering multi-mapping fusions by alignment score and read support (remaining=475152)
[2026-06-08T08:42:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=472417)
[2026-06-08T08:42:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=287786)
[2026-06-08T08:42:54] Filtering fusions with <2 supporting reads (remaining=23216)
[2026-06-08T08:42:55] Filtering fusions with an e-value >=0.3 (remaining=4661)
[2026-06-08T08:42:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4737)
[2026-06-08T08:43:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4573)
[2026-06-08T08:43:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4573)
[2026-06-08T08:43:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4367)
[2026-06-08T08:43:14] Searching for fusions with spliced split reads (remaining=4467)
[2026-06-08T08:43:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=2944)
[2026-06-08T08:43:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2910)
[2026-06-08T08:43:25] Searching for fusions with >=4 spliced events (remaining=3370)
[2026-06-08T08:43:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1338)
[2026-06-08T08:43:44] Filtering fusions with anchors <=23nt (remaining=1039)
[2026-06-08T08:43:45] Filtering end-to-end fusions with low support (remaining=1019)
[2026-06-08T08:43:46] Filtering fusions with no coverage around the breakpoints (remaining=1000)
[2026-06-08T08:43:47] Indexing gene sequences 
[2026-06-08T08:43:55] Filtering genes with >=30% identity (remaining=323)
[2026-06-08T08:43:59] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=160)
[2026-06-08T08:44:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T08:44:05] Searching for additional isoforms (remaining=183)
[2026-06-08T08:44:07] Assigning confidence scores to events 
[2026-06-08T08:44:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:12] Writing fusions to file 'tih_rna_sample_00088_23H5VFLT4_s02.arriba.fusions.tsv' 
[2026-06-08T08:44:14] Writing discarded fusions to file 'tih_rna_sample_00088_23H5VFLT4_s02.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:02] Freeing resources
[2026-06-08T08:45:32] Done (elapsed time=00:14:54, CPU time=00:14:53, peak memory=16.6gb)