[2026-06-08T08:36:17] Launching Arriba 2.4.0
[2026-06-08T08:36:17] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:29] Reading chimeric alignments from 'tih_rna_sample_00166_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=9975415)
[2026-06-08T08:43:00] Marking multi-mapping alignments (marked=6176695)
[2026-06-08T08:43:03] Detecting strandedness (reverse)
[2026-06-08T08:43:03] Assigning strands to alignments 
[2026-06-08T08:43:05] Annotating alignments 
[2026-06-08T08:43:38] Filtering duplicates (remaining=3827549)
[2026-06-08T08:43:43] 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=3693619)
[2026-06-08T08:43:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3693619)
[2026-06-08T08:43:46] Filtering viral contigs with expression lower than the top 5 (remaining=3693619)
[2026-06-08T08:43:50] Filtering viral contigs with less than 5% coverage (remaining=3693619)
[2026-06-08T08:43:53] Estimating fragment length (mate gap mean=-87.2965, mate gap stddev=28.5277, read length mean=133.626)
[2026-06-08T08:43:53] Filtering read-through fragments with a distance <=10000bp (remaining=3469162)
[2026-06-08T08:43:55] Filtering inconsistently clipped mates (remaining=3417366)
[2026-06-08T08:43:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3314137)
[2026-06-08T08:44:00] Filtering fragments with small insert size (remaining=3313640)
[2026-06-08T08:44:02] Filtering alignments with long gaps (remaining=3313640)
[2026-06-08T08:44:04] Filtering fragments with both mates in the same gene (remaining=3312965)
[2026-06-08T08:44:06] Filtering fusions arising from hairpin structures (remaining=3177138)
[2026-06-08T08:44:08] Filtering reads with a mismatch p-value <=0.01 (remaining=1330211)
[2026-06-08T08:44:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=521739)
[2026-06-08T08:44:24] Finding fusions and counting supporting reads (total=432846)
[2026-06-08T08:44:38] Merging adjacent fusion breakpoints (remaining=429154)
[2026-06-08T08:44:39] Filtering multi-mapping fusions by alignment score and read support (remaining=270606)
[2026-06-08T08:45:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=269173)
[2026-06-08T08:45:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=133436)
[2026-06-08T08:45:17] Filtering fusions with <2 supporting reads (remaining=16253)
[2026-06-08T08:45:17] Filtering fusions with an e-value >=0.3 (remaining=4244)
[2026-06-08T08:45:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4277)
[2026-06-08T08:45:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4232)
[2026-06-08T08:45:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4232)
[2026-06-08T08:45:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3616)
[2026-06-08T08:45:26] Searching for fusions with spliced split reads (remaining=3698)
[2026-06-08T08:45:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=2608)
[2026-06-08T08:45:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2573)
[2026-06-08T08:45:32] Searching for fusions with >=4 spliced events (remaining=2992)
[2026-06-08T08:45:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=985)
[2026-06-08T08:45:45] Filtering fusions with anchors <=23nt (remaining=832)
[2026-06-08T08:45:46] Filtering end-to-end fusions with low support (remaining=815)
[2026-06-08T08:45:46] Filtering fusions with no coverage around the breakpoints (remaining=799)
[2026-06-08T08:45:47] Indexing gene sequences 
[2026-06-08T08:45:50] Filtering genes with >=30% identity (remaining=237)
[2026-06-08T08:45:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=95)
[2026-06-08T08:45:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=87)
[2026-06-08T08:45:54] Searching for additional isoforms (remaining=107)
[2026-06-08T08:45:55] Assigning confidence scores to events 
[2026-06-08T08:45:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:57] Writing fusions to file 'tih_rna_sample_00166_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:58] Writing discarded fusions to file 'tih_rna_sample_00166_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:20] Freeing resources
[2026-06-08T08:46:38] Done (elapsed time=00:10:21, CPU time=00:10:20, peak memory=14.4gb)