[2026-06-08T07:36:47] Launching Arriba 2.4.0
[2026-06-08T07:36:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:37:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:37:10] Reading chimeric alignments from 'tih_rna_sample_00461_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=1871748)
[2026-06-08T07:38:49] Marking multi-mapping alignments (marked=1231035)
[2026-06-08T07:38:50] Detecting strandedness (reverse)
[2026-06-08T07:38:50] Assigning strands to alignments 
[2026-06-08T07:38:50] Annotating alignments 
[2026-06-08T07:38:56] Filtering duplicates (remaining=424476)
[2026-06-08T07:38:57] 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=388839)
[2026-06-08T07:38:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=388839)
[2026-06-08T07:38:58] Filtering viral contigs with expression lower than the top 5 (remaining=388839)
[2026-06-08T07:38:59] Filtering viral contigs with less than 5% coverage (remaining=388839)
[2026-06-08T07:38:59] Estimating fragment length (mate gap mean=-85.4818, mate gap stddev=30.7227, read length mean=133.894)
[2026-06-08T07:39:00] Filtering read-through fragments with a distance <=10000bp (remaining=376115)
[2026-06-08T07:39:00] Filtering inconsistently clipped mates (remaining=368656)
[2026-06-08T07:39:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=353518)
[2026-06-08T07:39:01] Filtering fragments with small insert size (remaining=353412)
[2026-06-08T07:39:01] Filtering alignments with long gaps (remaining=353412)
[2026-06-08T07:39:01] Filtering fragments with both mates in the same gene (remaining=353205)
[2026-06-08T07:39:02] Filtering fusions arising from hairpin structures (remaining=342214)
[2026-06-08T07:39:02] Filtering reads with a mismatch p-value <=0.01 (remaining=130697)
[2026-06-08T07:39:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=36831)
[2026-06-08T07:39:05] Finding fusions and counting supporting reads (total=36090)
[2026-06-08T07:39:07] Merging adjacent fusion breakpoints (remaining=36048)
[2026-06-08T07:39:07] Filtering multi-mapping fusions by alignment score and read support (remaining=19496)
[2026-06-08T07:39:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:39:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=19266)
[2026-06-08T07:39:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=12549)
[2026-06-08T07:39:14] Filtering fusions with <2 supporting reads (remaining=670)
[2026-06-08T07:39:14] Filtering fusions with an e-value >=0.3 (remaining=225)
[2026-06-08T07:39:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=229)
[2026-06-08T07:39:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=219)
[2026-06-08T07:39:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=219)
[2026-06-08T07:39:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=191)
[2026-06-08T07:39:16] Searching for fusions with spliced split reads (remaining=219)
[2026-06-08T07:39:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=193)
[2026-06-08T07:39:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=190)
[2026-06-08T07:39:17] Searching for fusions with >=4 spliced events (remaining=196)
[2026-06-08T07:39:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=78)
[2026-06-08T07:39:36] Filtering fusions with anchors <=23nt (remaining=74)
[2026-06-08T07:39:37] Filtering end-to-end fusions with low support (remaining=69)
[2026-06-08T07:39:37] Filtering fusions with no coverage around the breakpoints (remaining=62)
[2026-06-08T07:39:37] Indexing gene sequences 
[2026-06-08T07:39:38] Filtering genes with >=30% identity (remaining=46)
[2026-06-08T07:39:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=36)
[2026-06-08T07:39:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=36)
[2026-06-08T07:39:39] Searching for additional isoforms (remaining=47)
[2026-06-08T07:39:39] Assigning confidence scores to events 
[2026-06-08T07:39:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:39:40] Writing fusions to file 'tih_rna_sample_00461_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:39:40] Writing discarded fusions to file 'tih_rna_sample_00461_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:39:44] Freeing resources
[2026-06-08T07:39:49] Done (elapsed time=00:03:02, CPU time=00:03:01, peak memory=5.94gb)