[2026-06-08T07:37:01] Launching Arriba 2.4.0
[2026-06-08T07:37:01] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:37:10] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:37:15] Reading chimeric alignments from 'tih_rna_sample_00723_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=5406595)
[2026-06-08T07:38:58] Marking multi-mapping alignments (marked=4156790)
[2026-06-08T07:39:00] Detecting strandedness (reverse)
[2026-06-08T07:39:00] Assigning strands to alignments 
[2026-06-08T07:39:01] Annotating alignments 
[2026-06-08T07:39:27] Filtering duplicates (remaining=1928665)
[2026-06-08T07:39:32] 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=1721382)
[2026-06-08T07:39:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1721382)
[2026-06-08T07:39:34] Filtering viral contigs with expression lower than the top 5 (remaining=1721382)
[2026-06-08T07:39:36] Filtering viral contigs with less than 5% coverage (remaining=1721382)
[2026-06-08T07:39:38] Estimating fragment length (mate gap mean=-86.0149, mate gap stddev=27.9294, read length mean=117.779)
[2026-06-08T07:39:38] Filtering read-through fragments with a distance <=10000bp (remaining=1696505)
[2026-06-08T07:39:39] Filtering inconsistently clipped mates (remaining=1672989)
[2026-06-08T07:39:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1636703)
[2026-06-08T07:39:42] Filtering fragments with small insert size (remaining=1636144)
[2026-06-08T07:39:43] Filtering alignments with long gaps (remaining=1636144)
[2026-06-08T07:39:44] Filtering fragments with both mates in the same gene (remaining=1635936)
[2026-06-08T07:39:45] Filtering fusions arising from hairpin structures (remaining=1568921)
[2026-06-08T07:39:46] Filtering reads with a mismatch p-value <=0.01 (remaining=389038)
[2026-06-08T07:39:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=166852)
[2026-06-08T07:39:54] Finding fusions and counting supporting reads (total=156881)
[2026-06-08T07:40:05] Merging adjacent fusion breakpoints (remaining=155684)
[2026-06-08T07:40:06] Filtering multi-mapping fusions by alignment score and read support (remaining=87025)
[2026-06-08T07:40:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:40:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=86813)
[2026-06-08T07:40:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=64505)
[2026-06-08T07:40:33] Filtering fusions with <2 supporting reads (remaining=3813)
[2026-06-08T07:40:34] Filtering fusions with an e-value >=0.3 (remaining=839)
[2026-06-08T07:40:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=853)
[2026-06-08T07:40:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=836)
[2026-06-08T07:40:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=836)
[2026-06-08T07:40:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=832)
[2026-06-08T07:40:40] Searching for fusions with spliced split reads (remaining=849)
[2026-06-08T07:40:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=752)
[2026-06-08T07:40:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=746)
[2026-06-08T07:40:44] Searching for fusions with >=4 spliced events (remaining=795)
[2026-06-08T07:40:45] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=483)
[2026-06-08T07:41:05] Filtering fusions with anchors <=23nt (remaining=286)
[2026-06-08T07:41:05] Filtering end-to-end fusions with low support (remaining=196)
[2026-06-08T07:41:05] Filtering fusions with no coverage around the breakpoints (remaining=167)
[2026-06-08T07:41:06] Indexing gene sequences 
[2026-06-08T07:41:09] Filtering genes with >=30% identity (remaining=114)
[2026-06-08T07:41:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=94)
[2026-06-08T07:41:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=67)
[2026-06-08T07:41:11] Searching for additional isoforms (remaining=72)
[2026-06-08T07:41:11] Assigning confidence scores to events 
[2026-06-08T07:41:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:41:13] Writing fusions to file 'tih_rna_sample_00723_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:41:13] Writing discarded fusions to file 'tih_rna_sample_00723_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:41:31] Freeing resources
[2026-06-08T07:41:45] Done (elapsed time=00:04:44, CPU time=00:04:43, peak memory=9.81gb)