[2026-06-08T08:26:22] Launching Arriba 2.4.0
[2026-06-08T08:26:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:35] Reading chimeric alignments from 'tih_rna_sample_00572_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=9174155)
[2026-06-08T08:31:37] Marking multi-mapping alignments (marked=5899007)
[2026-06-08T08:31:41] Detecting strandedness (reverse)
[2026-06-08T08:31:41] Assigning strands to alignments 
[2026-06-08T08:31:43] Annotating alignments 
[2026-06-08T08:32:13] Filtering duplicates (remaining=5371255)
[2026-06-08T08:32:19] 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=5036317)
[2026-06-08T08:32:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5036317)
[2026-06-08T08:32:23] Filtering viral contigs with expression lower than the top 5 (remaining=5036317)
[2026-06-08T08:32:27] Filtering viral contigs with less than 5% coverage (remaining=5036317)
[2026-06-08T08:32:29] Estimating fragment length (mate gap mean=-87.5831, mate gap stddev=29.3567, read length mean=129.597)
[2026-06-08T08:32:30] Filtering read-through fragments with a distance <=10000bp (remaining=4784657)
[2026-06-08T08:32:31] Filtering inconsistently clipped mates (remaining=4694414)
[2026-06-08T08:32:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4585557)
[2026-06-08T08:32:37] Filtering fragments with small insert size (remaining=4584840)
[2026-06-08T08:32:39] Filtering alignments with long gaps (remaining=4584840)
[2026-06-08T08:32:41] Filtering fragments with both mates in the same gene (remaining=4584010)
[2026-06-08T08:32:43] Filtering fusions arising from hairpin structures (remaining=4277310)
[2026-06-08T08:32:45] Filtering reads with a mismatch p-value <=0.01 (remaining=1993442)
[2026-06-08T08:32:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=663654)
[2026-06-08T08:33:06] Finding fusions and counting supporting reads (total=501925)
[2026-06-08T08:33:21] Merging adjacent fusion breakpoints (remaining=495365)
[2026-06-08T08:33:23] Filtering multi-mapping fusions by alignment score and read support (remaining=313217)
[2026-06-08T08:33:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=311264)
[2026-06-08T08:34:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=173161)
[2026-06-08T08:34:01] Filtering fusions with <2 supporting reads (remaining=22877)
[2026-06-08T08:34:02] Filtering fusions with an e-value >=0.3 (remaining=6612)
[2026-06-08T08:34:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6670)
[2026-06-08T08:34:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6578)
[2026-06-08T08:34:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6578)
[2026-06-08T08:34:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5285)
[2026-06-08T08:34:12] Searching for fusions with spliced split reads (remaining=5372)
[2026-06-08T08:34:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=3707)
[2026-06-08T08:34:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3643)
[2026-06-08T08:34:19] Searching for fusions with >=4 spliced events (remaining=4109)
[2026-06-08T08:34:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1521)
[2026-06-08T08:34:35] Filtering fusions with anchors <=23nt (remaining=1140)
[2026-06-08T08:34:35] Filtering end-to-end fusions with low support (remaining=1094)
[2026-06-08T08:34:36] Filtering fusions with no coverage around the breakpoints (remaining=1058)
[2026-06-08T08:34:37] Indexing gene sequences 
[2026-06-08T08:34:41] Filtering genes with >=30% identity (remaining=339)
[2026-06-08T08:34:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=170)
[2026-06-08T08:34:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=162)
[2026-06-08T08:34:47] Searching for additional isoforms (remaining=187)
[2026-06-08T08:34:48] Assigning confidence scores to events 
[2026-06-08T08:34:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:51] Writing fusions to file 'tih_rna_sample_00572_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:53] Writing discarded fusions to file 'tih_rna_sample_00572_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:20] Freeing resources
[2026-06-08T08:35:35] Done (elapsed time=00:09:13, CPU time=00:09:11, peak memory=13.7gb)