[2026-06-08T08:53:33] Launching Arriba 2.4.0
[2026-06-08T08:53:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:53] Reading chimeric alignments from 'tih_rna_sample_00604_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10185811)
[2026-06-08T09:02:04] Marking multi-mapping alignments (marked=6194814)
[2026-06-08T09:02:08] Detecting strandedness (reverse)
[2026-06-08T09:02:08] Assigning strands to alignments 
[2026-06-08T09:02:10] Annotating alignments 
[2026-06-08T09:02:42] Filtering duplicates (remaining=7086735)
[2026-06-08T09:02:49] 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=6797737)
[2026-06-08T09:02:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6797737)
[2026-06-08T09:02:53] Filtering viral contigs with expression lower than the top 5 (remaining=6797737)
[2026-06-08T09:02:58] Filtering viral contigs with less than 5% coverage (remaining=6797737)
[2026-06-08T09:03:00] Estimating fragment length (mate gap mean=-86.3115, mate gap stddev=30.6527, read length mean=135.088)
[2026-06-08T09:03:00] Filtering read-through fragments with a distance <=10000bp (remaining=6432524)
[2026-06-08T09:03:02] Filtering inconsistently clipped mates (remaining=6324560)
[2026-06-08T09:03:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6194260)
[2026-06-08T09:03:09] Filtering fragments with small insert size (remaining=6193551)
[2026-06-08T09:03:11] Filtering alignments with long gaps (remaining=6193550)
[2026-06-08T09:03:13] Filtering fragments with both mates in the same gene (remaining=6192412)
[2026-06-08T09:03:15] Filtering fusions arising from hairpin structures (remaining=5778418)
[2026-06-08T09:03:18] Filtering reads with a mismatch p-value <=0.01 (remaining=3021682)
[2026-06-08T09:03:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=1039670)
[2026-06-08T09:03:46] Finding fusions and counting supporting reads (total=760580)
[2026-06-08T09:04:03] Merging adjacent fusion breakpoints (remaining=752201)
[2026-06-08T09:04:04] Filtering multi-mapping fusions by alignment score and read support (remaining=500433)
[2026-06-08T09:04:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=497027)
[2026-06-08T09:04:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=270215)
[2026-06-08T09:04:45] Filtering fusions with <2 supporting reads (remaining=39374)
[2026-06-08T09:04:45] Filtering fusions with an e-value >=0.3 (remaining=12528)
[2026-06-08T09:04:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12593)
[2026-06-08T09:04:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12490)
[2026-06-08T09:04:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12490)
[2026-06-08T09:04:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8392)
[2026-06-08T09:04:57] Searching for fusions with spliced split reads (remaining=8410)
[2026-06-08T09:05:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=5052)
[2026-06-08T09:05:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4974)
[2026-06-08T09:05:04] Searching for fusions with >=4 spliced events (remaining=5927)
[2026-06-08T09:05:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2159)
[2026-06-08T09:05:25] Filtering fusions with anchors <=23nt (remaining=1600)
[2026-06-08T09:05:26] Filtering end-to-end fusions with low support (remaining=1553)
[2026-06-08T09:05:27] Filtering fusions with no coverage around the breakpoints (remaining=1516)
[2026-06-08T09:05:27] Indexing gene sequences 
[2026-06-08T09:05:34] Filtering genes with >=30% identity (remaining=509)
[2026-06-08T09:05:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=228)
[2026-06-08T09:05:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=189)
[2026-06-08T09:05:45] Searching for additional isoforms (remaining=268)
[2026-06-08T09:05:46] Assigning confidence scores to events 
[2026-06-08T09:05:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:50] Writing fusions to file 'tih_rna_sample_00604_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:53] Writing discarded fusions to file 'tih_rna_sample_00604_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:26] Freeing resources
[2026-06-08T09:06:43] Done (elapsed time=00:13:10, CPU time=00:13:08, peak memory=14.7gb)