[2026-06-08T08:41:31] Launching Arriba 2.4.0
[2026-06-08T08:41:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:44] Reading chimeric alignments from 'tih_rna_sample_00729_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=12046667)
[2026-06-08T08:48:40] Marking multi-mapping alignments (marked=7983005)
[2026-06-08T08:48:46] Detecting strandedness (reverse)
[2026-06-08T08:48:46] Assigning strands to alignments 
[2026-06-08T08:48:48] Annotating alignments 
[2026-06-08T08:49:29] Filtering duplicates (remaining=6951543)
[2026-06-08T08:49:38] 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=6481400)
[2026-06-08T08:49:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6481400)
[2026-06-08T08:49:43] Filtering viral contigs with expression lower than the top 5 (remaining=6481400)
[2026-06-08T08:49:49] Filtering viral contigs with less than 5% coverage (remaining=6481400)
[2026-06-08T08:49:52] Estimating fragment length (mate gap mean=-88.5408, mate gap stddev=29.0702, read length mean=131.465)
[2026-06-08T08:49:52] Filtering read-through fragments with a distance <=10000bp (remaining=6169512)
[2026-06-08T08:49:54] Filtering inconsistently clipped mates (remaining=6080865)
[2026-06-08T08:49:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5953900)
[2026-06-08T08:50:02] Filtering fragments with small insert size (remaining=5953224)
[2026-06-08T08:50:05] Filtering alignments with long gaps (remaining=5953223)
[2026-06-08T08:50:07] Filtering fragments with both mates in the same gene (remaining=5952255)
[2026-06-08T08:50:10] Filtering fusions arising from hairpin structures (remaining=5673589)
[2026-06-08T08:50:13] Filtering reads with a mismatch p-value <=0.01 (remaining=2450637)
[2026-06-08T08:50:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=861989)
[2026-06-08T08:50:39] Finding fusions and counting supporting reads (total=626548)
[2026-06-08T08:50:59] Merging adjacent fusion breakpoints (remaining=618968)
[2026-06-08T08:51:01] Filtering multi-mapping fusions by alignment score and read support (remaining=387454)
[2026-06-08T08:51:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=385354)
[2026-06-08T08:51:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=233552)
[2026-06-08T08:51:52] Filtering fusions with <2 supporting reads (remaining=29365)
[2026-06-08T08:51:53] Filtering fusions with an e-value >=0.3 (remaining=7719)
[2026-06-08T08:51:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7767)
[2026-06-08T08:51:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7692)
[2026-06-08T08:51:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7692)
[2026-06-08T08:52:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6352)
[2026-06-08T08:52:06] Searching for fusions with spliced split reads (remaining=6461)
[2026-06-08T08:52:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=4279)
[2026-06-08T08:52:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4224)
[2026-06-08T08:52:14] Searching for fusions with >=4 spliced events (remaining=4863)
[2026-06-08T08:52:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1903)
[2026-06-08T08:52:30] Filtering fusions with anchors <=23nt (remaining=1371)
[2026-06-08T08:52:31] Filtering end-to-end fusions with low support (remaining=1259)
[2026-06-08T08:52:32] Filtering fusions with no coverage around the breakpoints (remaining=1217)
[2026-06-08T08:52:32] Indexing gene sequences 
[2026-06-08T08:52:37] Filtering genes with >=30% identity (remaining=369)
[2026-06-08T08:52:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=191)
[2026-06-08T08:52:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=183)
[2026-06-08T08:52:46] Searching for additional isoforms (remaining=218)
[2026-06-08T08:52:48] Assigning confidence scores to events 
[2026-06-08T08:52:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:51] Writing fusions to file 'tih_rna_sample_00729_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:53] Writing discarded fusions to file 'tih_rna_sample_00729_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:25] Freeing resources
[2026-06-08T08:53:44] Done (elapsed time=00:12:13, CPU time=00:12:12, peak memory=16.8gb)