[2026-06-08T08:50:39] Launching Arriba 2.4.0
[2026-06-08T08:50:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:52] Reading chimeric alignments from 'tih_rna_sample_00618_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=10624677)
[2026-06-08T08:58:04] Marking multi-mapping alignments (marked=6413299)
[2026-06-08T08:58:09] Detecting strandedness (reverse)
[2026-06-08T08:58:09] Assigning strands to alignments 
[2026-06-08T08:58:11] Annotating alignments 
[2026-06-08T08:58:56] Filtering duplicates (remaining=7082364)
[2026-06-08T08:59:11] 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=6808397)
[2026-06-08T08:59:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6808397)
[2026-06-08T08:59:20] Filtering viral contigs with expression lower than the top 5 (remaining=6808397)
[2026-06-08T08:59:28] Filtering viral contigs with less than 5% coverage (remaining=6808397)
[2026-06-08T08:59:30] Estimating fragment length (mate gap mean=-87.9411, mate gap stddev=29.6498, read length mean=135.534)
[2026-06-08T08:59:31] Filtering read-through fragments with a distance <=10000bp (remaining=6436706)
[2026-06-08T08:59:33] Filtering inconsistently clipped mates (remaining=6343383)
[2026-06-08T08:59:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6213779)
[2026-06-08T08:59:42] Filtering fragments with small insert size (remaining=6213151)
[2026-06-08T08:59:45] Filtering alignments with long gaps (remaining=6213151)
[2026-06-08T08:59:47] Filtering fragments with both mates in the same gene (remaining=6211811)
[2026-06-08T08:59:50] Filtering fusions arising from hairpin structures (remaining=5865752)
[2026-06-08T08:59:53] Filtering reads with a mismatch p-value <=0.01 (remaining=2952459)
[2026-06-08T09:00:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=1033069)
[2026-06-08T09:00:21] Finding fusions and counting supporting reads (total=758515)
[2026-06-08T09:00:41] Merging adjacent fusion breakpoints (remaining=749098)
[2026-06-08T09:00:43] Filtering multi-mapping fusions by alignment score and read support (remaining=503456)
[2026-06-08T09:01:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=501057)
[2026-06-08T09:01:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=291436)
[2026-06-08T09:01:32] Filtering fusions with <2 supporting reads (remaining=49735)
[2026-06-08T09:01:33] Filtering fusions with an e-value >=0.3 (remaining=20981)
[2026-06-08T09:01:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=21038)
[2026-06-08T09:01:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=20934)
[2026-06-08T09:01:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=20934)
[2026-06-08T09:01:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8578)
[2026-06-08T09:01:54] Searching for fusions with spliced split reads (remaining=8610)
[2026-06-08T09:02:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=4937)
[2026-06-08T09:02:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4875)
[2026-06-08T09:02:03] Searching for fusions with >=4 spliced events (remaining=6006)
[2026-06-08T09:02:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2408)
[2026-06-08T09:02:19] Filtering fusions with anchors <=23nt (remaining=1963)
[2026-06-08T09:02:20] Filtering end-to-end fusions with low support (remaining=1895)
[2026-06-08T09:02:21] Filtering fusions with no coverage around the breakpoints (remaining=1836)
[2026-06-08T09:02:22] Indexing gene sequences 
[2026-06-08T09:02:29] Filtering genes with >=30% identity (remaining=558)
[2026-06-08T09:02:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=229)
[2026-06-08T09:02:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=202)
[2026-06-08T09:02:42] Searching for additional isoforms (remaining=260)
[2026-06-08T09:02:44] Assigning confidence scores to events 
[2026-06-08T09:02:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:48] Writing fusions to file 'tih_rna_sample_00618_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:02:51] Writing discarded fusions to file 'tih_rna_sample_00618_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:28] Freeing resources
[2026-06-08T09:03:47] Done (elapsed time=00:13:08, CPU time=00:13:07, peak memory=15.2gb)