[2026-06-08T09:07:36] Launching Arriba 2.4.0
[2026-06-08T09:07:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:07:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:07:50] Reading chimeric alignments from 'tih_rna_sample_00626_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam' (total=11329835)
[2026-06-08T09:14:43] Marking multi-mapping alignments (marked=6970356)
[2026-06-08T09:14:49] Detecting strandedness (reverse)
[2026-06-08T09:14:49] Assigning strands to alignments 
[2026-06-08T09:14:51] Annotating alignments 
[2026-06-08T09:15:30] Filtering duplicates (remaining=7451774)
[2026-06-08T09:15:39] 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=7143956)
[2026-06-08T09:15:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7143956)
[2026-06-08T09:15:44] Filtering viral contigs with expression lower than the top 5 (remaining=7143956)
[2026-06-08T09:15:49] Filtering viral contigs with less than 5% coverage (remaining=7143956)
[2026-06-08T09:15:52] Estimating fragment length (mate gap mean=-86.9865, mate gap stddev=28.0775, read length mean=129.979)
[2026-06-08T09:15:52] Filtering read-through fragments with a distance <=10000bp (remaining=6634447)
[2026-06-08T09:15:55] Filtering inconsistently clipped mates (remaining=6525465)
[2026-06-08T09:15:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6401754)
[2026-06-08T09:16:03] Filtering fragments with small insert size (remaining=6400656)
[2026-06-08T09:16:06] Filtering alignments with long gaps (remaining=6400656)
[2026-06-08T09:16:09] Filtering fragments with both mates in the same gene (remaining=6399568)
[2026-06-08T09:16:12] Filtering fusions arising from hairpin structures (remaining=6039637)
[2026-06-08T09:16:15] Filtering reads with a mismatch p-value <=0.01 (remaining=2970327)
[2026-06-08T09:16:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=1156949)
[2026-06-08T09:16:45] Finding fusions and counting supporting reads (total=861442)
[2026-06-08T09:17:05] Merging adjacent fusion breakpoints (remaining=846934)
[2026-06-08T09:17:07] Filtering multi-mapping fusions by alignment score and read support (remaining=549072)
[2026-06-08T09:17:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:17:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=547125)
[2026-06-08T09:17:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280550)
[2026-06-08T09:17:57] Filtering fusions with <2 supporting reads (remaining=38616)
[2026-06-08T09:17:58] Filtering fusions with an e-value >=0.3 (remaining=9760)
[2026-06-08T09:17:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9832)
[2026-06-08T09:18:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9718)
[2026-06-08T09:18:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9718)
[2026-06-08T09:18:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8049)
[2026-06-08T09:18:12] Searching for fusions with spliced split reads (remaining=8168)
[2026-06-08T09:18:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=5139)
[2026-06-08T09:18:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5091)
[2026-06-08T09:18:20] Searching for fusions with >=4 spliced events (remaining=6124)
[2026-06-08T09:18:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2475)
[2026-06-08T09:18:38] Filtering fusions with anchors <=23nt (remaining=1933)
[2026-06-08T09:18:39] Filtering end-to-end fusions with low support (remaining=1888)
[2026-06-08T09:18:40] Filtering fusions with no coverage around the breakpoints (remaining=1857)
[2026-06-08T09:18:41] Indexing gene sequences 
[2026-06-08T09:18:47] Filtering genes with >=30% identity (remaining=556)
[2026-06-08T09:18:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=179)
[2026-06-08T09:18:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=174)
[2026-06-08T09:18:56] Searching for additional isoforms (remaining=210)
[2026-06-08T09:18:57] Assigning confidence scores to events 
[2026-06-08T09:19:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:19:01] Writing fusions to file 'tih_rna_sample_00626_B23MVV7LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:19:03] Writing discarded fusions to file 'tih_rna_sample_00626_B23MVV7LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:19:39] Freeing resources
[2026-06-08T09:19:58] Done (elapsed time=00:12:22, CPU time=00:12:20, peak memory=16gb)