[2026-06-08T08:50:28] Launching Arriba 2.4.0
[2026-06-08T08:50:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:42] Reading chimeric alignments from 'aih-tih-sc-1d89ab-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12372124)
[2026-06-08T08:57:30] Marking multi-mapping alignments (marked=8138036)
[2026-06-08T08:57:35] Detecting strandedness (reverse)
[2026-06-08T08:57:35] Assigning strands to alignments 
[2026-06-08T08:57:37] Annotating alignments 
[2026-06-08T08:58:16] Filtering duplicates (remaining=6544297)
[2026-06-08T08:58:24] 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=6256150)
[2026-06-08T08:58:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6256150)
[2026-06-08T08:58:29] Filtering viral contigs with expression lower than the top 5 (remaining=6256150)
[2026-06-08T08:58:35] Filtering viral contigs with less than 5% coverage (remaining=6256150)
[2026-06-08T08:58:37] Estimating fragment length (mate gap mean=-86.2638, mate gap stddev=28.3527, read length mean=129.396)
[2026-06-08T08:58:38] Filtering read-through fragments with a distance <=10000bp (remaining=5971954)
[2026-06-08T08:58:40] Filtering inconsistently clipped mates (remaining=5866678)
[2026-06-08T08:58:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5713665)
[2026-06-08T08:58:47] Filtering fragments with small insert size (remaining=5712840)
[2026-06-08T08:58:49] Filtering alignments with long gaps (remaining=5712840)
[2026-06-08T08:58:51] Filtering fragments with both mates in the same gene (remaining=5711877)
[2026-06-08T08:58:54] Filtering fusions arising from hairpin structures (remaining=5431808)
[2026-06-08T08:58:57] Filtering reads with a mismatch p-value <=0.01 (remaining=2440670)
[2026-06-08T08:59:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=755851)
[2026-06-08T08:59:21] Finding fusions and counting supporting reads (total=587165)
[2026-06-08T08:59:39] Merging adjacent fusion breakpoints (remaining=578674)
[2026-06-08T08:59:41] Filtering multi-mapping fusions by alignment score and read support (remaining=341618)
[2026-06-08T09:00:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=340044)
[2026-06-08T09:00:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=195296)
[2026-06-08T09:00:29] Filtering fusions with <2 supporting reads (remaining=23290)
[2026-06-08T09:00:30] Filtering fusions with an e-value >=0.3 (remaining=5761)
[2026-06-08T09:00:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5803)
[2026-06-08T09:00:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5672)
[2026-06-08T09:00:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5672)
[2026-06-08T09:00:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5498)
[2026-06-08T09:00:43] Searching for fusions with spliced split reads (remaining=5600)
[2026-06-08T09:00:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=3882)
[2026-06-08T09:00:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3835)
[2026-06-08T09:00:51] Searching for fusions with >=4 spliced events (remaining=4436)
[2026-06-08T09:00:53] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1871)
[2026-06-08T09:01:12] Filtering fusions with anchors <=23nt (remaining=1499)
[2026-06-08T09:01:12] Filtering end-to-end fusions with low support (remaining=1455)
[2026-06-08T09:01:13] Filtering fusions with no coverage around the breakpoints (remaining=1422)
[2026-06-08T09:01:14] Indexing gene sequences 
[2026-06-08T09:01:22] Filtering genes with >=30% identity (remaining=622)
[2026-06-08T09:01:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=412)
[2026-06-08T09:01:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=308)
[2026-06-08T09:01:33] Searching for additional isoforms (remaining=405)
[2026-06-08T09:01:35] Assigning confidence scores to events 
[2026-06-08T09:01:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:39] Writing fusions to file 'aih-tih-sc-1d89ab-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:42] Writing discarded fusions to file 'aih-tih-sc-1d89ab-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:02:12] Freeing resources
[2026-06-08T09:02:31] Done (elapsed time=00:12:03, CPU time=00:12:02, peak memory=16.6gb)