[2026-06-08T08:32:30] Launching Arriba 2.4.0
[2026-06-08T08:32:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:42] Reading chimeric alignments from 'aih-tih-sc-3eb8dd-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8255531)
[2026-06-08T08:38:00] Marking multi-mapping alignments (marked=5531948)
[2026-06-08T08:38:04] Detecting strandedness (reverse)
[2026-06-08T08:38:04] Assigning strands to alignments 
[2026-06-08T08:38:05] Annotating alignments 
[2026-06-08T08:38:33] Filtering duplicates (remaining=5080007)
[2026-06-08T08:38:38] 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=4791415)
[2026-06-08T08:38:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4791415)
[2026-06-08T08:38:42] Filtering viral contigs with expression lower than the top 5 (remaining=4791415)
[2026-06-08T08:38:45] Filtering viral contigs with less than 5% coverage (remaining=4791415)
[2026-06-08T08:38:47] Estimating fragment length (mate gap mean=-86.2828, mate gap stddev=28.0181, read length mean=128.754)
[2026-06-08T08:38:47] Filtering read-through fragments with a distance <=10000bp (remaining=4404293)
[2026-06-08T08:38:49] Filtering inconsistently clipped mates (remaining=4320889)
[2026-06-08T08:38:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4217320)
[2026-06-08T08:38:53] Filtering fragments with small insert size (remaining=4216679)
[2026-06-08T08:38:55] Filtering alignments with long gaps (remaining=4216679)
[2026-06-08T08:38:57] Filtering fragments with both mates in the same gene (remaining=4215993)
[2026-06-08T08:38:59] Filtering fusions arising from hairpin structures (remaining=3935178)
[2026-06-08T08:39:01] Filtering reads with a mismatch p-value <=0.01 (remaining=1825121)
[2026-06-08T08:39:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=797793)
[2026-06-08T08:39:19] Finding fusions and counting supporting reads (total=641300)
[2026-06-08T08:39:33] Merging adjacent fusion breakpoints (remaining=631196)
[2026-06-08T08:39:34] Filtering multi-mapping fusions by alignment score and read support (remaining=376620)
[2026-06-08T08:40:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=374918)
[2026-06-08T08:40:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=200709)
[2026-06-08T08:40:10] Filtering fusions with <2 supporting reads (remaining=21456)
[2026-06-08T08:40:10] Filtering fusions with an e-value >=0.3 (remaining=6068)
[2026-06-08T08:40:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6127)
[2026-06-08T08:40:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6053)
[2026-06-08T08:40:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6056)
[2026-06-08T08:40:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4782)
[2026-06-08T08:40:20] Searching for fusions with spliced split reads (remaining=4874)
[2026-06-08T08:40:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=3070)
[2026-06-08T08:40:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3050)
[2026-06-08T08:40:27] Searching for fusions with >=4 spliced events (remaining=3655)
[2026-06-08T08:40:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1708)
[2026-06-08T08:40:44] Filtering fusions with anchors <=23nt (remaining=1369)
[2026-06-08T08:40:45] Filtering end-to-end fusions with low support (remaining=1330)
[2026-06-08T08:40:46] Filtering fusions with no coverage around the breakpoints (remaining=1299)
[2026-06-08T08:40:46] Indexing gene sequences 
[2026-06-08T08:40:53] Filtering genes with >=30% identity (remaining=408)
[2026-06-08T08:40:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=143)
[2026-06-08T08:40:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=118)
[2026-06-08T08:41:00] Searching for additional isoforms (remaining=173)
[2026-06-08T08:41:01] Assigning confidence scores to events 
[2026-06-08T08:41:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:04] Writing fusions to file 'aih-tih-sc-3eb8dd-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:05] Writing discarded fusions to file 'aih-tih-sc-3eb8dd-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:32] Freeing resources
[2026-06-08T08:41:47] Done (elapsed time=00:09:17, CPU time=00:09:16, peak memory=12.9gb)