[2026-06-08T08:50:19] Launching Arriba 2.4.0
[2026-06-08T08:50:19] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:29] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:33] Reading chimeric alignments from 'aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12343814)
[2026-06-08T08:57:50] Marking multi-mapping alignments (marked=7703251)
[2026-06-08T08:57:55] Detecting strandedness (reverse)
[2026-06-08T08:57:55] Assigning strands to alignments 
[2026-06-08T08:57:57] Annotating alignments 
[2026-06-08T08:58:38] Filtering duplicates (remaining=7649957)
[2026-06-08T08:58:47] 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=7395316)
[2026-06-08T08:58:50] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7395316)
[2026-06-08T08:58:52] Filtering viral contigs with expression lower than the top 5 (remaining=7395316)
[2026-06-08T08:58:57] Filtering viral contigs with less than 5% coverage (remaining=7395316)
[2026-06-08T08:59:00] Estimating fragment length (mate gap mean=-88.0185, mate gap stddev=30.0699, read length mean=134.842)
[2026-06-08T08:59:00] Filtering read-through fragments with a distance <=10000bp (remaining=6972460)
[2026-06-08T08:59:03] Filtering inconsistently clipped mates (remaining=6883267)
[2026-06-08T08:59:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6738635)
[2026-06-08T08:59:10] Filtering fragments with small insert size (remaining=6737982)
[2026-06-08T08:59:12] Filtering alignments with long gaps (remaining=6737982)
[2026-06-08T08:59:15] Filtering fragments with both mates in the same gene (remaining=6736919)
[2026-06-08T08:59:17] Filtering fusions arising from hairpin structures (remaining=6455618)
[2026-06-08T08:59:20] Filtering reads with a mismatch p-value <=0.01 (remaining=3073632)
[2026-06-08T08:59:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=1148502)
[2026-06-08T08:59:49] Finding fusions and counting supporting reads (total=850729)
[2026-06-08T09:00:09] Merging adjacent fusion breakpoints (remaining=837877)
[2026-06-08T09:00:11] Filtering multi-mapping fusions by alignment score and read support (remaining=531197)
[2026-06-08T09:00:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=529516)
[2026-06-08T09:00:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=305738)
[2026-06-08T09:01:01] Filtering fusions with <2 supporting reads (remaining=43457)
[2026-06-08T09:01:01] Filtering fusions with an e-value >=0.3 (remaining=13990)
[2026-06-08T09:01:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14040)
[2026-06-08T09:01:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13750)
[2026-06-08T09:01:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13750)
[2026-06-08T09:01:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9402)
[2026-06-08T09:01:16] Searching for fusions with spliced split reads (remaining=9426)
[2026-06-08T09:01:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=5458)
[2026-06-08T09:01:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5400)
[2026-06-08T09:01:24] Searching for fusions with >=4 spliced events (remaining=6561)
[2026-06-08T09:01:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2661)
[2026-06-08T09:01:48] Filtering fusions with anchors <=23nt (remaining=1932)
[2026-06-08T09:01:49] Filtering end-to-end fusions with low support (remaining=1879)
[2026-06-08T09:01:50] Filtering fusions with no coverage around the breakpoints (remaining=1838)
[2026-06-08T09:01:51] Indexing gene sequences 
[2026-06-08T09:01:57] Filtering genes with >=30% identity (remaining=506)
[2026-06-08T09:02:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=212)
[2026-06-08T09:02:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=201)
[2026-06-08T09:02:06] Searching for additional isoforms (remaining=259)
[2026-06-08T09:02:08] Assigning confidence scores to events 
[2026-06-08T09:02:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:12] Writing fusions to file 'aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:02:14] Writing discarded fusions to file 'aih-tih-sc-3e91d2-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:02:45] Freeing resources
[2026-06-08T09:03:04] Done (elapsed time=00:12:45, CPU time=00:12:43, peak memory=16.8gb)