[2026-06-08T08:40:08] Launching Arriba 2.4.0
[2026-06-08T08:40:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:20] Reading chimeric alignments from 'aih-tih-sc-3924cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10544358)
[2026-06-08T08:46:54] Marking multi-mapping alignments (marked=6596159)
[2026-06-08T08:46:58] Detecting strandedness (reverse)
[2026-06-08T08:46:58] Assigning strands to alignments 
[2026-06-08T08:47:00] Annotating alignments 
[2026-06-08T08:47:33] Filtering duplicates (remaining=6820461)
[2026-06-08T08:47:41] 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=6603823)
[2026-06-08T08:47:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6603823)
[2026-06-08T08:47:45] Filtering viral contigs with expression lower than the top 5 (remaining=6603823)
[2026-06-08T08:47:50] Filtering viral contigs with less than 5% coverage (remaining=6603823)
[2026-06-08T08:47:52] Estimating fragment length (mate gap mean=-86.9231, mate gap stddev=28.7432, read length mean=132.901)
[2026-06-08T08:47:52] Filtering read-through fragments with a distance <=10000bp (remaining=6242501)
[2026-06-08T08:47:54] Filtering inconsistently clipped mates (remaining=6158987)
[2026-06-08T08:47:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6010240)
[2026-06-08T08:48:00] Filtering fragments with small insert size (remaining=6009338)
[2026-06-08T08:48:02] Filtering alignments with long gaps (remaining=6009338)
[2026-06-08T08:48:04] Filtering fragments with both mates in the same gene (remaining=6008308)
[2026-06-08T08:48:06] Filtering fusions arising from hairpin structures (remaining=5775889)
[2026-06-08T08:48:09] Filtering reads with a mismatch p-value <=0.01 (remaining=2811819)
[2026-06-08T08:48:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=959790)
[2026-06-08T08:48:33] Finding fusions and counting supporting reads (total=704728)
[2026-06-08T08:48:49] Merging adjacent fusion breakpoints (remaining=698291)
[2026-06-08T08:48:51] Filtering multi-mapping fusions by alignment score and read support (remaining=444576)
[2026-06-08T08:49:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=443261)
[2026-06-08T08:49:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=264693)
[2026-06-08T08:49:34] Filtering fusions with <2 supporting reads (remaining=30888)
[2026-06-08T08:49:35] Filtering fusions with an e-value >=0.3 (remaining=7566)
[2026-06-08T08:49:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7614)
[2026-06-08T08:49:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7532)
[2026-06-08T08:49:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7532)
[2026-06-08T08:49:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6764)
[2026-06-08T08:49:46] Searching for fusions with spliced split reads (remaining=6881)
[2026-06-08T08:49:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=4324)
[2026-06-08T08:49:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4282)
[2026-06-08T08:49:53] Searching for fusions with >=4 spliced events (remaining=5283)
[2026-06-08T08:49:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2294)
[2026-06-08T08:50:11] Filtering fusions with anchors <=23nt (remaining=1897)
[2026-06-08T08:50:12] Filtering end-to-end fusions with low support (remaining=1860)
[2026-06-08T08:50:13] Filtering fusions with no coverage around the breakpoints (remaining=1822)
[2026-06-08T08:50:13] Indexing gene sequences 
[2026-06-08T08:50:19] Filtering genes with >=30% identity (remaining=547)
[2026-06-08T08:50:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=248)
[2026-06-08T08:50:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=208)
[2026-06-08T08:50:28] Searching for additional isoforms (remaining=271)
[2026-06-08T08:50:29] Assigning confidence scores to events 
[2026-06-08T08:50:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:33] Writing fusions to file 'aih-tih-sc-3924cb-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:35] Writing discarded fusions to file 'aih-tih-sc-3924cb-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:04] Freeing resources
[2026-06-08T08:51:21] Done (elapsed time=00:11:13, CPU time=00:11:11, peak memory=14.9gb)