[2026-06-08T08:20:11] Launching Arriba 2.4.0
[2026-06-08T08:20:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:23] Reading chimeric alignments from 'aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9202812)
[2026-06-08T08:25:03] Marking multi-mapping alignments (marked=6418979)
[2026-06-08T08:25:06] Detecting strandedness (reverse)
[2026-06-08T08:25:06] Assigning strands to alignments 
[2026-06-08T08:25:08] Annotating alignments 
[2026-06-08T08:25:38] Filtering duplicates (remaining=4215264)
[2026-06-08T08:25:42] 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=3853760)
[2026-06-08T08:25:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3853760)
[2026-06-08T08:25:46] Filtering viral contigs with expression lower than the top 5 (remaining=3853760)
[2026-06-08T08:25:49] Filtering viral contigs with less than 5% coverage (remaining=3853760)
[2026-06-08T08:25:51] Estimating fragment length (mate gap mean=-81.1324, mate gap stddev=27.4781, read length mean=115.923)
[2026-06-08T08:25:51] Filtering read-through fragments with a distance <=10000bp (remaining=3652114)
[2026-06-08T08:25:53] Filtering inconsistently clipped mates (remaining=3553004)
[2026-06-08T08:25:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3414269)
[2026-06-08T08:25:58] Filtering fragments with small insert size (remaining=3413325)
[2026-06-08T08:26:00] Filtering alignments with long gaps (remaining=3413325)
[2026-06-08T08:26:01] Filtering fragments with both mates in the same gene (remaining=3412403)
[2026-06-08T08:26:03] Filtering fusions arising from hairpin structures (remaining=3174539)
[2026-06-08T08:26:05] Filtering reads with a mismatch p-value <=0.01 (remaining=1123099)
[2026-06-08T08:26:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=509340)
[2026-06-08T08:26:19] Finding fusions and counting supporting reads (total=443567)
[2026-06-08T08:26:32] Merging adjacent fusion breakpoints (remaining=439027)
[2026-06-08T08:26:34] Filtering multi-mapping fusions by alignment score and read support (remaining=245404)
[2026-06-08T08:27:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=244441)
[2026-06-08T08:27:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=143942)
[2026-06-08T08:27:07] Filtering fusions with <2 supporting reads (remaining=13393)
[2026-06-08T08:27:08] Filtering fusions with an e-value >=0.3 (remaining=3207)
[2026-06-08T08:27:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3268)
[2026-06-08T08:27:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3210)
[2026-06-08T08:27:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3210)
[2026-06-08T08:27:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3185)
[2026-06-08T08:27:17] Searching for fusions with spliced split reads (remaining=3240)
[2026-06-08T08:27:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=2348)
[2026-06-08T08:27:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2320)
[2026-06-08T08:27:23] Searching for fusions with >=4 spliced events (remaining=2631)
[2026-06-08T08:27:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1045)
[2026-06-08T08:27:38] Filtering fusions with anchors <=23nt (remaining=780)
[2026-06-08T08:27:39] Filtering end-to-end fusions with low support (remaining=762)
[2026-06-08T08:27:39] Filtering fusions with no coverage around the breakpoints (remaining=744)
[2026-06-08T08:27:40] Indexing gene sequences 
[2026-06-08T08:27:44] Filtering genes with >=30% identity (remaining=244)
[2026-06-08T08:27:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=111)
[2026-06-08T08:27:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=96)
[2026-06-08T08:27:48] Searching for additional isoforms (remaining=121)
[2026-06-08T08:27:49] Assigning confidence scores to events 
[2026-06-08T08:27:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:52] Writing fusions to file 'aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:27:53] Writing discarded fusions to file 'aih-tih-sc-ffd2af-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:13] Freeing resources
[2026-06-08T08:28:27] Done (elapsed time=00:08:16, CPU time=00:08:15, peak memory=13.8gb)