[2026-06-08T08:08:46] Launching Arriba 2.4.0
[2026-06-08T08:08:46] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:09:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:09:04] Reading chimeric alignments from 'aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=3651480)
[2026-06-08T08:11:23] Marking multi-mapping alignments (marked=2500192)
[2026-06-08T08:11:25] Detecting strandedness (reverse)
[2026-06-08T08:11:25] Assigning strands to alignments 
[2026-06-08T08:11:25] Annotating alignments 
[2026-06-08T08:11:37] Filtering duplicates (remaining=1277855)
[2026-06-08T08:11:39] 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=1191705)
[2026-06-08T08:11:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1191705)
[2026-06-08T08:11:40] Filtering viral contigs with expression lower than the top 5 (remaining=1191705)
[2026-06-08T08:11:41] Filtering viral contigs with less than 5% coverage (remaining=1191705)
[2026-06-08T08:11:42] Estimating fragment length (mate gap mean=-83.0926, mate gap stddev=28.9079, read length mean=124.154)
[2026-06-08T08:11:42] Filtering read-through fragments with a distance <=10000bp (remaining=1149417)
[2026-06-08T08:11:43] Filtering inconsistently clipped mates (remaining=1124054)
[2026-06-08T08:11:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1075362)
[2026-06-08T08:11:45] Filtering fragments with small insert size (remaining=1075084)
[2026-06-08T08:11:45] Filtering alignments with long gaps (remaining=1075084)
[2026-06-08T08:11:46] Filtering fragments with both mates in the same gene (remaining=1074753)
[2026-06-08T08:11:47] Filtering fusions arising from hairpin structures (remaining=1023151)
[2026-06-08T08:11:47] Filtering reads with a mismatch p-value <=0.01 (remaining=433279)
[2026-06-08T08:11:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=116900)
[2026-06-08T08:11:53] Finding fusions and counting supporting reads (total=108176)
[2026-06-08T08:11:57] Merging adjacent fusion breakpoints (remaining=107858)
[2026-06-08T08:11:58] Filtering multi-mapping fusions by alignment score and read support (remaining=54857)
[2026-06-08T08:12:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:12:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=54303)
[2026-06-08T08:12:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=32563)
[2026-06-08T08:12:11] Filtering fusions with <2 supporting reads (remaining=2288)
[2026-06-08T08:12:11] Filtering fusions with an e-value >=0.3 (remaining=721)
[2026-06-08T08:12:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=742)
[2026-06-08T08:12:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=709)
[2026-06-08T08:12:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=709)
[2026-06-08T08:12:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=688)
[2026-06-08T08:12:14] Searching for fusions with spliced split reads (remaining=762)
[2026-06-08T08:12:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=570)
[2026-06-08T08:12:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=557)
[2026-06-08T08:12:16] Searching for fusions with >=4 spliced events (remaining=604)
[2026-06-08T08:12:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=166)
[2026-06-08T08:12:29] Filtering fusions with anchors <=23nt (remaining=146)
[2026-06-08T08:12:29] Filtering end-to-end fusions with low support (remaining=142)
[2026-06-08T08:12:29] Filtering fusions with no coverage around the breakpoints (remaining=138)
[2026-06-08T08:12:30] Indexing gene sequences 
[2026-06-08T08:12:31] Filtering genes with >=30% identity (remaining=49)
[2026-06-08T08:12:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=23)
[2026-06-08T08:12:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=20)
[2026-06-08T08:12:32] Searching for additional isoforms (remaining=24)
[2026-06-08T08:12:32] Assigning confidence scores to events 
[2026-06-08T08:12:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:12:33] Writing fusions to file 'aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:12:34] Writing discarded fusions to file 'aih-tih-sc-cf89e7-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:12:40] Freeing resources
[2026-06-08T08:12:47] Done (elapsed time=00:04:01, CPU time=00:04:00, peak memory=7.77gb)