[2026-06-08T08:27:04] Launching Arriba 2.4.0
[2026-06-08T08:27:04] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:27:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:23] Reading chimeric alignments from 'aih-tih-sc-070e1d-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=13810853)
[2026-06-08T08:34:14] Marking multi-mapping alignments (marked=9353988)
[2026-06-08T08:34:20] Detecting strandedness (reverse)
[2026-06-08T08:34:20] Assigning strands to alignments 
[2026-06-08T08:34:23] Annotating alignments 
[2026-06-08T08:35:05] Filtering duplicates (remaining=5260449)
[2026-06-08T08:35:12] 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=4930561)
[2026-06-08T08:35:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4930561)
[2026-06-08T08:35:17] Filtering viral contigs with expression lower than the top 5 (remaining=4930561)
[2026-06-08T08:35:23] Filtering viral contigs with less than 5% coverage (remaining=4930561)
[2026-06-08T08:35:26] Estimating fragment length (mate gap mean=-83.5542, mate gap stddev=27.7954, read length mean=121.77)
[2026-06-08T08:35:26] Filtering read-through fragments with a distance <=10000bp (remaining=4675968)
[2026-06-08T08:35:28] Filtering inconsistently clipped mates (remaining=4598985)
[2026-06-08T08:35:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4408204)
[2026-06-08T08:35:35] Filtering fragments with small insert size (remaining=4407060)
[2026-06-08T08:35:38] Filtering alignments with long gaps (remaining=4407060)
[2026-06-08T08:35:41] Filtering fragments with both mates in the same gene (remaining=4405628)
[2026-06-08T08:35:43] Filtering fusions arising from hairpin structures (remaining=4240611)
[2026-06-08T08:35:46] Filtering reads with a mismatch p-value <=0.01 (remaining=1726779)
[2026-06-08T08:35:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=575140)
[2026-06-08T08:36:06] Finding fusions and counting supporting reads (total=489260)
[2026-06-08T08:36:24] Merging adjacent fusion breakpoints (remaining=483513)
[2026-06-08T08:36:25] Filtering multi-mapping fusions by alignment score and read support (remaining=261286)
[2026-06-08T08:37:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=260290)
[2026-06-08T08:37:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=152290)
[2026-06-08T08:37:12] Filtering fusions with <2 supporting reads (remaining=17067)
[2026-06-08T08:37:12] Filtering fusions with an e-value >=0.3 (remaining=3884)
[2026-06-08T08:37:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3926)
[2026-06-08T08:37:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3809)
[2026-06-08T08:37:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3809)
[2026-06-08T08:37:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3728)
[2026-06-08T08:37:24] Searching for fusions with spliced split reads (remaining=3768)
[2026-06-08T08:37:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=2731)
[2026-06-08T08:37:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2711)
[2026-06-08T08:37:31] Searching for fusions with >=4 spliced events (remaining=3064)
[2026-06-08T08:37:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1248)
[2026-06-08T08:37:51] Filtering fusions with anchors <=23nt (remaining=965)
[2026-06-08T08:37:51] Filtering end-to-end fusions with low support (remaining=933)
[2026-06-08T08:37:52] Filtering fusions with no coverage around the breakpoints (remaining=904)
[2026-06-08T08:37:53] Indexing gene sequences 
[2026-06-08T08:37:57] Filtering genes with >=30% identity (remaining=262)
[2026-06-08T08:37:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=68)
[2026-06-08T08:37:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=65)
[2026-06-08T08:38:00] Searching for additional isoforms (remaining=73)
[2026-06-08T08:38:01] Assigning confidence scores to events 
[2026-06-08T08:38:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:38:04] Writing fusions to file 'aih-tih-sc-070e1d-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:38:05] Writing discarded fusions to file 'aih-tih-sc-070e1d-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:28] Freeing resources
[2026-06-08T08:38:48] Done (elapsed time=00:11:44, CPU time=00:11:43, peak memory=17.9gb)