[2026-06-08T07:32:51] Launching Arriba 2.4.0
[2026-06-08T07:32:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:33:09] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:33:16] Reading chimeric alignments from 'aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=2026378)
[2026-06-08T07:34:35] Marking multi-mapping alignments (marked=1547020)
[2026-06-08T07:34:36] Detecting strandedness (no)
[2026-06-08T07:34:36] Annotating alignments 
[2026-06-08T07:34:46] Filtering duplicates (remaining=695583)
[2026-06-08T07:34:47] 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=594393)
[2026-06-08T07:34:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=594393)
[2026-06-08T07:34:48] Filtering viral contigs with expression lower than the top 5 (remaining=594393)
[2026-06-08T07:34:49] Filtering viral contigs with less than 5% coverage (remaining=594393)
[2026-06-08T07:34:49] Estimating fragment length (mate gap mean=-72.2092, mate gap stddev=27.4851, read length mean=105.762)
[2026-06-08T07:34:49] Filtering read-through fragments with a distance <=10000bp (remaining=575125)
[2026-06-08T07:34:50] Filtering inconsistently clipped mates (remaining=553517)
[2026-06-08T07:34:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=519915)
[2026-06-08T07:34:51] Filtering fragments with small insert size (remaining=519328)
[2026-06-08T07:34:51] Filtering alignments with long gaps (remaining=519328)
[2026-06-08T07:34:52] Filtering fragments with both mates in the same gene (remaining=518886)
[2026-06-08T07:34:52] Filtering fusions arising from hairpin structures (remaining=478856)
[2026-06-08T07:34:53] Filtering reads with a mismatch p-value <=0.01 (remaining=127366)
[2026-06-08T07:34:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=59059)
[2026-06-08T07:34:55] Finding fusions and counting supporting reads (total=59942)
[2026-06-08T07:34:58] Merging adjacent fusion breakpoints (remaining=59668)
[2026-06-08T07:34:59] Filtering multi-mapping fusions by alignment score and read support (remaining=27031)
[2026-06-08T07:35:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:35:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=26777)
[2026-06-08T07:35:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=18187)
[2026-06-08T07:35:08] Filtering fusions with <2 supporting reads (remaining=637)
[2026-06-08T07:35:08] Filtering fusions with an e-value >=0.3 (remaining=261)
[2026-06-08T07:35:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=274)
[2026-06-08T07:35:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=253)
[2026-06-08T07:35:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=253)
[2026-06-08T07:35:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=240)
[2026-06-08T07:35:10] Searching for fusions with spliced split reads (remaining=251)
[2026-06-08T07:35:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=193)
[2026-06-08T07:35:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=190)
[2026-06-08T07:35:11] Searching for fusions with >=4 spliced events (remaining=190)
[2026-06-08T07:35:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=61)
[2026-06-08T07:35:36] Filtering fusions with anchors <=23nt (remaining=51)
[2026-06-08T07:35:36] Filtering end-to-end fusions with low support (remaining=44)
[2026-06-08T07:35:36] Filtering fusions with no coverage around the breakpoints (remaining=41)
[2026-06-08T07:35:37] Indexing gene sequences 
[2026-06-08T07:35:37] Filtering genes with >=30% identity (remaining=8)
[2026-06-08T07:35:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-06-08T07:35:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-06-08T07:35:38] Searching for additional isoforms (remaining=3)
[2026-06-08T07:35:38] Assigning confidence scores to events 
[2026-06-08T07:35:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:35:39] Writing fusions to file 'aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:35:39] Writing discarded fusions to file 'aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:35:44] Freeing resources
[2026-06-08T07:35:49] Done (elapsed time=00:02:58, CPU time=00:02:57, peak memory=6.22gb)