[2026-06-08T07:30:53] Launching Arriba 2.4.0
[2026-06-08T07:30:53] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:31:11] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:31:18] Reading chimeric alignments from '1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=604236)
[2026-06-08T07:31:47] Marking multi-mapping alignments (marked=417374)
[2026-06-08T07:31:47] Detecting strandedness (reverse)
[2026-06-08T07:31:47] Assigning strands to alignments 
[2026-06-08T07:31:47] Annotating alignments 
[2026-06-08T07:31:50] Filtering duplicates (remaining=525822)
[2026-06-08T07:31:51] 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=464221)
[2026-06-08T07:31:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=464221)
[2026-06-08T07:31:51] Filtering viral contigs with expression lower than the top 5 (remaining=464221)
[2026-06-08T07:31:51] Filtering viral contigs with less than 5% coverage (remaining=464221)
[2026-06-08T07:31:51] Estimating fragment length (mate gap mean=-81.1537, mate gap stddev=26.1206, read length mean=120.996)
[2026-06-08T07:31:52] Filtering read-through fragments with a distance <=10000bp (remaining=452217)
[2026-06-08T07:31:52] Filtering inconsistently clipped mates (remaining=445488)
[2026-06-08T07:31:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=437773)
[2026-06-08T07:31:52] Filtering fragments with small insert size (remaining=437717)
[2026-06-08T07:31:52] Filtering alignments with long gaps (remaining=437717)
[2026-06-08T07:31:52] Filtering fragments with both mates in the same gene (remaining=437643)
[2026-06-08T07:31:52] Filtering fusions arising from hairpin structures (remaining=418944)
[2026-06-08T07:31:53] Filtering reads with a mismatch p-value <=0.01 (remaining=219713)
[2026-06-08T07:31:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=102676)
[2026-06-08T07:31:55] Finding fusions and counting supporting reads (total=104809)
[2026-06-08T07:31:56] Merging adjacent fusion breakpoints (remaining=104642)
[2026-06-08T07:31:56] Filtering multi-mapping fusions by alignment score and read support (remaining=56559)
[2026-06-08T07:31:59] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:31:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=56438)
[2026-06-08T07:31:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=48118)
[2026-06-08T07:31:59] Filtering fusions with <2 supporting reads (remaining=950)
[2026-06-08T07:32:00] Filtering fusions with an e-value >=0.3 (remaining=421)
[2026-06-08T07:32:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=443)
[2026-06-08T07:32:00] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=439)
[2026-06-08T07:32:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=439)
[2026-06-08T07:32:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=428)
[2026-06-08T07:32:00] Searching for fusions with spliced split reads (remaining=432)
[2026-06-08T07:32:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=362)
[2026-06-08T07:32:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=358)
[2026-06-08T07:32:01] Searching for fusions with >=4 spliced events (remaining=358)
[2026-06-08T07:32:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=103)
[2026-06-08T07:32:23] Filtering fusions with anchors <=23nt (remaining=78)
[2026-06-08T07:32:23] Filtering end-to-end fusions with low support (remaining=76)
[2026-06-08T07:32:23] Filtering fusions with no coverage around the breakpoints (remaining=72)
[2026-06-08T07:32:23] Indexing gene sequences 
[2026-06-08T07:32:24] Filtering genes with >=30% identity (remaining=49)
[2026-06-08T07:32:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=40)
[2026-06-08T07:32:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=40)
[2026-06-08T07:32:24] Searching for additional isoforms (remaining=41)
[2026-06-08T07:32:24] Assigning confidence scores to events 
[2026-06-08T07:32:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:32:25] Writing fusions to file '1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:32:25] Writing discarded fusions to file '1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:32:30] Freeing resources
[2026-06-08T07:32:32] Done (elapsed time=00:01:39, CPU time=00:01:38, peak memory=4.73gb)