[2026-06-08T07:27:52] Launching Arriba 2.4.0
[2026-06-08T07:27:52] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:28:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:28:04] Reading chimeric alignments from '1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=1038772)
[2026-06-08T07:28:20] Marking multi-mapping alignments (marked=834076)
[2026-06-08T07:28:20] Detecting strandedness (no)
[2026-06-08T07:28:20] Annotating alignments 
[2026-06-08T07:28:23] Filtering duplicates (remaining=324074)
[2026-06-08T07:28:24] 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=254107)
[2026-06-08T07:28:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=254107)
[2026-06-08T07:28:24] Filtering viral contigs with expression lower than the top 5 (remaining=254107)
[2026-06-08T07:28:24] Filtering viral contigs with less than 5% coverage (remaining=254107)
[2026-06-08T07:28:25] Estimating fragment length (mate gap mean=-59.8378, mate gap stddev=28.3301, read length mean=104.041)
[2026-06-08T07:28:25] Filtering read-through fragments with a distance <=10000bp (remaining=249476)
[2026-06-08T07:28:25] Filtering inconsistently clipped mates (remaining=241708)
[2026-06-08T07:28:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=236070)
[2026-06-08T07:28:26] Filtering fragments with small insert size (remaining=235617)
[2026-06-08T07:28:26] Filtering alignments with long gaps (remaining=235617)
[2026-06-08T07:28:26] Filtering fragments with both mates in the same gene (remaining=235556)
[2026-06-08T07:28:26] Filtering fusions arising from hairpin structures (remaining=221668)
[2026-06-08T07:28:26] Filtering reads with a mismatch p-value <=0.01 (remaining=77578)
[2026-06-08T07:28:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=12421)
[2026-06-08T07:28:27] Finding fusions and counting supporting reads (total=10525)
[2026-06-08T07:28:28] Merging adjacent fusion breakpoints (remaining=10432)
[2026-06-08T07:28:28] Filtering multi-mapping fusions by alignment score and read support (remaining=4840)
[2026-06-08T07:28:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:28:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=4714)
[2026-06-08T07:28:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=2977)
[2026-06-08T07:28:30] Filtering fusions with <2 supporting reads (remaining=153)
[2026-06-08T07:28:30] Filtering fusions with an e-value >=0.3 (remaining=89)
[2026-06-08T07:28:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=90)
[2026-06-08T07:28:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=77)
[2026-06-08T07:28:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=77)
[2026-06-08T07:28:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=70)
[2026-06-08T07:28:31] Searching for fusions with spliced split reads (remaining=71)
[2026-06-08T07:28:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=67)
[2026-06-08T07:28:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=67)
[2026-06-08T07:28:31] Searching for fusions with >=4 spliced events (remaining=67)
[2026-06-08T07:28:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=19)
[2026-06-08T07:28:46] Filtering fusions with anchors <=23nt (remaining=16)
[2026-06-08T07:28:46] Filtering end-to-end fusions with low support (remaining=16)
[2026-06-08T07:28:46] Filtering fusions with no coverage around the breakpoints (remaining=14)
[2026-06-08T07:28:46] Indexing gene sequences 
[2026-06-08T07:28:47] Filtering genes with >=30% identity (remaining=7)
[2026-06-08T07:28:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=4)
[2026-06-08T07:28:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=4)
[2026-06-08T07:28:47] Searching for additional isoforms (remaining=4)
[2026-06-08T07:28:47] Assigning confidence scores to events 
[2026-06-08T07:28:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:28:47] Writing fusions to file '1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:28:47] Writing discarded fusions to file '1173_KRT_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:28:49] Freeing resources
[2026-06-08T07:28:50] Done (elapsed time=00:00:58, CPU time=00:00:57, peak memory=5.06gb)