[2026-06-08T07:34:51] Launching Arriba 2.4.0
[2026-06-08T07:34:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:35:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:35:14] Reading chimeric alignments from '1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=2101689)
[2026-06-08T07:36:34] Marking multi-mapping alignments (marked=1540280)
[2026-06-08T07:36:35] Detecting strandedness (reverse)
[2026-06-08T07:36:35] Assigning strands to alignments 
[2026-06-08T07:36:35] Annotating alignments 
[2026-06-08T07:36:42] Filtering duplicates (remaining=587279)
[2026-06-08T07:36:43] 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=516287)
[2026-06-08T07:36:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=516287)
[2026-06-08T07:36:44] Filtering viral contigs with expression lower than the top 5 (remaining=516287)
[2026-06-08T07:36:45] Filtering viral contigs with less than 5% coverage (remaining=516287)
[2026-06-08T07:36:45] Estimating fragment length (mate gap mean=-78.9154, mate gap stddev=30.337, read length mean=124.95)
[2026-06-08T07:36:46] Filtering read-through fragments with a distance <=10000bp (remaining=503020)
[2026-06-08T07:36:46] Filtering inconsistently clipped mates (remaining=492608)
[2026-06-08T07:36:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=473650)
[2026-06-08T07:36:47] Filtering fragments with small insert size (remaining=473489)
[2026-06-08T07:36:47] Filtering alignments with long gaps (remaining=473489)
[2026-06-08T07:36:48] Filtering fragments with both mates in the same gene (remaining=473361)
[2026-06-08T07:36:48] Filtering fusions arising from hairpin structures (remaining=456197)
[2026-06-08T07:36:49] Filtering reads with a mismatch p-value <=0.01 (remaining=172977)
[2026-06-08T07:36:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=32598)
[2026-06-08T07:36:51] Finding fusions and counting supporting reads (total=29404)
[2026-06-08T07:36:54] Merging adjacent fusion breakpoints (remaining=29306)
[2026-06-08T07:36:54] Filtering multi-mapping fusions by alignment score and read support (remaining=13475)
[2026-06-08T07:37:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:37:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=13241)
[2026-06-08T07:37:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=8318)
[2026-06-08T07:37:02] Filtering fusions with <2 supporting reads (remaining=392)
[2026-06-08T07:37:02] Filtering fusions with an e-value >=0.3 (remaining=162)
[2026-06-08T07:37:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=164)
[2026-06-08T07:37:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=141)
[2026-06-08T07:37:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=141)
[2026-06-08T07:37:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=134)
[2026-06-08T07:37:04] Searching for fusions with spliced split reads (remaining=151)
[2026-06-08T07:37:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=128)
[2026-06-08T07:37:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=124)
[2026-06-08T07:37:05] Searching for fusions with >=4 spliced events (remaining=134)
[2026-06-08T07:37:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=42)
[2026-06-08T07:37:24] Filtering fusions with anchors <=23nt (remaining=33)
[2026-06-08T07:37:24] Filtering end-to-end fusions with low support (remaining=33)
[2026-06-08T07:37:24] Filtering fusions with no coverage around the breakpoints (remaining=30)
[2026-06-08T07:37:24] Indexing gene sequences 
[2026-06-08T07:37:25] Filtering genes with >=30% identity (remaining=16)
[2026-06-08T07:37:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=9)
[2026-06-08T07:37:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=6)
[2026-06-08T07:37:25] Searching for additional isoforms (remaining=6)
[2026-06-08T07:37:25] Assigning confidence scores to events 
[2026-06-08T07:37:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:37:26] Writing fusions to file '1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:37:26] Writing discarded fusions to file '1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:37:29] Freeing resources
[2026-06-08T07:37:34] Done (elapsed time=00:02:43, CPU time=00:02:42, peak memory=6.11gb)