[2026-06-08T07:43:05] Launching Arriba 2.4.0
[2026-06-08T07:43:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:43:25] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:43:32] Reading chimeric alignments from '1173_LAF_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=19130925)
[2026-06-08T07:50:28] Marking multi-mapping alignments (marked=16950379)
[2026-06-08T07:50:36] Detecting strandedness (no)
[2026-06-08T07:50:36] Annotating alignments 
[2026-06-08T07:52:02] Filtering duplicates (remaining=6663082)
[2026-06-08T07:52:18] 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=3694778)
[2026-06-08T07:52:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3694778)
[2026-06-08T07:52:26] Filtering viral contigs with expression lower than the top 5 (remaining=3694778)
[2026-06-08T07:52:35] Filtering viral contigs with less than 5% coverage (remaining=3694778)
[2026-06-08T07:52:39] Estimating fragment length (mate gap mean=-57.9338, mate gap stddev=27.0808, read length mean=88.4302)
[2026-06-08T07:52:39] Filtering read-through fragments with a distance <=10000bp (remaining=3629635)
[2026-06-08T07:52:44] Filtering inconsistently clipped mates (remaining=3587985)
[2026-06-08T07:52:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3486585)
[2026-06-08T07:52:54] Filtering fragments with small insert size (remaining=3484998)
[2026-06-08T07:52:58] Filtering alignments with long gaps (remaining=3484997)
[2026-06-08T07:53:03] Filtering fragments with both mates in the same gene (remaining=3483879)
[2026-06-08T07:53:08] Filtering fusions arising from hairpin structures (remaining=3414534)
[2026-06-08T07:53:13] Filtering reads with a mismatch p-value <=0.01 (remaining=1103700)
[2026-06-08T07:53:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=553599)
[2026-06-08T07:53:39] Finding fusions and counting supporting reads (total=545037)
[2026-06-08T07:54:13] Merging adjacent fusion breakpoints (remaining=541811)
[2026-06-08T07:54:16] Filtering multi-mapping fusions by alignment score and read support (remaining=169019)
[2026-06-08T07:55:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:55:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=165342)
[2026-06-08T07:55:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=152627)
[2026-06-08T07:55:30] Filtering fusions with <2 supporting reads (remaining=3874)
[2026-06-08T07:55:31] Filtering fusions with an e-value >=0.3 (remaining=747)
[2026-06-08T07:55:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=773)
[2026-06-08T07:55:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=763)
[2026-06-08T07:55:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=763)
[2026-06-08T07:55:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=763)
[2026-06-08T07:55:52] Searching for fusions with spliced split reads (remaining=799)
[2026-06-08T07:56:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=613)
[2026-06-08T07:56:04] Filtering read-through fusions with breakpoints near the gene boundary (remaining=606)
[2026-06-08T07:56:05] Searching for fusions with >=4 spliced events (remaining=636)
[2026-06-08T07:56:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=237)
[2026-06-08T07:56:30] Filtering fusions with anchors <=23nt (remaining=174)
[2026-06-08T07:56:31] Filtering end-to-end fusions with low support (remaining=166)
[2026-06-08T07:56:32] Filtering fusions with no coverage around the breakpoints (remaining=161)
[2026-06-08T07:56:33] Indexing gene sequences 
[2026-06-08T07:56:36] Filtering genes with >=30% identity (remaining=90)
[2026-06-08T07:56:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=66)
[2026-06-08T07:56:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=62)
[2026-06-08T07:56:41] Searching for additional isoforms (remaining=64)
[2026-06-08T07:56:43] Assigning confidence scores to events 
[2026-06-08T07:56:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:56:48] Writing fusions to file '1173_LAF_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T07:56:49] Writing discarded fusions to file '1173_LAF_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T07:57:33] Freeing resources
[2026-06-08T07:58:16] Done (elapsed time=00:15:11, CPU time=00:15:09, peak memory=24gb)