[2026-06-08T07:59:09] Launching Arriba 2.4.0
[2026-06-08T07:59:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:59:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:59:33] Reading chimeric alignments from '1173_QJL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=7051426)
[2026-06-08T08:04:56] Marking multi-mapping alignments (marked=4912105)
[2026-06-08T08:04:59] Detecting strandedness (no)
[2026-06-08T08:04:59] Annotating alignments 
[2026-06-08T08:05:30] Filtering duplicates (remaining=5352280)
[2026-06-08T08:05:36] 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=4774643)
[2026-06-08T08:05:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4774643)
[2026-06-08T08:05:38] Filtering viral contigs with expression lower than the top 5 (remaining=4774643)
[2026-06-08T08:05:42] Filtering viral contigs with less than 5% coverage (remaining=4774643)
[2026-06-08T08:05:43] Estimating fragment length (mate gap mean=-79.4315, mate gap stddev=26.8615, read length mean=117.216)
[2026-06-08T08:05:44] Filtering read-through fragments with a distance <=10000bp (remaining=4606522)
[2026-06-08T08:05:45] Filtering inconsistently clipped mates (remaining=4556004)
[2026-06-08T08:05:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4472480)
[2026-06-08T08:05:50] Filtering fragments with small insert size (remaining=4471847)
[2026-06-08T08:05:51] Filtering alignments with long gaps (remaining=4471847)
[2026-06-08T08:05:52] Filtering fragments with both mates in the same gene (remaining=4470943)
[2026-06-08T08:05:54] Filtering fusions arising from hairpin structures (remaining=4355694)
[2026-06-08T08:05:56] Filtering reads with a mismatch p-value <=0.01 (remaining=2073418)
[2026-06-08T08:06:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=881286)
[2026-06-08T08:06:17] Finding fusions and counting supporting reads (total=803389)
[2026-06-08T08:06:29] Merging adjacent fusion breakpoints (remaining=799463)
[2026-06-08T08:06:31] Filtering multi-mapping fusions by alignment score and read support (remaining=413346)
[2026-06-08T08:06:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:07:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=412549)
[2026-06-08T08:07:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=346323)
[2026-06-08T08:07:04] Filtering fusions with <2 supporting reads (remaining=13752)
[2026-06-08T08:07:05] Filtering fusions with an e-value >=0.3 (remaining=2794)
[2026-06-08T08:07:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2832)
[2026-06-08T08:07:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2804)
[2026-06-08T08:07:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2814)
[2026-06-08T08:07:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2800)
[2026-06-08T08:07:15] Searching for fusions with spliced split reads (remaining=2854)
[2026-06-08T08:07:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=2156)
[2026-06-08T08:07:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2122)
[2026-06-08T08:07:21] Searching for fusions with >=4 spliced events (remaining=2368)
[2026-06-08T08:07:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=994)
[2026-06-08T08:07:38] Filtering fusions with anchors <=23nt (remaining=819)
[2026-06-08T08:07:39] Filtering end-to-end fusions with low support (remaining=799)
[2026-06-08T08:07:40] Filtering fusions with no coverage around the breakpoints (remaining=782)
[2026-06-08T08:07:40] Indexing gene sequences 
[2026-06-08T08:07:46] Filtering genes with >=30% identity (remaining=397)
[2026-06-08T08:07:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=277)
[2026-06-08T08:07:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=217)
[2026-06-08T08:07:57] Searching for additional isoforms (remaining=270)
[2026-06-08T08:07:58] Assigning confidence scores to events 
[2026-06-08T08:08:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:08:02] Writing fusions to file '1173_QJL_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:08:04] Writing discarded fusions to file '1173_QJL_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:08:32] Freeing resources
[2026-06-08T08:08:43] Done (elapsed time=00:09:34, CPU time=00:09:34, peak memory=11.5gb)