[2026-06-08T08:40:33] Launching Arriba 2.4.0
[2026-06-08T08:40:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:45] Reading chimeric alignments from '1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=16637897)
[2026-06-08T08:47:55] Marking multi-mapping alignments (marked=11388388)
[2026-06-08T08:48:01] Detecting strandedness (reverse)
[2026-06-08T08:48:01] Assigning strands to alignments 
[2026-06-08T08:48:05] Annotating alignments 
[2026-06-08T08:48:57] Filtering duplicates (remaining=9853002)
[2026-06-08T08:49:08] 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=9244215)
[2026-06-08T08:49:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9244215)
[2026-06-08T08:49:14] Filtering viral contigs with expression lower than the top 5 (remaining=9244215)
[2026-06-08T08:49:22] Filtering viral contigs with less than 5% coverage (remaining=9244215)
[2026-06-08T08:49:26] Estimating fragment length (mate gap mean=-83.3, mate gap stddev=27.0206, read length mean=125.294)
[2026-06-08T08:49:26] Filtering read-through fragments with a distance <=10000bp (remaining=8952263)
[2026-06-08T08:49:29] Filtering inconsistently clipped mates (remaining=8748672)
[2026-06-08T08:49:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8589743)
[2026-06-08T08:49:39] Filtering fragments with small insert size (remaining=8587981)
[2026-06-08T08:49:42] Filtering alignments with long gaps (remaining=8587981)
[2026-06-08T08:49:45] Filtering fragments with both mates in the same gene (remaining=8586654)
[2026-06-08T08:49:49] Filtering fusions arising from hairpin structures (remaining=8064223)
[2026-06-08T08:49:53] Filtering reads with a mismatch p-value <=0.01 (remaining=3659873)
[2026-06-08T08:50:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=1409445)
[2026-06-08T08:50:28] Finding fusions and counting supporting reads (total=1244939)
[2026-06-08T08:50:54] Merging adjacent fusion breakpoints (remaining=1235368)
[2026-06-08T08:50:57] Filtering multi-mapping fusions by alignment score and read support (remaining=687339)
[2026-06-08T08:51:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=686160)
[2026-06-08T08:52:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=514011)
[2026-06-08T08:52:07] Filtering fusions with <2 supporting reads (remaining=24892)
[2026-06-08T08:52:08] Filtering fusions with an e-value >=0.3 (remaining=4276)
[2026-06-08T08:52:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4386)
[2026-06-08T08:52:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4259)
[2026-06-08T08:52:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4259)
[2026-06-08T08:52:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4232)
[2026-06-08T08:52:29] Searching for fusions with spliced split reads (remaining=4307)
[2026-06-08T08:52:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=3096)
[2026-06-08T08:52:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3072)
[2026-06-08T08:52:41] Searching for fusions with >=4 spliced events (remaining=3881)
[2026-06-08T08:52:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1607)
[2026-06-08T08:53:00] Filtering fusions with anchors <=23nt (remaining=1346)
[2026-06-08T08:53:01] Filtering end-to-end fusions with low support (remaining=1321)
[2026-06-08T08:53:03] Filtering fusions with no coverage around the breakpoints (remaining=1293)
[2026-06-08T08:53:04] Indexing gene sequences 
[2026-06-08T08:53:10] Filtering genes with >=30% identity (remaining=374)
[2026-06-08T08:53:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=139)
[2026-06-08T08:53:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=130)
[2026-06-08T08:53:18] Searching for additional isoforms (remaining=169)
[2026-06-08T08:53:20] Assigning confidence scores to events 
[2026-06-08T08:53:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:26] Writing fusions to file '1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:53:28] Writing discarded fusions to file '1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:20] Freeing resources
[2026-06-08T08:54:49] Done (elapsed time=00:14:16, CPU time=00:14:15, peak memory=21.1gb)