[2026-06-08T08:37:33] Launching Arriba 2.4.0
[2026-06-08T08:37:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:51] Reading chimeric alignments from '1173_MHK_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=17094203)
[2026-06-08T08:46:39] Marking multi-mapping alignments (marked=11979072)
[2026-06-08T08:46:47] Detecting strandedness (reverse)
[2026-06-08T08:46:47] Assigning strands to alignments 
[2026-06-08T08:46:50] Annotating alignments 
[2026-06-08T08:47:42] Filtering duplicates (remaining=11038530)
[2026-06-08T08:47:54] 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=9976448)
[2026-06-08T08:47:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9976448)
[2026-06-08T08:48:01] Filtering viral contigs with expression lower than the top 5 (remaining=9976448)
[2026-06-08T08:48:09] Filtering viral contigs with less than 5% coverage (remaining=9976448)
[2026-06-08T08:48:13] Estimating fragment length (mate gap mean=-82.7475, mate gap stddev=26.8022, read length mean=123.283)
[2026-06-08T08:48:13] Filtering read-through fragments with a distance <=10000bp (remaining=9665667)
[2026-06-08T08:48:17] Filtering inconsistently clipped mates (remaining=9462157)
[2026-06-08T08:48:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9280896)
[2026-06-08T08:48:27] Filtering fragments with small insert size (remaining=9279284)
[2026-06-08T08:48:31] Filtering alignments with long gaps (remaining=9279284)
[2026-06-08T08:48:35] Filtering fragments with both mates in the same gene (remaining=9277775)
[2026-06-08T08:48:38] Filtering fusions arising from hairpin structures (remaining=8742403)
[2026-06-08T08:48:42] Filtering reads with a mismatch p-value <=0.01 (remaining=4421454)
[2026-06-08T08:49:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=2159432)
[2026-06-08T08:49:25] Finding fusions and counting supporting reads (total=1973630)
[2026-06-08T08:49:52] Merging adjacent fusion breakpoints (remaining=1962106)
[2026-06-08T08:49:56] Filtering multi-mapping fusions by alignment score and read support (remaining=1014612)
[2026-06-08T08:50:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1013355)
[2026-06-08T08:51:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=859578)
[2026-06-08T08:51:01] Filtering fusions with <2 supporting reads (remaining=24880)
[2026-06-08T08:51:02] Filtering fusions with an e-value >=0.3 (remaining=4416)
[2026-06-08T08:51:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4538)
[2026-06-08T08:51:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4426)
[2026-06-08T08:51:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4426)
[2026-06-08T08:51:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4405)
[2026-06-08T08:51:23] Searching for fusions with spliced split reads (remaining=4529)
[2026-06-08T08:51:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=3251)
[2026-06-08T08:51:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3213)
[2026-06-08T08:51:36] Searching for fusions with >=4 spliced events (remaining=3869)
[2026-06-08T08:51:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1693)
[2026-06-08T08:51:57] Filtering fusions with anchors <=23nt (remaining=1368)
[2026-06-08T08:51:58] Filtering end-to-end fusions with low support (remaining=1312)
[2026-06-08T08:51:59] Filtering fusions with no coverage around the breakpoints (remaining=1274)
[2026-06-08T08:52:00] Indexing gene sequences 
[2026-06-08T08:52:09] Filtering genes with >=30% identity (remaining=473)
[2026-06-08T08:52:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=234)
[2026-06-08T08:52:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=174)
[2026-06-08T08:52:22] Searching for additional isoforms (remaining=226)
[2026-06-08T08:52:25] Assigning confidence scores to events 
[2026-06-08T08:52:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:52:31] Writing fusions to file '1173_MHK_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:52:34] Writing discarded fusions to file '1173_MHK_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:31] Freeing resources
[2026-06-08T08:54:01] Done (elapsed time=00:16:28, CPU time=00:16:27, peak memory=22gb)