[2026-06-08T08:29:32] Launching Arriba 2.4.0
[2026-06-08T08:29:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:44] Reading chimeric alignments from '1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=15553888)
[2026-06-08T08:36:53] Marking multi-mapping alignments (marked=10597807)
[2026-06-08T08:36:59] Detecting strandedness (reverse)
[2026-06-08T08:36:59] Assigning strands to alignments 
[2026-06-08T08:37:02] Annotating alignments 
[2026-06-08T08:37:54] Filtering duplicates (remaining=11568052)
[2026-06-08T08:38:06] 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=10034076)
[2026-06-08T08:38:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10034076)
[2026-06-08T08:38:12] Filtering viral contigs with expression lower than the top 5 (remaining=10034076)
[2026-06-08T08:38:19] Filtering viral contigs with less than 5% coverage (remaining=10034076)
[2026-06-08T08:38:22] Estimating fragment length (mate gap mean=-82.4137, mate gap stddev=27.013, read length mean=125.402)
[2026-06-08T08:38:23] Filtering read-through fragments with a distance <=10000bp (remaining=9741070)
[2026-06-08T08:38:26] Filtering inconsistently clipped mates (remaining=9624582)
[2026-06-08T08:38:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9444137)
[2026-06-08T08:38:36] Filtering fragments with small insert size (remaining=9443070)
[2026-06-08T08:38:39] Filtering alignments with long gaps (remaining=9443070)
[2026-06-08T08:38:42] Filtering fragments with both mates in the same gene (remaining=9441586)
[2026-06-08T08:38:45] Filtering fusions arising from hairpin structures (remaining=9152922)
[2026-06-08T08:38:49] Filtering reads with a mismatch p-value <=0.01 (remaining=4785303)
[2026-06-08T08:39:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=2621272)
[2026-06-08T08:39:30] Finding fusions and counting supporting reads (total=2452308)
[2026-06-08T08:39:58] Merging adjacent fusion breakpoints (remaining=2445241)
[2026-06-08T08:40:01] Filtering multi-mapping fusions by alignment score and read support (remaining=1324149)
[2026-06-08T08:40:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1322898)
[2026-06-08T08:41:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1177645)
[2026-06-08T08:41:09] Filtering fusions with <2 supporting reads (remaining=30631)
[2026-06-08T08:41:10] Filtering fusions with an e-value >=0.3 (remaining=4644)
[2026-06-08T08:41:12] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4717)
[2026-06-08T08:41:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4664)
[2026-06-08T08:41:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4664)
[2026-06-08T08:41:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4573)
[2026-06-08T08:41:32] Searching for fusions with spliced split reads (remaining=4616)
[2026-06-08T08:41:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=3289)
[2026-06-08T08:41:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3227)
[2026-06-08T08:41:46] Searching for fusions with >=4 spliced events (remaining=4051)
[2026-06-08T08:41:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1617)
[2026-06-08T08:42:03] Filtering fusions with anchors <=23nt (remaining=1255)
[2026-06-08T08:42:04] Filtering end-to-end fusions with low support (remaining=1236)
[2026-06-08T08:42:06] Filtering fusions with no coverage around the breakpoints (remaining=1199)
[2026-06-08T08:42:07] Indexing gene sequences 
[2026-06-08T08:42:13] Filtering genes with >=30% identity (remaining=403)
[2026-06-08T08:42:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=208)
[2026-06-08T08:42:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=159)
[2026-06-08T08:42:23] Searching for additional isoforms (remaining=227)
[2026-06-08T08:42:26] Assigning confidence scores to events 
[2026-06-08T08:42:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:33] Writing fusions to file '1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:35] Writing discarded fusions to file '1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:32] Freeing resources
[2026-06-08T08:43:56] Done (elapsed time=00:14:24, CPU time=00:14:24, peak memory=20.9gb)