[2026-06-08T08:34:30] Launching Arriba 2.4.0
[2026-06-08T08:34:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:53] Reading chimeric alignments from '1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=16544069)
[2026-06-08T08:44:55] Marking multi-mapping alignments (marked=11111738)
[2026-06-08T08:45:02] Detecting strandedness (reverse)
[2026-06-08T08:45:02] Assigning strands to alignments 
[2026-06-08T08:45:05] Annotating alignments 
[2026-06-08T08:45:59] Filtering duplicates (remaining=11584948)
[2026-06-08T08:46:11] 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=10594941)
[2026-06-08T08:46:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10594941)
[2026-06-08T08:46:18] Filtering viral contigs with expression lower than the top 5 (remaining=10594941)
[2026-06-08T08:46:25] Filtering viral contigs with less than 5% coverage (remaining=10594941)
[2026-06-08T08:46:29] Estimating fragment length (mate gap mean=-77.8049, mate gap stddev=26.135, read length mean=120.317)
[2026-06-08T08:46:29] Filtering read-through fragments with a distance <=10000bp (remaining=10354712)
[2026-06-08T08:46:33] Filtering inconsistently clipped mates (remaining=10186958)
[2026-06-08T08:46:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=10037743)
[2026-06-08T08:46:43] Filtering fragments with small insert size (remaining=10035943)
[2026-06-08T08:46:46] Filtering alignments with long gaps (remaining=10035942)
[2026-06-08T08:46:49] Filtering fragments with both mates in the same gene (remaining=10033946)
[2026-06-08T08:46:52] Filtering fusions arising from hairpin structures (remaining=9593070)
[2026-06-08T08:46:55] Filtering reads with a mismatch p-value <=0.01 (remaining=5003045)
[2026-06-08T08:47:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=2490086)
[2026-06-08T08:47:45] Finding fusions and counting supporting reads (total=2436674)
[2026-06-08T08:48:14] Merging adjacent fusion breakpoints (remaining=2426870)
[2026-06-08T08:48:17] Filtering multi-mapping fusions by alignment score and read support (remaining=1341616)
[2026-06-08T08:49:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1340488)
[2026-06-08T08:49:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1192155)
[2026-06-08T08:49:29] Filtering fusions with <2 supporting reads (remaining=22277)
[2026-06-08T08:49:30] Filtering fusions with an e-value >=0.3 (remaining=3089)
[2026-06-08T08:49:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3194)
[2026-06-08T08:49:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3132)
[2026-06-08T08:49:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3132)
[2026-06-08T08:49:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3127)
[2026-06-08T08:49:51] Searching for fusions with spliced split reads (remaining=3219)
[2026-06-08T08:50:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=2334)
[2026-06-08T08:50:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2314)
[2026-06-08T08:50:04] Searching for fusions with >=4 spliced events (remaining=2865)
[2026-06-08T08:50:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1289)
[2026-06-08T08:50:31] Filtering fusions with anchors <=23nt (remaining=1100)
[2026-06-08T08:50:32] Filtering end-to-end fusions with low support (remaining=1076)
[2026-06-08T08:50:33] Filtering fusions with no coverage around the breakpoints (remaining=1059)
[2026-06-08T08:50:35] Indexing gene sequences 
[2026-06-08T08:50:41] Filtering genes with >=30% identity (remaining=329)
[2026-06-08T08:50:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=186)
[2026-06-08T08:50:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=150)
[2026-06-08T08:50:51] Searching for additional isoforms (remaining=185)
[2026-06-08T08:50:54] Assigning confidence scores to events 
[2026-06-08T08:51:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:00] Writing fusions to file '1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:02] Writing discarded fusions to file '1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:05] Freeing resources
[2026-06-08T08:52:33] Done (elapsed time=00:18:03, CPU time=00:18:01, peak memory=21.2gb)