[2026-06-08T08:28:42] Launching Arriba 2.4.0
[2026-06-08T08:28:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:54] Reading chimeric alignments from '1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=17161168)
[2026-06-08T08:35:53] Marking multi-mapping alignments (marked=12091623)
[2026-06-08T08:36:00] Detecting strandedness (reverse)
[2026-06-08T08:36:00] Assigning strands to alignments 
[2026-06-08T08:36:04] Annotating alignments 
[2026-06-08T08:36:58] Filtering duplicates (remaining=11652232)
[2026-06-08T08:37:10] 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=10519981)
[2026-06-08T08:37:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=10519981)
[2026-06-08T08:37:17] Filtering viral contigs with expression lower than the top 5 (remaining=10519981)
[2026-06-08T08:37:25] Filtering viral contigs with less than 5% coverage (remaining=10519981)
[2026-06-08T08:37:29] Estimating fragment length (mate gap mean=-80.001, mate gap stddev=26.6686, read length mean=121.476)
[2026-06-08T08:37:29] Filtering read-through fragments with a distance <=10000bp (remaining=10240663)
[2026-06-08T08:37:32] Filtering inconsistently clipped mates (remaining=10053424)
[2026-06-08T08:37:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=9883827)
[2026-06-08T08:37:42] Filtering fragments with small insert size (remaining=9882130)
[2026-06-08T08:37:46] Filtering alignments with long gaps (remaining=9882130)
[2026-06-08T08:37:49] Filtering fragments with both mates in the same gene (remaining=9880618)
[2026-06-08T08:37:53] Filtering fusions arising from hairpin structures (remaining=9386642)
[2026-06-08T08:37:57] Filtering reads with a mismatch p-value <=0.01 (remaining=4568328)
[2026-06-08T08:38:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=2095318)
[2026-06-08T08:38:38] Finding fusions and counting supporting reads (total=1952507)
[2026-06-08T08:39:10] Merging adjacent fusion breakpoints (remaining=1942323)
[2026-06-08T08:39:14] Filtering multi-mapping fusions by alignment score and read support (remaining=1004842)
[2026-06-08T08:40:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=1003397)
[2026-06-08T08:40:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=857564)
[2026-06-08T08:40:25] Filtering fusions with <2 supporting reads (remaining=23528)
[2026-06-08T08:40:27] Filtering fusions with an e-value >=0.3 (remaining=4065)
[2026-06-08T08:40:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4192)
[2026-06-08T08:40:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4117)
[2026-06-08T08:40:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4117)
[2026-06-08T08:40:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4067)
[2026-06-08T08:40:49] Searching for fusions with spliced split reads (remaining=4178)
[2026-06-08T08:40:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=3035)
[2026-06-08T08:41:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2991)
[2026-06-08T08:41:03] Searching for fusions with >=4 spliced events (remaining=3595)
[2026-06-08T08:41:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1452)
[2026-06-08T08:41:19] Filtering fusions with anchors <=23nt (remaining=1249)
[2026-06-08T08:41:20] Filtering end-to-end fusions with low support (remaining=1214)
[2026-06-08T08:41:22] Filtering fusions with no coverage around the breakpoints (remaining=1197)
[2026-06-08T08:41:23] Indexing gene sequences 
[2026-06-08T08:41:29] Filtering genes with >=30% identity (remaining=398)
[2026-06-08T08:41:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=199)
[2026-06-08T08:41:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-06-08T08:41:40] Searching for additional isoforms (remaining=219)
[2026-06-08T08:41:43] Assigning confidence scores to events 
[2026-06-08T08:41:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:49] Writing fusions to file '1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:52] Writing discarded fusions to file '1173_NMN_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:44] Freeing resources
[2026-06-08T08:43:09] Done (elapsed time=00:14:27, CPU time=00:14:26, peak memory=21.8gb)