[2026-06-08T08:23:26] Launching Arriba 2.4.0
[2026-06-08T08:23:26] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:38] Reading chimeric alignments from '1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam' (total=15786414)
[2026-06-08T08:29:55] Marking multi-mapping alignments (marked=10964559)
[2026-06-08T08:30:01] Detecting strandedness (reverse)
[2026-06-08T08:30:01] Assigning strands to alignments 
[2026-06-08T08:30:04] Annotating alignments 
[2026-06-08T08:30:52] Filtering duplicates (remaining=9801876)
[2026-06-08T08:31:03] 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=9089271)
[2026-06-08T08:31:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=9089271)
[2026-06-08T08:31:10] Filtering viral contigs with expression lower than the top 5 (remaining=9089271)
[2026-06-08T08:31:17] Filtering viral contigs with less than 5% coverage (remaining=9089271)
[2026-06-08T08:31:20] Estimating fragment length (mate gap mean=-80.5933, mate gap stddev=27.4241, read length mean=123.482)
[2026-06-08T08:31:20] Filtering read-through fragments with a distance <=10000bp (remaining=8829154)
[2026-06-08T08:31:23] Filtering inconsistently clipped mates (remaining=8646508)
[2026-06-08T08:31:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=8513697)
[2026-06-08T08:31:33] Filtering fragments with small insert size (remaining=8512177)
[2026-06-08T08:31:36] Filtering alignments with long gaps (remaining=8512177)
[2026-06-08T08:31:39] Filtering fragments with both mates in the same gene (remaining=8510989)
[2026-06-08T08:31:43] Filtering fusions arising from hairpin structures (remaining=8028750)
[2026-06-08T08:31:46] Filtering reads with a mismatch p-value <=0.01 (remaining=3866994)
[2026-06-08T08:32:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=1541693)
[2026-06-08T08:32:21] Finding fusions and counting supporting reads (total=1377661)
[2026-06-08T08:32:47] Merging adjacent fusion breakpoints (remaining=1369730)
[2026-06-08T08:32:50] Filtering multi-mapping fusions by alignment score and read support (remaining=752353)
[2026-06-08T08:33:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=751061)
[2026-06-08T08:33:54] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=609712)
[2026-06-08T08:33:56] Filtering fusions with <2 supporting reads (remaining=21432)
[2026-06-08T08:33:57] Filtering fusions with an e-value >=0.3 (remaining=3892)
[2026-06-08T08:33:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4019)
[2026-06-08T08:34:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3961)
[2026-06-08T08:34:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3961)
[2026-06-08T08:34:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3889)
[2026-06-08T08:34:16] Searching for fusions with spliced split reads (remaining=3983)
[2026-06-08T08:34:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=2881)
[2026-06-08T08:34:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2843)
[2026-06-08T08:34:28] Searching for fusions with >=4 spliced events (remaining=3382)
[2026-06-08T08:34:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1378)
[2026-06-08T08:34:45] Filtering fusions with anchors <=23nt (remaining=1170)
[2026-06-08T08:34:47] Filtering end-to-end fusions with low support (remaining=1144)
[2026-06-08T08:34:48] Filtering fusions with no coverage around the breakpoints (remaining=1116)
[2026-06-08T08:34:49] Indexing gene sequences 
[2026-06-08T08:34:55] Filtering genes with >=30% identity (remaining=386)
[2026-06-08T08:34:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=192)
[2026-06-08T08:35:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-08T08:35:05] Searching for additional isoforms (remaining=197)
[2026-06-08T08:35:07] Assigning confidence scores to events 
[2026-06-08T08:35:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:12] Writing fusions to file '1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:35:15] Writing discarded fusions to file '1173_NMN_T1_RNA_SLD_01_A23T55JLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:02] Freeing resources
[2026-06-08T08:36:28] Done (elapsed time=00:13:02, CPU time=00:13:00, peak memory=20.2gb)