[2026-06-08T08:34:29] Launching Arriba 2.4.0
[2026-06-08T08:34:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:46] Reading chimeric alignments from '1173_S9Q_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=17476599)
[2026-06-08T08:43:05] Marking multi-mapping alignments (marked=12426340)
[2026-06-08T08:43:13] Detecting strandedness (no)
[2026-06-08T08:43:13] Annotating alignments 
[2026-06-08T08:44:17] Filtering duplicates (remaining=9499532)
[2026-06-08T08:44:32] 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=8468480)
[2026-06-08T08:44:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8468480)
[2026-06-08T08:44:39] Filtering viral contigs with expression lower than the top 5 (remaining=8468480)
[2026-06-08T08:44:47] Filtering viral contigs with less than 5% coverage (remaining=8468480)
[2026-06-08T08:44:51] Estimating fragment length (mate gap mean=-82.1876, mate gap stddev=27.1829, read length mean=120.848)
[2026-06-08T08:44:51] Filtering read-through fragments with a distance <=10000bp (remaining=8176127)
[2026-06-08T08:44:55] Filtering inconsistently clipped mates (remaining=7967596)
[2026-06-08T08:44:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7807709)
[2026-06-08T08:45:05] Filtering fragments with small insert size (remaining=7805925)
[2026-06-08T08:45:08] Filtering alignments with long gaps (remaining=7805925)
[2026-06-08T08:45:12] Filtering fragments with both mates in the same gene (remaining=7804450)
[2026-06-08T08:45:15] Filtering fusions arising from hairpin structures (remaining=7267692)
[2026-06-08T08:45:19] Filtering reads with a mismatch p-value <=0.01 (remaining=3375476)
[2026-06-08T08:45:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=1513960)
[2026-06-08T08:45:54] Finding fusions and counting supporting reads (total=1354413)
[2026-06-08T08:46:24] Merging adjacent fusion breakpoints (remaining=1342833)
[2026-06-08T08:46:27] Filtering multi-mapping fusions by alignment score and read support (remaining=701170)
[2026-06-08T08:47:37] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=699922)
[2026-06-08T08:47:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=543654)
[2026-06-08T08:47:54] Filtering fusions with <2 supporting reads (remaining=22854)
[2026-06-08T08:47:56] Filtering fusions with an e-value >=0.3 (remaining=4444)
[2026-06-08T08:47:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4598)
[2026-06-08T08:48:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4483)
[2026-06-08T08:48:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4483)
[2026-06-08T08:48:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4460)
[2026-06-08T08:48:17] Searching for fusions with spliced split reads (remaining=4544)
[2026-06-08T08:48:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=3303)
[2026-06-08T08:48:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3261)
[2026-06-08T08:48:30] Searching for fusions with >=4 spliced events (remaining=3739)
[2026-06-08T08:48:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1397)
[2026-06-08T08:48:51] Filtering fusions with anchors <=23nt (remaining=1117)
[2026-06-08T08:48:53] Filtering end-to-end fusions with low support (remaining=1084)
[2026-06-08T08:48:54] Filtering fusions with no coverage around the breakpoints (remaining=1060)
[2026-06-08T08:48:55] Indexing gene sequences 
[2026-06-08T08:49:04] Filtering genes with >=30% identity (remaining=353)
[2026-06-08T08:49:07] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=182)
[2026-06-08T08:49:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=175)
[2026-06-08T08:49:13] Searching for additional isoforms (remaining=210)
[2026-06-08T08:49:16] Assigning confidence scores to events 
[2026-06-08T08:49:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:21] Writing fusions to file '1173_S9Q_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:24] Writing discarded fusions to file '1173_S9Q_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:50:13] Freeing resources
[2026-06-08T08:50:52] Done (elapsed time=00:16:23, CPU time=00:16:23, peak memory=22.4gb)