[2026-06-08T09:16:26] Launching Arriba 2.4.0
[2026-06-08T09:16:26] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:16:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:16:41] Reading chimeric alignments from 'aih-tih-sc-63c8b4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10565790)
[2026-06-08T09:23:23] Marking multi-mapping alignments (marked=6786182)
[2026-06-08T09:23:27] Detecting strandedness (reverse)
[2026-06-08T09:23:27] Assigning strands to alignments 
[2026-06-08T09:23:29] Annotating alignments 
[2026-06-08T09:24:03] Filtering duplicates (remaining=4854281)
[2026-06-08T09:24:09] 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=4584513)
[2026-06-08T09:24:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4584513)
[2026-06-08T09:24:13] Filtering viral contigs with expression lower than the top 5 (remaining=4584513)
[2026-06-08T09:24:18] Filtering viral contigs with less than 5% coverage (remaining=4584513)
[2026-06-08T09:24:20] Estimating fragment length (mate gap mean=-87.0626, mate gap stddev=28.1345, read length mean=128.637)
[2026-06-08T09:24:20] Filtering read-through fragments with a distance <=10000bp (remaining=4394776)
[2026-06-08T09:24:22] Filtering inconsistently clipped mates (remaining=4330189)
[2026-06-08T09:24:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4201087)
[2026-06-08T09:24:27] Filtering fragments with small insert size (remaining=4200524)
[2026-06-08T09:24:29] Filtering alignments with long gaps (remaining=4200524)
[2026-06-08T09:24:31] Filtering fragments with both mates in the same gene (remaining=4199460)
[2026-06-08T09:24:34] Filtering fusions arising from hairpin structures (remaining=4039940)
[2026-06-08T09:24:36] Filtering reads with a mismatch p-value <=0.01 (remaining=1758462)
[2026-06-08T09:24:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=496592)
[2026-06-08T09:24:55] Finding fusions and counting supporting reads (total=362870)
[2026-06-08T09:25:10] Merging adjacent fusion breakpoints (remaining=358845)
[2026-06-08T09:25:11] Filtering multi-mapping fusions by alignment score and read support (remaining=217396)
[2026-06-08T09:25:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:25:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=216324)
[2026-06-08T09:25:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=133220)
[2026-06-08T09:25:51] Filtering fusions with <2 supporting reads (remaining=17812)
[2026-06-08T09:25:52] Filtering fusions with an e-value >=0.3 (remaining=4377)
[2026-06-08T09:25:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4412)
[2026-06-08T09:25:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4331)
[2026-06-08T09:25:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4332)
[2026-06-08T09:25:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4078)
[2026-06-08T09:26:02] Searching for fusions with spliced split reads (remaining=4148)
[2026-06-08T09:26:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=2928)
[2026-06-08T09:26:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2896)
[2026-06-08T09:26:08] Searching for fusions with >=4 spliced events (remaining=3280)
[2026-06-08T09:26:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1054)
[2026-06-08T09:26:23] Filtering fusions with anchors <=23nt (remaining=839)
[2026-06-08T09:26:24] Filtering end-to-end fusions with low support (remaining=818)
[2026-06-08T09:26:25] Filtering fusions with no coverage around the breakpoints (remaining=799)
[2026-06-08T09:26:25] Indexing gene sequences 
[2026-06-08T09:26:29] Filtering genes with >=30% identity (remaining=275)
[2026-06-08T09:26:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=141)
[2026-06-08T09:26:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=134)
[2026-06-08T09:26:33] Searching for additional isoforms (remaining=154)
[2026-06-08T09:26:35] Assigning confidence scores to events 
[2026-06-08T09:26:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:26:37] Writing fusions to file 'aih-tih-sc-63c8b4-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:26:38] Writing discarded fusions to file 'aih-tih-sc-63c8b4-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:26:59] Freeing resources
[2026-06-08T09:27:15] Done (elapsed time=00:10:49, CPU time=00:10:48, peak memory=14.7gb)