[2026-06-08T08:41:09] Launching Arriba 2.4.0
[2026-06-08T08:41:09] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:22] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:26] Reading chimeric alignments from 'aih-tih-sc-9114fc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11059235)
[2026-06-08T08:49:27] Marking multi-mapping alignments (marked=7069863)
[2026-06-08T08:49:32] Detecting strandedness (reverse)
[2026-06-08T08:49:32] Assigning strands to alignments 
[2026-06-08T08:49:34] Annotating alignments 
[2026-06-08T08:50:11] Filtering duplicates (remaining=7212144)
[2026-06-08T08:50:20] 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=6858397)
[2026-06-08T08:50:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6858397)
[2026-06-08T08:50:25] Filtering viral contigs with expression lower than the top 5 (remaining=6858397)
[2026-06-08T08:50:30] Filtering viral contigs with less than 5% coverage (remaining=6858397)
[2026-06-08T08:50:34] Estimating fragment length (mate gap mean=-86.9209, mate gap stddev=30.0404, read length mean=138.171)
[2026-06-08T08:50:34] Filtering read-through fragments with a distance <=10000bp (remaining=6560058)
[2026-06-08T08:50:37] Filtering inconsistently clipped mates (remaining=6475141)
[2026-06-08T08:50:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6309479)
[2026-06-08T08:50:45] Filtering fragments with small insert size (remaining=6308993)
[2026-06-08T08:50:47] Filtering alignments with long gaps (remaining=6308992)
[2026-06-08T08:50:50] Filtering fragments with both mates in the same gene (remaining=6307837)
[2026-06-08T08:50:53] Filtering fusions arising from hairpin structures (remaining=6015085)
[2026-06-08T08:50:56] Filtering reads with a mismatch p-value <=0.01 (remaining=3096168)
[2026-06-08T08:51:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=1001528)
[2026-06-08T08:51:28] Finding fusions and counting supporting reads (total=748854)
[2026-06-08T08:51:50] Merging adjacent fusion breakpoints (remaining=742918)
[2026-06-08T08:51:52] Filtering multi-mapping fusions by alignment score and read support (remaining=471122)
[2026-06-08T08:52:33] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:42] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=467341)
[2026-06-08T08:52:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=281157)
[2026-06-08T08:52:45] Filtering fusions with <2 supporting reads (remaining=33260)
[2026-06-08T08:52:46] Filtering fusions with an e-value >=0.3 (remaining=10435)
[2026-06-08T08:52:46] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10489)
[2026-06-08T08:52:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10396)
[2026-06-08T08:52:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10396)
[2026-06-08T08:52:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7098)
[2026-06-08T08:53:00] Searching for fusions with spliced split reads (remaining=7112)
[2026-06-08T08:53:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=4206)
[2026-06-08T08:53:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4159)
[2026-06-08T08:53:09] Searching for fusions with >=4 spliced events (remaining=5036)
[2026-06-08T08:53:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1895)
[2026-06-08T08:53:33] Filtering fusions with anchors <=23nt (remaining=1491)
[2026-06-08T08:53:34] Filtering end-to-end fusions with low support (remaining=1450)
[2026-06-08T08:53:34] Filtering fusions with no coverage around the breakpoints (remaining=1419)
[2026-06-08T08:53:35] Indexing gene sequences 
[2026-06-08T08:53:42] Filtering genes with >=30% identity (remaining=418)
[2026-06-08T08:53:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=204)
[2026-06-08T08:53:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-08T08:53:50] Searching for additional isoforms (remaining=236)
[2026-06-08T08:53:52] Assigning confidence scores to events 
[2026-06-08T08:53:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:55] Writing fusions to file 'aih-tih-sc-9114fc-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:58] Writing discarded fusions to file 'aih-tih-sc-9114fc-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:36] Freeing resources
[2026-06-08T08:54:57] Done (elapsed time=00:13:48, CPU time=00:13:47, peak memory=15.5gb)