[2026-06-08T08:35:06] Launching Arriba 2.4.0
[2026-06-08T08:35:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:22] Reading chimeric alignments from 'aih-tih-sc-3376ed-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11107188)
[2026-06-08T08:42:08] Marking multi-mapping alignments (marked=6828081)
[2026-06-08T08:42:12] Detecting strandedness (reverse)
[2026-06-08T08:42:12] Assigning strands to alignments 
[2026-06-08T08:42:14] Annotating alignments 
[2026-06-08T08:42:44] Filtering duplicates (remaining=6687180)
[2026-06-08T08:42:51] 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=6480162)
[2026-06-08T08:42:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6480162)
[2026-06-08T08:42:55] Filtering viral contigs with expression lower than the top 5 (remaining=6480162)
[2026-06-08T08:43:00] Filtering viral contigs with less than 5% coverage (remaining=6480162)
[2026-06-08T08:43:02] Estimating fragment length (mate gap mean=-86.527, mate gap stddev=29.5151, read length mean=137.632)
[2026-06-08T08:43:03] Filtering read-through fragments with a distance <=10000bp (remaining=6147853)
[2026-06-08T08:43:05] Filtering inconsistently clipped mates (remaining=6073719)
[2026-06-08T08:43:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5951463)
[2026-06-08T08:43:10] Filtering fragments with small insert size (remaining=5950914)
[2026-06-08T08:43:12] Filtering alignments with long gaps (remaining=5950913)
[2026-06-08T08:43:14] Filtering fragments with both mates in the same gene (remaining=5949879)
[2026-06-08T08:43:16] Filtering fusions arising from hairpin structures (remaining=5710998)
[2026-06-08T08:43:19] Filtering reads with a mismatch p-value <=0.01 (remaining=2881875)
[2026-06-08T08:43:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=956628)
[2026-06-08T08:43:44] Finding fusions and counting supporting reads (total=680823)
[2026-06-08T08:43:59] Merging adjacent fusion breakpoints (remaining=675283)
[2026-06-08T08:44:00] Filtering multi-mapping fusions by alignment score and read support (remaining=446844)
[2026-06-08T08:44:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=444373)
[2026-06-08T08:44:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=232651)
[2026-06-08T08:44:39] Filtering fusions with <2 supporting reads (remaining=36379)
[2026-06-08T08:44:40] Filtering fusions with an e-value >=0.3 (remaining=10711)
[2026-06-08T08:44:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10750)
[2026-06-08T08:44:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10685)
[2026-06-08T08:44:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10685)
[2026-06-08T08:44:46] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7900)
[2026-06-08T08:44:50] Searching for fusions with spliced split reads (remaining=7932)
[2026-06-08T08:44:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=4511)
[2026-06-08T08:44:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4470)
[2026-06-08T08:44:57] Searching for fusions with >=4 spliced events (remaining=5587)
[2026-06-08T08:44:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2146)
[2026-06-08T08:45:12] Filtering fusions with anchors <=23nt (remaining=1771)
[2026-06-08T08:45:12] Filtering end-to-end fusions with low support (remaining=1737)
[2026-06-08T08:45:13] Filtering fusions with no coverage around the breakpoints (remaining=1705)
[2026-06-08T08:45:14] Indexing gene sequences 
[2026-06-08T08:45:19] Filtering genes with >=30% identity (remaining=538)
[2026-06-08T08:45:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=258)
[2026-06-08T08:45:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=189)
[2026-06-08T08:45:31] Searching for additional isoforms (remaining=267)
[2026-06-08T08:45:32] Assigning confidence scores to events 
[2026-06-08T08:45:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:35] Writing fusions to file 'aih-tih-sc-3376ed-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:37] Writing discarded fusions to file 'aih-tih-sc-3376ed-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:01] Freeing resources
[2026-06-08T08:46:18] Done (elapsed time=00:11:12, CPU time=00:11:11, peak memory=15.4gb)