[2026-06-08T08:22:58] Launching Arriba 2.4.0
[2026-06-08T08:22:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:17] Reading chimeric alignments from 'aih-tih-sc-487f7f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=7571315)
[2026-06-08T08:27:27] Marking multi-mapping alignments (marked=5181165)
[2026-06-08T08:27:29] Detecting strandedness (reverse)
[2026-06-08T08:27:29] Assigning strands to alignments 
[2026-06-08T08:27:31] Annotating alignments 
[2026-06-08T08:27:51] Filtering duplicates (remaining=2118624)
[2026-06-08T08:27:54] 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=1938547)
[2026-06-08T08:27:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1938547)
[2026-06-08T08:27:57] Filtering viral contigs with expression lower than the top 5 (remaining=1938547)
[2026-06-08T08:27:59] Filtering viral contigs with less than 5% coverage (remaining=1938547)
[2026-06-08T08:28:01] Estimating fragment length (mate gap mean=-81.9956, mate gap stddev=27.7207, read length mean=119.73)
[2026-06-08T08:28:01] Filtering read-through fragments with a distance <=10000bp (remaining=1872002)
[2026-06-08T08:28:02] Filtering inconsistently clipped mates (remaining=1828739)
[2026-06-08T08:28:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1749188)
[2026-06-08T08:28:05] Filtering fragments with small insert size (remaining=1748555)
[2026-06-08T08:28:06] Filtering alignments with long gaps (remaining=1748555)
[2026-06-08T08:28:07] Filtering fragments with both mates in the same gene (remaining=1747998)
[2026-06-08T08:28:09] Filtering fusions arising from hairpin structures (remaining=1661494)
[2026-06-08T08:28:10] Filtering reads with a mismatch p-value <=0.01 (remaining=643318)
[2026-06-08T08:28:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=195092)
[2026-06-08T08:28:18] Finding fusions and counting supporting reads (total=180050)
[2026-06-08T08:28:26] Merging adjacent fusion breakpoints (remaining=178850)
[2026-06-08T08:28:26] Filtering multi-mapping fusions by alignment score and read support (remaining=93231)
[2026-06-08T08:28:46] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=92447)
[2026-06-08T08:28:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=56470)
[2026-06-08T08:28:49] Filtering fusions with <2 supporting reads (remaining=4342)
[2026-06-08T08:28:49] Filtering fusions with an e-value >=0.3 (remaining=1152)
[2026-06-08T08:28:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1169)
[2026-06-08T08:28:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1131)
[2026-06-08T08:28:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1131)
[2026-06-08T08:28:52] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1098)
[2026-06-08T08:28:54] Searching for fusions with spliced split reads (remaining=1167)
[2026-06-08T08:28:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=885)
[2026-06-08T08:28:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=873)
[2026-06-08T08:28:57] Searching for fusions with >=4 spliced events (remaining=939)
[2026-06-08T08:28:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=251)
[2026-06-08T08:29:09] Filtering fusions with anchors <=23nt (remaining=218)
[2026-06-08T08:29:09] Filtering end-to-end fusions with low support (remaining=206)
[2026-06-08T08:29:09] Filtering fusions with no coverage around the breakpoints (remaining=197)
[2026-06-08T08:29:09] Indexing gene sequences 
[2026-06-08T08:29:11] Filtering genes with >=30% identity (remaining=70)
[2026-06-08T08:29:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=30)
[2026-06-08T08:29:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=30)
[2026-06-08T08:29:12] Searching for additional isoforms (remaining=38)
[2026-06-08T08:29:13] Assigning confidence scores to events 
[2026-06-08T08:29:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:14] Writing fusions to file 'aih-tih-sc-487f7f-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:29:14] Writing discarded fusions to file 'aih-tih-sc-487f7f-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:23] Freeing resources
[2026-06-08T08:29:34] Done (elapsed time=00:06:36, CPU time=00:06:35, peak memory=11.7gb)