[2026-06-08T07:56:37] Launching Arriba 2.4.0
[2026-06-08T07:56:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:56:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:56:59] Reading chimeric alignments from 'aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=5112796)
[2026-06-08T08:00:47] Marking multi-mapping alignments (marked=3499796)
[2026-06-08T08:00:50] Detecting strandedness (reverse)
[2026-06-08T08:00:50] Assigning strands to alignments 
[2026-06-08T08:00:51] Annotating alignments 
[2026-06-08T08:01:11] Filtering duplicates (remaining=1972912)
[2026-06-08T08:01:14] 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=1860684)
[2026-06-08T08:01:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1860684)
[2026-06-08T08:01:16] Filtering viral contigs with expression lower than the top 5 (remaining=1860684)
[2026-06-08T08:01:18] Filtering viral contigs with less than 5% coverage (remaining=1860684)
[2026-06-08T08:01:19] Estimating fragment length (mate gap mean=-83.0162, mate gap stddev=27.1301, read length mean=120.502)
[2026-06-08T08:01:19] Filtering read-through fragments with a distance <=10000bp (remaining=1774693)
[2026-06-08T08:01:20] Filtering inconsistently clipped mates (remaining=1732038)
[2026-06-08T08:01:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1672935)
[2026-06-08T08:01:23] Filtering fragments with small insert size (remaining=1672461)
[2026-06-08T08:01:24] Filtering alignments with long gaps (remaining=1672461)
[2026-06-08T08:01:25] Filtering fragments with both mates in the same gene (remaining=1671939)
[2026-06-08T08:01:26] Filtering fusions arising from hairpin structures (remaining=1579050)
[2026-06-08T08:01:27] Filtering reads with a mismatch p-value <=0.01 (remaining=644567)
[2026-06-08T08:01:32] Filtering reads with low entropy (k-mer content >=60%) (remaining=201140)
[2026-06-08T08:01:37] Finding fusions and counting supporting reads (total=181484)
[2026-06-08T08:01:45] Merging adjacent fusion breakpoints (remaining=179887)
[2026-06-08T08:01:46] Filtering multi-mapping fusions by alignment score and read support (remaining=96198)
[2026-06-08T08:02:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:02:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=95713)
[2026-06-08T08:02:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=54674)
[2026-06-08T08:02:08] Filtering fusions with <2 supporting reads (remaining=5007)
[2026-06-08T08:02:08] Filtering fusions with an e-value >=0.3 (remaining=1297)
[2026-06-08T08:02:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1331)
[2026-06-08T08:02:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1297)
[2026-06-08T08:02:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1297)
[2026-06-08T08:02:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1289)
[2026-06-08T08:02:13] Searching for fusions with spliced split reads (remaining=1374)
[2026-06-08T08:02:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=1100)
[2026-06-08T08:02:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1090)
[2026-06-08T08:02:16] Searching for fusions with >=4 spliced events (remaining=1178)
[2026-06-08T08:02:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=369)
[2026-06-08T08:02:35] Filtering fusions with anchors <=23nt (remaining=316)
[2026-06-08T08:02:36] Filtering end-to-end fusions with low support (remaining=313)
[2026-06-08T08:02:36] Filtering fusions with no coverage around the breakpoints (remaining=309)
[2026-06-08T08:02:36] Indexing gene sequences 
[2026-06-08T08:02:38] Filtering genes with >=30% identity (remaining=118)
[2026-06-08T08:02:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=79)
[2026-06-08T08:02:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-06-08T08:02:40] Searching for additional isoforms (remaining=90)
[2026-06-08T08:02:41] Assigning confidence scores to events 
[2026-06-08T08:02:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:02:42] Writing fusions to file 'aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:02:43] Writing discarded fusions to file 'aih-tih-sc-13a2f6-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:02:54] Freeing resources
[2026-06-08T08:03:02] Done (elapsed time=00:06:25, CPU time=00:06:25, peak memory=9.25gb)