[2026-06-08T08:17:51] Launching Arriba 2.4.0
[2026-06-08T08:17:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:18:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:18:04] Reading chimeric alignments from 'aih-tih-sc-7dd1d5-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10743702)
[2026-06-08T08:22:55] Marking multi-mapping alignments (marked=7312885)
[2026-06-08T08:22:59] Detecting strandedness (reverse)
[2026-06-08T08:22:59] Assigning strands to alignments 
[2026-06-08T08:23:01] Annotating alignments 
[2026-06-08T08:23:34] Filtering duplicates (remaining=4737284)
[2026-06-08T08:23:39] 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=4403309)
[2026-06-08T08:23:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4403309)
[2026-06-08T08:23:43] Filtering viral contigs with expression lower than the top 5 (remaining=4403309)
[2026-06-08T08:23:47] Filtering viral contigs with less than 5% coverage (remaining=4403309)
[2026-06-08T08:23:49] Estimating fragment length (mate gap mean=-85.4707, mate gap stddev=28.2798, read length mean=125.746)
[2026-06-08T08:23:50] Filtering read-through fragments with a distance <=10000bp (remaining=4169727)
[2026-06-08T08:23:52] Filtering inconsistently clipped mates (remaining=4088212)
[2026-06-08T08:23:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3985767)
[2026-06-08T08:23:57] Filtering fragments with small insert size (remaining=3985037)
[2026-06-08T08:23:59] Filtering alignments with long gaps (remaining=3985037)
[2026-06-08T08:24:01] Filtering fragments with both mates in the same gene (remaining=3984160)
[2026-06-08T08:24:03] Filtering fusions arising from hairpin structures (remaining=3777747)
[2026-06-08T08:24:06] Filtering reads with a mismatch p-value <=0.01 (remaining=1611740)
[2026-06-08T08:24:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=515869)
[2026-06-08T08:24:23] Finding fusions and counting supporting reads (total=402781)
[2026-06-08T08:24:37] Merging adjacent fusion breakpoints (remaining=396914)
[2026-06-08T08:24:39] Filtering multi-mapping fusions by alignment score and read support (remaining=237644)
[2026-06-08T08:25:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:25:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=236409)
[2026-06-08T08:25:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=127359)
[2026-06-08T08:25:17] Filtering fusions with <2 supporting reads (remaining=16773)
[2026-06-08T08:25:18] Filtering fusions with an e-value >=0.3 (remaining=4596)
[2026-06-08T08:25:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4648)
[2026-06-08T08:25:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4552)
[2026-06-08T08:25:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4554)
[2026-06-08T08:25:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4398)
[2026-06-08T08:25:28] Searching for fusions with spliced split reads (remaining=4449)
[2026-06-08T08:25:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=3179)
[2026-06-08T08:25:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3137)
[2026-06-08T08:25:34] Searching for fusions with >=4 spliced events (remaining=3428)
[2026-06-08T08:25:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1130)
[2026-06-08T08:25:54] Filtering fusions with anchors <=23nt (remaining=798)
[2026-06-08T08:25:55] Filtering end-to-end fusions with low support (remaining=781)
[2026-06-08T08:25:55] Filtering fusions with no coverage around the breakpoints (remaining=762)
[2026-06-08T08:25:56] Indexing gene sequences 
[2026-06-08T08:25:59] Filtering genes with >=30% identity (remaining=274)
[2026-06-08T08:26:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=140)
[2026-06-08T08:26:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=140)
[2026-06-08T08:26:04] Searching for additional isoforms (remaining=154)
[2026-06-08T08:26:05] Assigning confidence scores to events 
[2026-06-08T08:26:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:26:08] Writing fusions to file 'aih-tih-sc-7dd1d5-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:26:09] Writing discarded fusions to file 'aih-tih-sc-7dd1d5-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:26:28] Freeing resources
[2026-06-08T08:26:43] Done (elapsed time=00:08:52, CPU time=00:08:51, peak memory=15gb)