[2026-06-08T08:58:14] Launching Arriba 2.4.0
[2026-06-08T08:58:14] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:27] Reading chimeric alignments from 'aih-tih-sc-693ffe-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=13523136)
[2026-06-08T09:05:30] Marking multi-mapping alignments (marked=9439508)
[2026-06-08T09:05:36] Detecting strandedness (reverse)
[2026-06-08T09:05:36] Assigning strands to alignments 
[2026-06-08T09:05:39] Annotating alignments 
[2026-06-08T09:06:27] Filtering duplicates (remaining=4808683)
[2026-06-08T09:06:34] 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=4361823)
[2026-06-08T09:06:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4361823)
[2026-06-08T09:06:40] Filtering viral contigs with expression lower than the top 5 (remaining=4361823)
[2026-06-08T09:06:46] Filtering viral contigs with less than 5% coverage (remaining=4361823)
[2026-06-08T09:06:50] Estimating fragment length (mate gap mean=-87.801, mate gap stddev=27.1765, read length mean=125.171)
[2026-06-08T09:06:50] Filtering read-through fragments with a distance <=10000bp (remaining=4199408)
[2026-06-08T09:06:53] Filtering inconsistently clipped mates (remaining=4129699)
[2026-06-08T09:06:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4011492)
[2026-06-08T09:07:01] Filtering fragments with small insert size (remaining=4010521)
[2026-06-08T09:07:04] Filtering alignments with long gaps (remaining=4010521)
[2026-06-08T09:07:06] Filtering fragments with both mates in the same gene (remaining=4009781)
[2026-06-08T09:07:09] Filtering fusions arising from hairpin structures (remaining=3806507)
[2026-06-08T09:07:12] Filtering reads with a mismatch p-value <=0.01 (remaining=1306726)
[2026-06-08T09:07:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=523434)
[2026-06-08T09:07:33] Finding fusions and counting supporting reads (total=458382)
[2026-06-08T09:07:53] Merging adjacent fusion breakpoints (remaining=453810)
[2026-06-08T09:07:54] Filtering multi-mapping fusions by alignment score and read support (remaining=260037)
[2026-06-08T09:08:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=258876)
[2026-06-08T09:08:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=160227)
[2026-06-08T09:08:48] Filtering fusions with <2 supporting reads (remaining=13542)
[2026-06-08T09:08:49] Filtering fusions with an e-value >=0.3 (remaining=2843)
[2026-06-08T09:08:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2877)
[2026-06-08T09:08:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2815)
[2026-06-08T09:08:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2815)
[2026-06-08T09:08:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2731)
[2026-06-08T09:09:01] Searching for fusions with spliced split reads (remaining=2781)
[2026-06-08T09:09:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=2155)
[2026-06-08T09:09:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2121)
[2026-06-08T09:09:08] Searching for fusions with >=4 spliced events (remaining=2372)
[2026-06-08T09:09:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1047)
[2026-06-08T09:09:22] Filtering fusions with anchors <=23nt (remaining=768)
[2026-06-08T09:09:23] Filtering end-to-end fusions with low support (remaining=690)
[2026-06-08T09:09:23] Filtering fusions with no coverage around the breakpoints (remaining=662)
[2026-06-08T09:09:24] Indexing gene sequences 
[2026-06-08T09:09:28] Filtering genes with >=30% identity (remaining=286)
[2026-06-08T09:09:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=193)
[2026-06-08T09:09:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=167)
[2026-06-08T09:09:34] Searching for additional isoforms (remaining=204)
[2026-06-08T09:09:36] Assigning confidence scores to events 
[2026-06-08T09:09:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:38] Writing fusions to file 'aih-tih-sc-693ffe-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:09:40] Writing discarded fusions to file 'aih-tih-sc-693ffe-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:06] Freeing resources
[2026-06-08T09:10:27] Done (elapsed time=00:12:13, CPU time=00:12:11, peak memory=18.4gb)