[2026-06-08T08:49:07] Launching Arriba 2.4.0
[2026-06-08T08:49:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:23] Reading chimeric alignments from 'aih-tih-sc-445ab1-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11468882)
[2026-06-08T08:56:03] Marking multi-mapping alignments (marked=7415889)
[2026-06-08T08:56:07] Detecting strandedness (no)
[2026-06-08T08:56:07] Annotating alignments 
[2026-06-08T08:56:42] Filtering duplicates (remaining=6254322)
[2026-06-08T08:56:49] 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=5987609)
[2026-06-08T08:56:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5987609)
[2026-06-08T08:56:53] Filtering viral contigs with expression lower than the top 5 (remaining=5987609)
[2026-06-08T08:56:58] Filtering viral contigs with less than 5% coverage (remaining=5987609)
[2026-06-08T08:57:00] Estimating fragment length (mate gap mean=-86.7887, mate gap stddev=29.7303, read length mean=135.88)
[2026-06-08T08:57:00] Filtering read-through fragments with a distance <=10000bp (remaining=5748420)
[2026-06-08T08:57:02] Filtering inconsistently clipped mates (remaining=5651763)
[2026-06-08T08:57:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5498385)
[2026-06-08T08:57:09] Filtering fragments with small insert size (remaining=5497813)
[2026-06-08T08:57:11] Filtering alignments with long gaps (remaining=5497813)
[2026-06-08T08:57:14] Filtering fragments with both mates in the same gene (remaining=5496881)
[2026-06-08T08:57:16] Filtering fusions arising from hairpin structures (remaining=5192828)
[2026-06-08T08:57:18] Filtering reads with a mismatch p-value <=0.01 (remaining=2532294)
[2026-06-08T08:57:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=777868)
[2026-06-08T08:57:44] Finding fusions and counting supporting reads (total=548968)
[2026-06-08T08:57:59] Merging adjacent fusion breakpoints (remaining=542886)
[2026-06-08T08:58:01] Filtering multi-mapping fusions by alignment score and read support (remaining=336621)
[2026-06-08T08:58:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=334162)
[2026-06-08T08:58:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=193480)
[2026-06-08T08:58:42] Filtering fusions with <2 supporting reads (remaining=27121)
[2026-06-08T08:58:42] Filtering fusions with an e-value >=0.3 (remaining=8840)
[2026-06-08T08:58:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8901)
[2026-06-08T08:58:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8726)
[2026-06-08T08:58:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8726)
[2026-06-08T08:58:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6751)
[2026-06-08T08:58:53] Searching for fusions with spliced split reads (remaining=6760)
[2026-06-08T08:58:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=4213)
[2026-06-08T08:58:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4154)
[2026-06-08T08:59:00] Searching for fusions with >=4 spliced events (remaining=4871)
[2026-06-08T08:59:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1797)
[2026-06-08T08:59:17] Filtering fusions with anchors <=23nt (remaining=1462)
[2026-06-08T08:59:18] Filtering end-to-end fusions with low support (remaining=1419)
[2026-06-08T08:59:18] Filtering fusions with no coverage around the breakpoints (remaining=1379)
[2026-06-08T08:59:19] Indexing gene sequences 
[2026-06-08T08:59:25] Filtering genes with >=30% identity (remaining=560)
[2026-06-08T08:59:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=396)
[2026-06-08T08:59:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=269)
[2026-06-08T08:59:43] Searching for additional isoforms (remaining=363)
[2026-06-08T08:59:44] Assigning confidence scores to events 
[2026-06-08T08:59:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:47] Writing fusions to file 'aih-tih-sc-445ab1-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:50] Writing discarded fusions to file 'aih-tih-sc-445ab1-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:13] Freeing resources
[2026-06-08T09:00:30] Done (elapsed time=00:11:23, CPU time=00:11:22, peak memory=15.8gb)