[2026-06-08T08:48:33] Launching Arriba 2.4.0
[2026-06-08T08:48:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:48] Reading chimeric alignments from 'aih-tih-sc-7de750-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11010586)
[2026-06-08T08:55:44] Marking multi-mapping alignments (marked=7247452)
[2026-06-08T08:55:49] Detecting strandedness (reverse)
[2026-06-08T08:55:49] Assigning strands to alignments 
[2026-06-08T08:55:52] Annotating alignments 
[2026-06-08T08:56:30] Filtering duplicates (remaining=5106447)
[2026-06-08T08:56:37] 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=4761843)
[2026-06-08T08:56:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4761843)
[2026-06-08T08:56:41] Filtering viral contigs with expression lower than the top 5 (remaining=4761843)
[2026-06-08T08:56:46] Filtering viral contigs with less than 5% coverage (remaining=4761843)
[2026-06-08T08:56:49] Estimating fragment length (mate gap mean=-87.3765, mate gap stddev=28.8455, read length mean=127.847)
[2026-06-08T08:56:49] Filtering read-through fragments with a distance <=10000bp (remaining=4487063)
[2026-06-08T08:56:51] Filtering inconsistently clipped mates (remaining=4407995)
[2026-06-08T08:56:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4300025)
[2026-06-08T08:56:58] Filtering fragments with small insert size (remaining=4299092)
[2026-06-08T08:57:00] Filtering alignments with long gaps (remaining=4299092)
[2026-06-08T08:57:03] Filtering fragments with both mates in the same gene (remaining=4298254)
[2026-06-08T08:57:06] Filtering fusions arising from hairpin structures (remaining=4071975)
[2026-06-08T08:57:08] Filtering reads with a mismatch p-value <=0.01 (remaining=1656815)
[2026-06-08T08:57:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=632507)
[2026-06-08T08:57:29] Finding fusions and counting supporting reads (total=529072)
[2026-06-08T08:57:46] Merging adjacent fusion breakpoints (remaining=521159)
[2026-06-08T08:57:48] Filtering multi-mapping fusions by alignment score and read support (remaining=320474)
[2026-06-08T08:58:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=318414)
[2026-06-08T08:58:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=171815)
[2026-06-08T08:58:34] Filtering fusions with <2 supporting reads (remaining=20072)
[2026-06-08T08:58:35] Filtering fusions with an e-value >=0.3 (remaining=5362)
[2026-06-08T08:58:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5399)
[2026-06-08T08:58:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5232)
[2026-06-08T08:58:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5232)
[2026-06-08T08:58:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4718)
[2026-06-08T08:58:46] Searching for fusions with spliced split reads (remaining=4789)
[2026-06-08T08:58:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=3283)
[2026-06-08T08:58:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3237)
[2026-06-08T08:58:52] Searching for fusions with >=4 spliced events (remaining=3627)
[2026-06-08T08:58:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1396)
[2026-06-08T08:59:11] Filtering fusions with anchors <=23nt (remaining=921)
[2026-06-08T08:59:11] Filtering end-to-end fusions with low support (remaining=883)
[2026-06-08T08:59:12] Filtering fusions with no coverage around the breakpoints (remaining=853)
[2026-06-08T08:59:13] Indexing gene sequences 
[2026-06-08T08:59:17] Filtering genes with >=30% identity (remaining=262)
[2026-06-08T08:59:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=104)
[2026-06-08T08:59:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=99)
[2026-06-08T08:59:21] Searching for additional isoforms (remaining=127)
[2026-06-08T08:59:22] Assigning confidence scores to events 
[2026-06-08T08:59:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:25] Writing fusions to file 'aih-tih-sc-7de750-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:26] Writing discarded fusions to file 'aih-tih-sc-7de750-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:54] Freeing resources
[2026-06-08T09:00:12] Done (elapsed time=00:11:39, CPU time=00:11:37, peak memory=15.6gb)