[2026-06-08T08:21:02] Launching Arriba 2.4.0
[2026-06-08T08:21:02] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:21:19] Reading chimeric alignments from 'aih-tih-sc-550807-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=6858246)
[2026-06-08T08:25:34] Marking multi-mapping alignments (marked=4606916)
[2026-06-08T08:25:36] Detecting strandedness (reverse)
[2026-06-08T08:25:36] Assigning strands to alignments 
[2026-06-08T08:25:37] Annotating alignments 
[2026-06-08T08:25:57] Filtering duplicates (remaining=3778409)
[2026-06-08T08:26:01] 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=3552536)
[2026-06-08T08:26:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3552536)
[2026-06-08T08:26:03] Filtering viral contigs with expression lower than the top 5 (remaining=3552536)
[2026-06-08T08:26:06] Filtering viral contigs with less than 5% coverage (remaining=3552536)
[2026-06-08T08:26:07] Estimating fragment length (mate gap mean=-87.6595, mate gap stddev=28.5854, read length mean=128.535)
[2026-06-08T08:26:08] Filtering read-through fragments with a distance <=10000bp (remaining=3352300)
[2026-06-08T08:26:09] Filtering inconsistently clipped mates (remaining=3290599)
[2026-06-08T08:26:10] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3214188)
[2026-06-08T08:26:12] Filtering fragments with small insert size (remaining=3213649)
[2026-06-08T08:26:13] Filtering alignments with long gaps (remaining=3213649)
[2026-06-08T08:26:15] Filtering fragments with both mates in the same gene (remaining=3213022)
[2026-06-08T08:26:16] Filtering fusions arising from hairpin structures (remaining=3016892)
[2026-06-08T08:26:17] Filtering reads with a mismatch p-value <=0.01 (remaining=1388477)
[2026-06-08T08:26:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=536103)
[2026-06-08T08:26:31] Finding fusions and counting supporting reads (total=433423)
[2026-06-08T08:26:41] Merging adjacent fusion breakpoints (remaining=430033)
[2026-06-08T08:26:42] Filtering multi-mapping fusions by alignment score and read support (remaining=262989)
[2026-06-08T08:27:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=261495)
[2026-06-08T08:27:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=147197)
[2026-06-08T08:27:07] Filtering fusions with <2 supporting reads (remaining=18901)
[2026-06-08T08:27:07] Filtering fusions with an e-value >=0.3 (remaining=5141)
[2026-06-08T08:27:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5194)
[2026-06-08T08:27:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5117)
[2026-06-08T08:27:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5119)
[2026-06-08T08:27:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4423)
[2026-06-08T08:27:14] Searching for fusions with spliced split reads (remaining=4511)
[2026-06-08T08:27:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=3154)
[2026-06-08T08:27:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3110)
[2026-06-08T08:27:18] Searching for fusions with >=4 spliced events (remaining=3548)
[2026-06-08T08:27:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1284)
[2026-06-08T08:27:35] Filtering fusions with anchors <=23nt (remaining=984)
[2026-06-08T08:27:36] Filtering end-to-end fusions with low support (remaining=966)
[2026-06-08T08:27:36] Filtering fusions with no coverage around the breakpoints (remaining=938)
[2026-06-08T08:27:36] Indexing gene sequences 
[2026-06-08T08:27:42] Filtering genes with >=30% identity (remaining=366)
[2026-06-08T08:27:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=241)
[2026-06-08T08:27:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-08T08:27:47] Searching for additional isoforms (remaining=263)
[2026-06-08T08:27:48] Assigning confidence scores to events 
[2026-06-08T08:27:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:50] Writing fusions to file 'aih-tih-sc-550807-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:27:52] Writing discarded fusions to file 'aih-tih-sc-550807-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:09] Freeing resources
[2026-06-08T08:28:19] Done (elapsed time=00:07:17, CPU time=00:07:16, peak memory=11.4gb)