[2026-06-08T08:53:22] Launching Arriba 2.4.0
[2026-06-08T08:53:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:34] Reading chimeric alignments from 'aih-tih-sc-0992e4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10072592)
[2026-06-08T09:00:59] Marking multi-mapping alignments (marked=6169012)
[2026-06-08T09:01:05] Detecting strandedness (reverse)
[2026-06-08T09:01:05] Assigning strands to alignments 
[2026-06-08T09:01:07] Annotating alignments 
[2026-06-08T09:01:47] Filtering duplicates (remaining=6246830)
[2026-06-08T09:01:55] 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=5958414)
[2026-06-08T09:01:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5958414)
[2026-06-08T09:02:00] Filtering viral contigs with expression lower than the top 5 (remaining=5958414)
[2026-06-08T09:02:06] Filtering viral contigs with less than 5% coverage (remaining=5958414)
[2026-06-08T09:02:08] Estimating fragment length (mate gap mean=-86.9143, mate gap stddev=29.388, read length mean=132.622)
[2026-06-08T09:02:09] Filtering read-through fragments with a distance <=10000bp (remaining=5510606)
[2026-06-08T09:02:11] Filtering inconsistently clipped mates (remaining=5405809)
[2026-06-08T09:02:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5276231)
[2026-06-08T09:02:18] Filtering fragments with small insert size (remaining=5275171)
[2026-06-08T09:02:21] Filtering alignments with long gaps (remaining=5275171)
[2026-06-08T09:02:23] Filtering fragments with both mates in the same gene (remaining=5274296)
[2026-06-08T09:02:26] Filtering fusions arising from hairpin structures (remaining=4915496)
[2026-06-08T09:02:28] Filtering reads with a mismatch p-value <=0.01 (remaining=2296983)
[2026-06-08T09:02:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=1020164)
[2026-06-08T09:02:54] Finding fusions and counting supporting reads (total=788785)
[2026-06-08T09:03:14] Merging adjacent fusion breakpoints (remaining=780344)
[2026-06-08T09:03:15] Filtering multi-mapping fusions by alignment score and read support (remaining=515183)
[2026-06-08T09:03:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=512364)
[2026-06-08T09:04:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=266890)
[2026-06-08T09:04:02] Filtering fusions with <2 supporting reads (remaining=37251)
[2026-06-08T09:04:03] Filtering fusions with an e-value >=0.3 (remaining=13358)
[2026-06-08T09:04:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13439)
[2026-06-08T09:04:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13358)
[2026-06-08T09:04:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13358)
[2026-06-08T09:04:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6870)
[2026-06-08T09:04:15] Searching for fusions with spliced split reads (remaining=7013)
[2026-06-08T09:04:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4219)
[2026-06-08T09:04:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4158)
[2026-06-08T09:04:23] Searching for fusions with >=4 spliced events (remaining=5049)
[2026-06-08T09:04:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2047)
[2026-06-08T09:04:40] Filtering fusions with anchors <=23nt (remaining=1665)
[2026-06-08T09:04:40] Filtering end-to-end fusions with low support (remaining=1612)
[2026-06-08T09:04:41] Filtering fusions with no coverage around the breakpoints (remaining=1585)
[2026-06-08T09:04:42] Indexing gene sequences 
[2026-06-08T09:04:48] Filtering genes with >=30% identity (remaining=436)
[2026-06-08T09:04:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=191)
[2026-06-08T09:04:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=188)
[2026-06-08T09:04:57] Searching for additional isoforms (remaining=244)
[2026-06-08T09:04:58] Assigning confidence scores to events 
[2026-06-08T09:05:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:02] Writing fusions to file 'aih-tih-sc-0992e4-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:04] Writing discarded fusions to file 'aih-tih-sc-0992e4-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:37] Freeing resources
[2026-06-08T09:05:54] Done (elapsed time=00:12:32, CPU time=00:12:31, peak memory=14.8gb)