[2026-06-08T08:50:30] Launching Arriba 2.4.0
[2026-06-08T08:50:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:50:44] Reading chimeric alignments from 'aih-tih-sc-a8a787-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=9915987)
[2026-06-08T08:57:56] Marking multi-mapping alignments (marked=6389492)
[2026-06-08T08:58:00] Detecting strandedness (reverse)
[2026-06-08T08:58:00] Assigning strands to alignments 
[2026-06-08T08:58:02] Annotating alignments 
[2026-06-08T08:58:37] Filtering duplicates (remaining=7188036)
[2026-06-08T08:58:45] 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=6664774)
[2026-06-08T08:58:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6664774)
[2026-06-08T08:58:49] Filtering viral contigs with expression lower than the top 5 (remaining=6664774)
[2026-06-08T08:58:54] Filtering viral contigs with less than 5% coverage (remaining=6664774)
[2026-06-08T08:58:56] Estimating fragment length (mate gap mean=-85.6962, mate gap stddev=31.6061, read length mean=134.323)
[2026-06-08T08:58:57] Filtering read-through fragments with a distance <=10000bp (remaining=6334193)
[2026-06-08T08:58:59] Filtering inconsistently clipped mates (remaining=6231183)
[2026-06-08T08:59:01] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6064792)
[2026-06-08T08:59:06] Filtering fragments with small insert size (remaining=6064025)
[2026-06-08T08:59:08] Filtering alignments with long gaps (remaining=6064023)
[2026-06-08T08:59:10] Filtering fragments with both mates in the same gene (remaining=6062844)
[2026-06-08T08:59:12] Filtering fusions arising from hairpin structures (remaining=5667809)
[2026-06-08T08:59:15] Filtering reads with a mismatch p-value <=0.01 (remaining=2548063)
[2026-06-08T08:59:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=1186508)
[2026-06-08T08:59:42] Finding fusions and counting supporting reads (total=927300)
[2026-06-08T09:00:01] Merging adjacent fusion breakpoints (remaining=919006)
[2026-06-08T09:00:03] Filtering multi-mapping fusions by alignment score and read support (remaining=611561)
[2026-06-08T09:00:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=608842)
[2026-06-08T09:00:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=380588)
[2026-06-08T09:00:49] Filtering fusions with <2 supporting reads (remaining=51655)
[2026-06-08T09:00:50] Filtering fusions with an e-value >=0.3 (remaining=23450)
[2026-06-08T09:00:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=23513)
[2026-06-08T09:00:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=23417)
[2026-06-08T09:00:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=23417)
[2026-06-08T09:00:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8690)
[2026-06-08T09:01:03] Searching for fusions with spliced split reads (remaining=8727)
[2026-06-08T09:01:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=4347)
[2026-06-08T09:01:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4304)
[2026-06-08T09:01:11] Searching for fusions with >=4 spliced events (remaining=5392)
[2026-06-08T09:01:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2159)
[2026-06-08T09:01:27] Filtering fusions with anchors <=23nt (remaining=1657)
[2026-06-08T09:01:28] Filtering end-to-end fusions with low support (remaining=1591)
[2026-06-08T09:01:29] Filtering fusions with no coverage around the breakpoints (remaining=1553)
[2026-06-08T09:01:30] Indexing gene sequences 
[2026-06-08T09:01:36] Filtering genes with >=30% identity (remaining=504)
[2026-06-08T09:01:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=261)
[2026-06-08T09:01:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-08T09:01:48] Searching for additional isoforms (remaining=274)
[2026-06-08T09:01:49] Assigning confidence scores to events 
[2026-06-08T09:01:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:54] Writing fusions to file 'aih-tih-sc-a8a787-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:56] Writing discarded fusions to file 'aih-tih-sc-a8a787-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:02:34] Freeing resources
[2026-06-08T09:02:51] Done (elapsed time=00:12:21, CPU time=00:12:20, peak memory=14.8gb)