[2026-06-08T08:57:22] Launching Arriba 2.4.0
[2026-06-08T08:57:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:57:31] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:57:35] Reading chimeric alignments from 'aih-tih-sc-606237-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10451827)
[2026-06-08T09:04:49] Marking multi-mapping alignments (marked=6753001)
[2026-06-08T09:04:53] Detecting strandedness (reverse)
[2026-06-08T09:04:53] Assigning strands to alignments 
[2026-06-08T09:04:55] Annotating alignments 
[2026-06-08T09:05:30] Filtering duplicates (remaining=6629676)
[2026-06-08T09:05:38] 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=6387195)
[2026-06-08T09:05:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6387195)
[2026-06-08T09:05:42] Filtering viral contigs with expression lower than the top 5 (remaining=6387195)
[2026-06-08T09:05:47] Filtering viral contigs with less than 5% coverage (remaining=6387195)
[2026-06-08T09:05:50] Estimating fragment length (mate gap mean=-83.3227, mate gap stddev=32.0035, read length mean=134.647)
[2026-06-08T09:05:50] Filtering read-through fragments with a distance <=10000bp (remaining=6048383)
[2026-06-08T09:05:52] Filtering inconsistently clipped mates (remaining=5967131)
[2026-06-08T09:05:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5818630)
[2026-06-08T09:05:58] Filtering fragments with small insert size (remaining=5818110)
[2026-06-08T09:06:00] Filtering alignments with long gaps (remaining=5818109)
[2026-06-08T09:06:02] Filtering fragments with both mates in the same gene (remaining=5817152)
[2026-06-08T09:06:05] Filtering fusions arising from hairpin structures (remaining=5488714)
[2026-06-08T09:06:07] Filtering reads with a mismatch p-value <=0.01 (remaining=2741271)
[2026-06-08T09:06:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=1020817)
[2026-06-08T09:06:33] Finding fusions and counting supporting reads (total=794025)
[2026-06-08T09:06:51] Merging adjacent fusion breakpoints (remaining=787159)
[2026-06-08T09:06:53] Filtering multi-mapping fusions by alignment score and read support (remaining=526028)
[2026-06-08T09:07:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:07:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=523339)
[2026-06-08T09:07:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=288430)
[2026-06-08T09:07:37] Filtering fusions with <2 supporting reads (remaining=39638)
[2026-06-08T09:07:38] Filtering fusions with an e-value >=0.3 (remaining=14906)
[2026-06-08T09:07:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14960)
[2026-06-08T09:07:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14867)
[2026-06-08T09:07:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14867)
[2026-06-08T09:07:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8657)
[2026-06-08T09:07:50] Searching for fusions with spliced split reads (remaining=8677)
[2026-06-08T09:07:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=4459)
[2026-06-08T09:07:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4417)
[2026-06-08T09:07:57] Searching for fusions with >=4 spliced events (remaining=5433)
[2026-06-08T09:07:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2022)
[2026-06-08T09:08:13] Filtering fusions with anchors <=23nt (remaining=1557)
[2026-06-08T09:08:14] Filtering end-to-end fusions with low support (remaining=1505)
[2026-06-08T09:08:15] Filtering fusions with no coverage around the breakpoints (remaining=1469)
[2026-06-08T09:08:15] Indexing gene sequences 
[2026-06-08T09:08:21] Filtering genes with >=30% identity (remaining=423)
[2026-06-08T09:08:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=181)
[2026-06-08T09:08:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=157)
[2026-06-08T09:08:27] Searching for additional isoforms (remaining=216)
[2026-06-08T09:08:29] Assigning confidence scores to events 
[2026-06-08T09:08:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:08:32] Writing fusions to file 'aih-tih-sc-606237-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:08:34] Writing discarded fusions to file 'aih-tih-sc-606237-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:09:07] Freeing resources
[2026-06-08T09:09:24] Done (elapsed time=00:12:02, CPU time=00:12:00, peak memory=15.1gb)