[2026-06-08T08:49:22] Launching Arriba 2.4.0
[2026-06-08T08:49:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:38] Reading chimeric alignments from 'aih-tih-sc-3377ac-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10605960)
[2026-06-08T08:56:45] Marking multi-mapping alignments (marked=7218037)
[2026-06-08T08:56:49] Detecting strandedness (reverse)
[2026-06-08T08:56:49] Assigning strands to alignments 
[2026-06-08T08:56:50] Annotating alignments 
[2026-06-08T08:57:22] Filtering duplicates (remaining=5472471)
[2026-06-08T08:57:27] 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=4980107)
[2026-06-08T08:57:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4980107)
[2026-06-08T08:57:31] Filtering viral contigs with expression lower than the top 5 (remaining=4980107)
[2026-06-08T08:57:35] Filtering viral contigs with less than 5% coverage (remaining=4980107)
[2026-06-08T08:57:38] Estimating fragment length (mate gap mean=-83.2974, mate gap stddev=28.2761, read length mean=121.498)
[2026-06-08T08:57:38] Filtering read-through fragments with a distance <=10000bp (remaining=4717134)
[2026-06-08T08:57:40] Filtering inconsistently clipped mates (remaining=4586802)
[2026-06-08T08:57:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4463641)
[2026-06-08T08:57:45] Filtering fragments with small insert size (remaining=4462180)
[2026-06-08T08:57:47] Filtering alignments with long gaps (remaining=4462180)
[2026-06-08T08:57:49] Filtering fragments with both mates in the same gene (remaining=4460932)
[2026-06-08T08:57:51] Filtering fusions arising from hairpin structures (remaining=4104037)
[2026-06-08T08:57:53] Filtering reads with a mismatch p-value <=0.01 (remaining=1619501)
[2026-06-08T08:58:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=779141)
[2026-06-08T08:58:12] Finding fusions and counting supporting reads (total=613114)
[2026-06-08T08:58:27] Merging adjacent fusion breakpoints (remaining=604848)
[2026-06-08T08:58:28] Filtering multi-mapping fusions by alignment score and read support (remaining=356478)
[2026-06-08T08:58:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=354845)
[2026-06-08T08:59:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=223752)
[2026-06-08T08:59:03] Filtering fusions with <2 supporting reads (remaining=22012)
[2026-06-08T08:59:04] Filtering fusions with an e-value >=0.3 (remaining=4786)
[2026-06-08T08:59:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4857)
[2026-06-08T08:59:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4735)
[2026-06-08T08:59:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4735)
[2026-06-08T08:59:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4516)
[2026-06-08T08:59:14] Searching for fusions with spliced split reads (remaining=4601)
[2026-06-08T08:59:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=3229)
[2026-06-08T08:59:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3203)
[2026-06-08T08:59:21] Searching for fusions with >=4 spliced events (remaining=3670)
[2026-06-08T08:59:22] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1410)
[2026-06-08T08:59:36] Filtering fusions with anchors <=23nt (remaining=1179)
[2026-06-08T08:59:37] Filtering end-to-end fusions with low support (remaining=1151)
[2026-06-08T08:59:37] Filtering fusions with no coverage around the breakpoints (remaining=1135)
[2026-06-08T08:59:38] Indexing gene sequences 
[2026-06-08T08:59:43] Filtering genes with >=30% identity (remaining=366)
[2026-06-08T08:59:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=190)
[2026-06-08T08:59:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-08T08:59:49] Searching for additional isoforms (remaining=208)
[2026-06-08T08:59:50] Assigning confidence scores to events 
[2026-06-08T08:59:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:53] Writing fusions to file 'aih-tih-sc-3377ac-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:54] Writing discarded fusions to file 'aih-tih-sc-3377ac-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:19] Freeing resources
[2026-06-08T09:00:35] Done (elapsed time=00:11:13, CPU time=00:11:11, peak memory=15.3gb)