[2026-06-08T08:35:11] Launching Arriba 2.4.0
[2026-06-08T08:35:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:24] Reading chimeric alignments from 'aih-tih-sc-408cca-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8710084)
[2026-06-08T08:40:46] Marking multi-mapping alignments (marked=5618890)
[2026-06-08T08:40:49] Detecting strandedness (reverse)
[2026-06-08T08:40:49] Assigning strands to alignments 
[2026-06-08T08:40:51] Annotating alignments 
[2026-06-08T08:41:20] Filtering duplicates (remaining=3864143)
[2026-06-08T08:41:25] 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=3685416)
[2026-06-08T08:41:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3685416)
[2026-06-08T08:41:28] Filtering viral contigs with expression lower than the top 5 (remaining=3685416)
[2026-06-08T08:41:31] Filtering viral contigs with less than 5% coverage (remaining=3685416)
[2026-06-08T08:41:33] Estimating fragment length (mate gap mean=-85.9997, mate gap stddev=28.4009, read length mean=128.542)
[2026-06-08T08:41:34] Filtering read-through fragments with a distance <=10000bp (remaining=3500994)
[2026-06-08T08:41:35] Filtering inconsistently clipped mates (remaining=3435464)
[2026-06-08T08:41:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3316117)
[2026-06-08T08:41:40] Filtering fragments with small insert size (remaining=3315500)
[2026-06-08T08:41:41] Filtering alignments with long gaps (remaining=3315499)
[2026-06-08T08:41:43] Filtering fragments with both mates in the same gene (remaining=3314595)
[2026-06-08T08:41:45] Filtering fusions arising from hairpin structures (remaining=3143615)
[2026-06-08T08:41:46] Filtering reads with a mismatch p-value <=0.01 (remaining=1445704)
[2026-06-08T08:41:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=506690)
[2026-06-08T08:42:02] Finding fusions and counting supporting reads (total=404731)
[2026-06-08T08:42:15] Merging adjacent fusion breakpoints (remaining=402329)
[2026-06-08T08:42:16] Filtering multi-mapping fusions by alignment score and read support (remaining=241262)
[2026-06-08T08:42:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=240212)
[2026-06-08T08:42:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=136743)
[2026-06-08T08:42:50] Filtering fusions with <2 supporting reads (remaining=15221)
[2026-06-08T08:42:50] Filtering fusions with an e-value >=0.3 (remaining=3718)
[2026-06-08T08:42:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3757)
[2026-06-08T08:42:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3709)
[2026-06-08T08:42:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3709)
[2026-06-08T08:42:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3577)
[2026-06-08T08:42:58] Searching for fusions with spliced split reads (remaining=3643)
[2026-06-08T08:43:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=2615)
[2026-06-08T08:43:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2578)
[2026-06-08T08:43:03] Searching for fusions with >=4 spliced events (remaining=2950)
[2026-06-08T08:43:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1017)
[2026-06-08T08:43:17] Filtering fusions with anchors <=23nt (remaining=873)
[2026-06-08T08:43:18] Filtering end-to-end fusions with low support (remaining=841)
[2026-06-08T08:43:19] Filtering fusions with no coverage around the breakpoints (remaining=813)
[2026-06-08T08:43:19] Indexing gene sequences 
[2026-06-08T08:43:24] Filtering genes with >=30% identity (remaining=258)
[2026-06-08T08:43:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=121)
[2026-06-08T08:43:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=117)
[2026-06-08T08:43:29] Searching for additional isoforms (remaining=148)
[2026-06-08T08:43:30] Assigning confidence scores to events 
[2026-06-08T08:43:32] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:32] Writing fusions to file 'aih-tih-sc-408cca-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:34] Writing discarded fusions to file 'aih-tih-sc-408cca-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:59] Freeing resources
[2026-06-08T08:44:18] Done (elapsed time=00:09:07, CPU time=00:09:06, peak memory=13gb)