[2026-06-08T08:33:11] Launching Arriba 2.4.0
[2026-06-08T08:33:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:33:24] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:33:28] Reading chimeric alignments from 'aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11653336)
[2026-06-08T08:40:41] Marking multi-mapping alignments (marked=7567820)
[2026-06-08T08:40:46] Detecting strandedness (reverse)
[2026-06-08T08:40:46] Assigning strands to alignments 
[2026-06-08T08:40:48] Annotating alignments 
[2026-06-08T08:41:23] Filtering duplicates (remaining=7654404)
[2026-06-08T08:41:31] 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=7348440)
[2026-06-08T08:41:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7348440)
[2026-06-08T08:41:36] Filtering viral contigs with expression lower than the top 5 (remaining=7348440)
[2026-06-08T08:41:41] Filtering viral contigs with less than 5% coverage (remaining=7348440)
[2026-06-08T08:41:43] Estimating fragment length (mate gap mean=-86.3001, mate gap stddev=29.2041, read length mean=134.906)
[2026-06-08T08:41:44] Filtering read-through fragments with a distance <=10000bp (remaining=6961768)
[2026-06-08T08:41:46] Filtering inconsistently clipped mates (remaining=6871756)
[2026-06-08T08:41:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6701293)
[2026-06-08T08:41:53] Filtering fragments with small insert size (remaining=6700704)
[2026-06-08T08:41:55] Filtering alignments with long gaps (remaining=6700704)
[2026-06-08T08:41:58] Filtering fragments with both mates in the same gene (remaining=6699686)
[2026-06-08T08:42:00] Filtering fusions arising from hairpin structures (remaining=6395534)
[2026-06-08T08:42:03] Filtering reads with a mismatch p-value <=0.01 (remaining=3180527)
[2026-06-08T08:42:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=1091970)
[2026-06-08T08:42:37] Finding fusions and counting supporting reads (total=808727)
[2026-06-08T08:43:06] Merging adjacent fusion breakpoints (remaining=801362)
[2026-06-08T08:43:08] Filtering multi-mapping fusions by alignment score and read support (remaining=485657)
[2026-06-08T08:43:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=483399)
[2026-06-08T08:43:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=290895)
[2026-06-08T08:43:58] Filtering fusions with <2 supporting reads (remaining=34658)
[2026-06-08T08:43:59] Filtering fusions with an e-value >=0.3 (remaining=9648)
[2026-06-08T08:43:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9707)
[2026-06-08T08:44:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9590)
[2026-06-08T08:44:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9590)
[2026-06-08T08:44:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7508)
[2026-06-08T08:44:13] Searching for fusions with spliced split reads (remaining=7541)
[2026-06-08T08:44:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=4520)
[2026-06-08T08:44:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4483)
[2026-06-08T08:44:21] Searching for fusions with >=4 spliced events (remaining=5454)
[2026-06-08T08:44:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2250)
[2026-06-08T08:44:41] Filtering fusions with anchors <=23nt (remaining=1856)
[2026-06-08T08:44:42] Filtering end-to-end fusions with low support (remaining=1801)
[2026-06-08T08:44:43] Filtering fusions with no coverage around the breakpoints (remaining=1765)
[2026-06-08T08:44:43] Indexing gene sequences 
[2026-06-08T08:44:51] Filtering genes with >=30% identity (remaining=584)
[2026-06-08T08:44:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=238)
[2026-06-08T08:45:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=179)
[2026-06-08T08:45:11] Searching for additional isoforms (remaining=248)
[2026-06-08T08:45:13] Assigning confidence scores to events 
[2026-06-08T08:45:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:17] Writing fusions to file 'aih-tih-sc-f71b32-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:19] Writing discarded fusions to file 'aih-tih-sc-f71b32-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:51] Freeing resources
[2026-06-08T08:46:12] Done (elapsed time=00:13:01, CPU time=00:13:00, peak memory=16gb)