[2026-06-08T08:32:08] Launching Arriba 2.4.0
[2026-06-08T08:32:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:22] Reading chimeric alignments from 'aih-tih-sc-a3a521-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10574214)
[2026-06-08T08:39:15] Marking multi-mapping alignments (marked=6619518)
[2026-06-08T08:39:20] Detecting strandedness (reverse)
[2026-06-08T08:39:20] Assigning strands to alignments 
[2026-06-08T08:39:23] Annotating alignments 
[2026-06-08T08:40:02] Filtering duplicates (remaining=6799544)
[2026-06-08T08:40:11] 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=6558529)
[2026-06-08T08:40:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6558529)
[2026-06-08T08:40:17] Filtering viral contigs with expression lower than the top 5 (remaining=6558529)
[2026-06-08T08:40:23] Filtering viral contigs with less than 5% coverage (remaining=6558529)
[2026-06-08T08:40:25] Estimating fragment length (mate gap mean=-86.5289, mate gap stddev=28.7224, read length mean=131.462)
[2026-06-08T08:40:25] Filtering read-through fragments with a distance <=10000bp (remaining=6183979)
[2026-06-08T08:40:28] Filtering inconsistently clipped mates (remaining=6103424)
[2026-06-08T08:40:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5963534)
[2026-06-08T08:40:35] Filtering fragments with small insert size (remaining=5962954)
[2026-06-08T08:40:38] Filtering alignments with long gaps (remaining=5962954)
[2026-06-08T08:40:40] Filtering fragments with both mates in the same gene (remaining=5961965)
[2026-06-08T08:40:43] Filtering fusions arising from hairpin structures (remaining=5722788)
[2026-06-08T08:40:46] Filtering reads with a mismatch p-value <=0.01 (remaining=2836874)
[2026-06-08T08:41:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=1001496)
[2026-06-08T08:41:13] Finding fusions and counting supporting reads (total=748577)
[2026-06-08T08:41:35] Merging adjacent fusion breakpoints (remaining=740854)
[2026-06-08T08:41:37] Filtering multi-mapping fusions by alignment score and read support (remaining=465964)
[2026-06-08T08:42:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=464211)
[2026-06-08T08:42:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=268567)
[2026-06-08T08:42:36] Filtering fusions with <2 supporting reads (remaining=34499)
[2026-06-08T08:42:37] Filtering fusions with an e-value >=0.3 (remaining=8699)
[2026-06-08T08:42:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8742)
[2026-06-08T08:42:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8628)
[2026-06-08T08:42:44] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8628)
[2026-06-08T08:42:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7877)
[2026-06-08T08:42:54] Searching for fusions with spliced split reads (remaining=7882)
[2026-06-08T08:43:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=5045)
[2026-06-08T08:43:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4961)
[2026-06-08T08:43:04] Searching for fusions with >=4 spliced events (remaining=6053)
[2026-06-08T08:43:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2520)
[2026-06-08T08:43:28] Filtering fusions with anchors <=23nt (remaining=2059)
[2026-06-08T08:43:29] Filtering end-to-end fusions with low support (remaining=2001)
[2026-06-08T08:43:29] Filtering fusions with no coverage around the breakpoints (remaining=1963)
[2026-06-08T08:43:30] Indexing gene sequences 
[2026-06-08T08:43:42] Filtering genes with >=30% identity (remaining=670)
[2026-06-08T08:43:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=364)
[2026-06-08T08:43:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=299)
[2026-06-08T08:43:54] Searching for additional isoforms (remaining=387)
[2026-06-08T08:43:56] Assigning confidence scores to events 
[2026-06-08T08:44:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:01] Writing fusions to file 'aih-tih-sc-a3a521-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:44:06] Writing discarded fusions to file 'aih-tih-sc-a3a521-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:52] Freeing resources
[2026-06-08T08:45:18] Done (elapsed time=00:13:10, CPU time=00:13:08, peak memory=14.9gb)