[2026-06-08T08:49:39] Launching Arriba 2.4.0
[2026-06-08T08:49:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:54] Reading chimeric alignments from 'aih-tih-sc-7c610c-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=13224969)
[2026-06-08T08:56:59] Marking multi-mapping alignments (marked=9095102)
[2026-06-08T08:57:04] Detecting strandedness (reverse)
[2026-06-08T08:57:04] Assigning strands to alignments 
[2026-06-08T08:57:06] Annotating alignments 
[2026-06-08T08:57:46] Filtering duplicates (remaining=6906575)
[2026-06-08T08:57:54] 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=6543766)
[2026-06-08T08:57:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6543766)
[2026-06-08T08:57:59] Filtering viral contigs with expression lower than the top 5 (remaining=6543766)
[2026-06-08T08:58:05] Filtering viral contigs with less than 5% coverage (remaining=6543766)
[2026-06-08T08:58:07] Estimating fragment length (mate gap mean=-84.7859, mate gap stddev=27.3723, read length mean=124.671)
[2026-06-08T08:58:07] Filtering read-through fragments with a distance <=10000bp (remaining=6114418)
[2026-06-08T08:58:10] Filtering inconsistently clipped mates (remaining=6027890)
[2026-06-08T08:58:12] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5895610)
[2026-06-08T08:58:17] Filtering fragments with small insert size (remaining=5894876)
[2026-06-08T08:58:20] Filtering alignments with long gaps (remaining=5894876)
[2026-06-08T08:58:23] Filtering fragments with both mates in the same gene (remaining=5893846)
[2026-06-08T08:58:25] Filtering fusions arising from hairpin structures (remaining=5667943)
[2026-06-08T08:58:28] Filtering reads with a mismatch p-value <=0.01 (remaining=2502106)
[2026-06-08T08:58:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=862169)
[2026-06-08T08:58:52] Finding fusions and counting supporting reads (total=647084)
[2026-06-08T08:59:11] Merging adjacent fusion breakpoints (remaining=636743)
[2026-06-08T08:59:12] Filtering multi-mapping fusions by alignment score and read support (remaining=359895)
[2026-06-08T08:59:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=358691)
[2026-06-08T09:00:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=212148)
[2026-06-08T09:00:02] Filtering fusions with <2 supporting reads (remaining=26099)
[2026-06-08T09:00:02] Filtering fusions with an e-value >=0.3 (remaining=6347)
[2026-06-08T09:00:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6420)
[2026-06-08T09:00:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6297)
[2026-06-08T09:00:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6297)
[2026-06-08T09:00:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6180)
[2026-06-08T09:00:16] Searching for fusions with spliced split reads (remaining=6259)
[2026-06-08T09:00:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4186)
[2026-06-08T09:00:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4150)
[2026-06-08T09:00:24] Searching for fusions with >=4 spliced events (remaining=4860)
[2026-06-08T09:00:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1940)
[2026-06-08T09:00:46] Filtering fusions with anchors <=23nt (remaining=1469)
[2026-06-08T09:00:46] Filtering end-to-end fusions with low support (remaining=1438)
[2026-06-08T09:00:47] Filtering fusions with no coverage around the breakpoints (remaining=1410)
[2026-06-08T09:00:48] Indexing gene sequences 
[2026-06-08T09:00:54] Filtering genes with >=30% identity (remaining=382)
[2026-06-08T09:00:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=145)
[2026-06-08T09:00:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=129)
[2026-06-08T09:01:00] Searching for additional isoforms (remaining=154)
[2026-06-08T09:01:02] Assigning confidence scores to events 
[2026-06-08T09:01:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:05] Writing fusions to file 'aih-tih-sc-7c610c-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:07] Writing discarded fusions to file 'aih-tih-sc-7c610c-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:36] Freeing resources
[2026-06-08T09:01:55] Done (elapsed time=00:12:16, CPU time=00:12:15, peak memory=17.5gb)