[2026-06-03T20:41:39] Launching Arriba 2.4.0
[2026-06-03T20:41:39] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:41:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:41:50] Reading chimeric alignments from 'aih-tih-sc-184b05-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11993457)
[2026-06-03T20:48:51] Marking multi-mapping alignments (marked=8228645)
[2026-06-03T20:48:56] Detecting strandedness (reverse)
[2026-06-03T20:48:56] Assigning strands to alignments 
[2026-06-03T20:48:59] Annotating alignments 
[2026-06-03T20:49:37] Filtering duplicates (remaining=6935534)
[2026-06-03T20:49:45] 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=6375776)
[2026-06-03T20:49:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6375776)
[2026-06-03T20:49:49] Filtering viral contigs with expression lower than the top 5 (remaining=6375776)
[2026-06-03T20:49:55] Filtering viral contigs with less than 5% coverage (remaining=6375776)
[2026-06-03T20:49:58] Estimating fragment length (mate gap mean=-87.8404, mate gap stddev=28.4533, read length mean=129.647)
[2026-06-03T20:49:58] Filtering read-through fragments with a distance <=10000bp (remaining=5937278)
[2026-06-03T20:50:00] Filtering inconsistently clipped mates (remaining=5800405)
[2026-06-03T20:50:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5646419)
[2026-06-03T20:50:08] Filtering fragments with small insert size (remaining=5645425)
[2026-06-03T20:50:10] Filtering alignments with long gaps (remaining=5645425)
[2026-06-03T20:50:13] Filtering fragments with both mates in the same gene (remaining=5644339)
[2026-06-03T20:50:16] Filtering fusions arising from hairpin structures (remaining=5255326)
[2026-06-03T20:50:19] Filtering reads with a mismatch p-value <=0.01 (remaining=2179700)
[2026-06-03T20:50:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=992125)
[2026-06-03T20:50:47] Finding fusions and counting supporting reads (total=794885)
[2026-06-03T20:51:08] Merging adjacent fusion breakpoints (remaining=785406)
[2026-06-03T20:51:10] Filtering multi-mapping fusions by alignment score and read support (remaining=461350)
[2026-06-03T20:51:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:51:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=459052)
[2026-06-03T20:51:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=259141)
[2026-06-03T20:51:57] Filtering fusions with <2 supporting reads (remaining=27670)
[2026-06-03T20:51:57] Filtering fusions with an e-value >=0.3 (remaining=7902)
[2026-06-03T20:51:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7978)
[2026-06-03T20:52:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7870)
[2026-06-03T20:52:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7870)
[2026-06-03T20:52:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6098)
[2026-06-03T20:52:10] Searching for fusions with spliced split reads (remaining=6180)
[2026-06-03T20:52:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=3967)
[2026-06-03T20:52:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3925)
[2026-06-03T20:52:18] Searching for fusions with >=4 spliced events (remaining=4670)
[2026-06-03T20:52:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1992)
[2026-06-03T20:52:36] Filtering fusions with anchors <=23nt (remaining=1545)
[2026-06-03T20:52:37] Filtering end-to-end fusions with low support (remaining=1479)
[2026-06-03T20:52:38] Filtering fusions with no coverage around the breakpoints (remaining=1454)
[2026-06-03T20:52:38] Indexing gene sequences 
[2026-06-03T20:52:45] Filtering genes with >=30% identity (remaining=456)
[2026-06-03T20:52:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=200)
[2026-06-03T20:52:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=186)
[2026-06-03T20:52:52] Searching for additional isoforms (remaining=233)
[2026-06-03T20:52:53] Assigning confidence scores to events 
[2026-06-03T20:52:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:52:57] Writing fusions to file 'aih-tih-sc-184b05-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:52:59] Writing discarded fusions to file 'aih-tih-sc-184b05-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:53:31] Freeing resources
[2026-06-03T20:53:50] Done (elapsed time=00:12:11, CPU time=00:12:11, peak memory=17gb)