[2026-06-08T08:42:28] Launching Arriba 2.4.0
[2026-06-08T08:42:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:40] Reading chimeric alignments from 'aih-tih-sc-184b05-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=11993457)
[2026-06-08T08:50:02] Marking multi-mapping alignments (marked=8228645)
[2026-06-08T08:50:07] Detecting strandedness (reverse)
[2026-06-08T08:50:07] Assigning strands to alignments 
[2026-06-08T08:50:10] Annotating alignments 
[2026-06-08T08:50:48] Filtering duplicates (remaining=6935534)
[2026-06-08T08:50:56] 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)
[2026-06-08T08:50:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6375776)
[2026-06-08T08:51:01] Filtering viral contigs with expression lower than the top 5 (remaining=6375776)
[2026-06-08T08:51:06] Filtering viral contigs with less than 5% coverage (remaining=6375776)
[2026-06-08T08:51:09] Estimating fragment length (mate gap mean=-87.8404, mate gap stddev=28.4533, read length mean=129.647)
[2026-06-08T08:51:09] Filtering read-through fragments with a distance <=10000bp (remaining=5937278)
[2026-06-08T08:51:11] Filtering inconsistently clipped mates (remaining=5800405)
[2026-06-08T08:51:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5646419)
[2026-06-08T08:51:19] Filtering fragments with small insert size (remaining=5645425)
[2026-06-08T08:51:21] Filtering alignments with long gaps (remaining=5645425)
[2026-06-08T08:51:23] Filtering fragments with both mates in the same gene (remaining=5644339)
[2026-06-08T08:51:26] Filtering fusions arising from hairpin structures (remaining=5255326)
[2026-06-08T08:51:29] Filtering reads with a mismatch p-value <=0.01 (remaining=2179700)
[2026-06-08T08:51:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=992125)
[2026-06-08T08:51:55] Finding fusions and counting supporting reads (total=794885)
[2026-06-08T08:52:16] Merging adjacent fusion breakpoints (remaining=785406)
[2026-06-08T08:52:18] Filtering multi-mapping fusions by alignment score and read support (remaining=461350)
[2026-06-08T08:53:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=459052)
[2026-06-08T08:53:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=259141)
[2026-06-08T08:53:11] Filtering fusions with <2 supporting reads (remaining=27670)
[2026-06-08T08:53:12] Filtering fusions with an e-value >=0.3 (remaining=7902)
[2026-06-08T08:53:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7978)
[2026-06-08T08:53:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7870)
[2026-06-08T08:53:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7870)
[2026-06-08T08:53:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6098)
[2026-06-08T08:53:27] Searching for fusions with spliced split reads (remaining=6180)
[2026-06-08T08:53:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=3967)
[2026-06-08T08:53:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3925)
[2026-06-08T08:53:35] Searching for fusions with >=4 spliced events (remaining=4670)
[2026-06-08T08:53:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1992)
[2026-06-08T08:53:54] Filtering fusions with anchors <=23nt (remaining=1545)
[2026-06-08T08:53:55] Filtering end-to-end fusions with low support (remaining=1479)
[2026-06-08T08:53:56] Filtering fusions with no coverage around the breakpoints (remaining=1454)
[2026-06-08T08:53:57] Indexing gene sequences 
[2026-06-08T08:54:04] Filtering genes with >=30% identity (remaining=456)
[2026-06-08T08:54:07] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=200)
[2026-06-08T08:54:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=186)
[2026-06-08T08:54:11] Searching for additional isoforms (remaining=233)
[2026-06-08T08:54:12] Assigning confidence scores to events 
[2026-06-08T08:54:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:17] Writing fusions to file 'aih-tih-sc-184b05-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:19] Writing discarded fusions to file 'aih-tih-sc-184b05-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:59] Freeing resources
[2026-06-08T08:55:21] Done (elapsed time=00:12:53, CPU time=00:12:51, peak memory=17gb)