[2026-06-08T08:40:27] Launching Arriba 2.4.0
[2026-06-08T08:40:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:40:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:40:40] Reading chimeric alignments from 'aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10624093)
[2026-06-08T08:47:37] Marking multi-mapping alignments (marked=6945797)
[2026-06-08T08:47:41] Detecting strandedness (reverse)
[2026-06-08T08:47:41] Assigning strands to alignments 
[2026-06-08T08:47:43] Annotating alignments 
[2026-06-08T08:48:16] Filtering duplicates (remaining=7070033)
[2026-06-08T08:48:23] 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=6644002)
[2026-06-08T08:48:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6644002)
[2026-06-08T08:48:27] Filtering viral contigs with expression lower than the top 5 (remaining=6644002)
[2026-06-08T08:48:31] Filtering viral contigs with less than 5% coverage (remaining=6644002)
[2026-06-08T08:48:34] Estimating fragment length (mate gap mean=-84.8289, mate gap stddev=28.1356, read length mean=125.823)
[2026-06-08T08:48:34] Filtering read-through fragments with a distance <=10000bp (remaining=6135698)
[2026-06-08T08:48:36] Filtering inconsistently clipped mates (remaining=6013659)
[2026-06-08T08:48:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5852200)
[2026-06-08T08:48:42] Filtering fragments with small insert size (remaining=5851184)
[2026-06-08T08:48:44] Filtering alignments with long gaps (remaining=5851182)
[2026-06-08T08:48:46] Filtering fragments with both mates in the same gene (remaining=5850030)
[2026-06-08T08:48:48] Filtering fusions arising from hairpin structures (remaining=5486991)
[2026-06-08T08:48:51] Filtering reads with a mismatch p-value <=0.01 (remaining=2357216)
[2026-06-08T08:49:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1342632)
[2026-06-08T08:49:14] Finding fusions and counting supporting reads (total=1038469)
[2026-06-08T08:49:30] Merging adjacent fusion breakpoints (remaining=1025647)
[2026-06-08T08:49:32] Filtering multi-mapping fusions by alignment score and read support (remaining=614173)
[2026-06-08T08:50:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=612047)
[2026-06-08T08:50:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=392401)
[2026-06-08T08:50:11] Filtering fusions with <2 supporting reads (remaining=40273)
[2026-06-08T08:50:12] Filtering fusions with an e-value >=0.3 (remaining=8348)
[2026-06-08T08:50:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8409)
[2026-06-08T08:50:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8270)
[2026-06-08T08:50:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8273)
[2026-06-08T08:50:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7550)
[2026-06-08T08:50:24] Searching for fusions with spliced split reads (remaining=7570)
[2026-06-08T08:50:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=4843)
[2026-06-08T08:50:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4785)
[2026-06-08T08:50:31] Searching for fusions with >=4 spliced events (remaining=6024)
[2026-06-08T08:50:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2530)
[2026-06-08T08:50:47] Filtering fusions with anchors <=23nt (remaining=2174)
[2026-06-08T08:50:48] Filtering end-to-end fusions with low support (remaining=2122)
[2026-06-08T08:50:49] Filtering fusions with no coverage around the breakpoints (remaining=2077)
[2026-06-08T08:50:50] Indexing gene sequences 
[2026-06-08T08:50:56] Filtering genes with >=30% identity (remaining=787)
[2026-06-08T08:51:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=460)
[2026-06-08T08:51:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=253)
[2026-06-08T08:51:09] Searching for additional isoforms (remaining=393)
[2026-06-08T08:51:11] Assigning confidence scores to events 
[2026-06-08T08:51:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:14] Writing fusions to file 'aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:17] Writing discarded fusions to file 'aih-tih-sc-6cc13c-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:47] Freeing resources
[2026-06-08T08:52:04] Done (elapsed time=00:11:37, CPU time=00:11:35, peak memory=15.6gb)