[2026-06-08T08:00:41] Launching Arriba 2.4.0
[2026-06-08T08:00:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:01:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:01:05] Reading chimeric alignments from 'aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=5840106)
[2026-06-08T08:05:30] Marking multi-mapping alignments (marked=4001855)
[2026-06-08T08:05:33] Detecting strandedness (reverse)
[2026-06-08T08:05:33] Assigning strands to alignments 
[2026-06-08T08:05:34] Annotating alignments 
[2026-06-08T08:06:02] Filtering duplicates (remaining=3261220)
[2026-06-08T08:06:08] 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=3080793)
[2026-06-08T08:06:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3080793)
[2026-06-08T08:06:11] Filtering viral contigs with expression lower than the top 5 (remaining=3080793)
[2026-06-08T08:06:14] Filtering viral contigs with less than 5% coverage (remaining=3080793)
[2026-06-08T08:06:16] Estimating fragment length (mate gap mean=-87.3194, mate gap stddev=27.3732, read length mean=127.591)
[2026-06-08T08:06:16] Filtering read-through fragments with a distance <=10000bp (remaining=2953855)
[2026-06-08T08:06:17] Filtering inconsistently clipped mates (remaining=2894969)
[2026-06-08T08:06:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2799017)
[2026-06-08T08:06:22] Filtering fragments with small insert size (remaining=2798534)
[2026-06-08T08:06:23] Filtering alignments with long gaps (remaining=2798534)
[2026-06-08T08:06:24] Filtering fragments with both mates in the same gene (remaining=2797932)
[2026-06-08T08:06:26] Filtering fusions arising from hairpin structures (remaining=2644837)
[2026-06-08T08:06:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1167920)
[2026-06-08T08:06:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=369270)
[2026-06-08T08:06:40] Finding fusions and counting supporting reads (total=301505)
[2026-06-08T08:06:50] Merging adjacent fusion breakpoints (remaining=298988)
[2026-06-08T08:06:51] Filtering multi-mapping fusions by alignment score and read support (remaining=164433)
[2026-06-08T08:07:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:07:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=163653)
[2026-06-08T08:07:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=100891)
[2026-06-08T08:07:15] Filtering fusions with <2 supporting reads (remaining=10082)
[2026-06-08T08:07:15] Filtering fusions with an e-value >=0.3 (remaining=2772)
[2026-06-08T08:07:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2828)
[2026-06-08T08:07:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2779)
[2026-06-08T08:07:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2779)
[2026-06-08T08:07:19] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2698)
[2026-06-08T08:07:22] Searching for fusions with spliced split reads (remaining=2738)
[2026-06-08T08:07:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=1981)
[2026-06-08T08:07:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1953)
[2026-06-08T08:07:27] Searching for fusions with >=4 spliced events (remaining=2155)
[2026-06-08T08:07:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=698)
[2026-06-08T08:07:45] Filtering fusions with anchors <=23nt (remaining=501)
[2026-06-08T08:07:46] Filtering end-to-end fusions with low support (remaining=491)
[2026-06-08T08:07:46] Filtering fusions with no coverage around the breakpoints (remaining=470)
[2026-06-08T08:07:46] Indexing gene sequences 
[2026-06-08T08:07:50] Filtering genes with >=30% identity (remaining=123)
[2026-06-08T08:07:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=52)
[2026-06-08T08:07:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=52)
[2026-06-08T08:07:53] Searching for additional isoforms (remaining=62)
[2026-06-08T08:07:53] Assigning confidence scores to events 
[2026-06-08T08:07:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:07:55] Writing fusions to file 'aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:07:56] Writing discarded fusions to file 'aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:08:13] Freeing resources
[2026-06-08T08:08:24] Done (elapsed time=00:07:43, CPU time=00:07:41, peak memory=10.1gb)