[2026-06-08T09:07:06] Launching Arriba 2.4.0
[2026-06-08T09:07:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:07:14] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:07:19] Reading chimeric alignments from 'aih-tih-sc-e9e54b-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=13309953)
[2026-06-08T09:13:55] Marking multi-mapping alignments (marked=9017284)
[2026-06-08T09:14:01] Detecting strandedness (reverse)
[2026-06-08T09:14:01] Assigning strands to alignments 
[2026-06-08T09:14:03] Annotating alignments 
[2026-06-08T09:14:50] Filtering duplicates (remaining=5700145)
[2026-06-08T09:14:58] 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=5335901)
[2026-06-08T09:15:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5335901)
[2026-06-08T09:15:03] Filtering viral contigs with expression lower than the top 5 (remaining=5335901)
[2026-06-08T09:15:10] Filtering viral contigs with less than 5% coverage (remaining=5335901)
[2026-06-08T09:15:13] Estimating fragment length (mate gap mean=-86.2001, mate gap stddev=27.8674, read length mean=126.594)
[2026-06-08T09:15:13] Filtering read-through fragments with a distance <=10000bp (remaining=5116305)
[2026-06-08T09:15:16] Filtering inconsistently clipped mates (remaining=5022385)
[2026-06-08T09:15:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4850825)
[2026-06-08T09:15:24] Filtering fragments with small insert size (remaining=4850090)
[2026-06-08T09:15:27] Filtering alignments with long gaps (remaining=4850090)
[2026-06-08T09:15:30] Filtering fragments with both mates in the same gene (remaining=4849087)
[2026-06-08T09:15:32] Filtering fusions arising from hairpin structures (remaining=4614192)
[2026-06-08T09:15:36] Filtering reads with a mismatch p-value <=0.01 (remaining=1986046)
[2026-06-08T09:15:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=594338)
[2026-06-08T09:15:58] Finding fusions and counting supporting reads (total=472572)
[2026-06-08T09:16:17] Merging adjacent fusion breakpoints (remaining=466282)
[2026-06-08T09:16:18] Filtering multi-mapping fusions by alignment score and read support (remaining=259013)
[2026-06-08T09:17:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:17:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=257633)
[2026-06-08T09:17:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=154512)
[2026-06-08T09:17:10] Filtering fusions with <2 supporting reads (remaining=16523)
[2026-06-08T09:17:11] Filtering fusions with an e-value >=0.3 (remaining=4366)
[2026-06-08T09:17:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4409)
[2026-06-08T09:17:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4270)
[2026-06-08T09:17:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4270)
[2026-06-08T09:17:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4156)
[2026-06-08T09:17:23] Searching for fusions with spliced split reads (remaining=4222)
[2026-06-08T09:17:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=3006)
[2026-06-08T09:17:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2975)
[2026-06-08T09:17:31] Searching for fusions with >=4 spliced events (remaining=3396)
[2026-06-08T09:17:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1280)
[2026-06-08T09:17:49] Filtering fusions with anchors <=23nt (remaining=975)
[2026-06-08T09:17:49] Filtering end-to-end fusions with low support (remaining=952)
[2026-06-08T09:17:50] Filtering fusions with no coverage around the breakpoints (remaining=919)
[2026-06-08T09:17:51] Indexing gene sequences 
[2026-06-08T09:17:55] Filtering genes with >=30% identity (remaining=310)
[2026-06-08T09:17:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=140)
[2026-06-08T09:17:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=137)
[2026-06-08T09:18:00] Searching for additional isoforms (remaining=158)
[2026-06-08T09:18:01] Assigning confidence scores to events 
[2026-06-08T09:18:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:18:05] Writing fusions to file 'aih-tih-sc-e9e54b-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:18:06] Writing discarded fusions to file 'aih-tih-sc-e9e54b-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:18:33] Freeing resources
[2026-06-08T09:18:52] Done (elapsed time=00:11:46, CPU time=00:11:46, peak memory=17.6gb)