[2026-06-08T08:43:07] Launching Arriba 2.4.0
[2026-06-08T08:43:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:20] Reading chimeric alignments from 'aih-tih-sc-7c6c07-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12831222)
[2026-06-08T08:50:16] Marking multi-mapping alignments (marked=8533398)
[2026-06-08T08:50:20] Detecting strandedness (no)
[2026-06-08T08:50:20] Annotating alignments 
[2026-06-08T08:51:04] Filtering duplicates (remaining=7988122)
[2026-06-08T08:51:13] 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=7631451)
[2026-06-08T08:51:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7631451)
[2026-06-08T08:51:18] Filtering viral contigs with expression lower than the top 5 (remaining=7631451)
[2026-06-08T08:51:23] Filtering viral contigs with less than 5% coverage (remaining=7631451)
[2026-06-08T08:51:26] Estimating fragment length (mate gap mean=-85.9198, mate gap stddev=28.4702, read length mean=132.256)
[2026-06-08T08:51:26] Filtering read-through fragments with a distance <=10000bp (remaining=7304825)
[2026-06-08T08:51:28] Filtering inconsistently clipped mates (remaining=7198336)
[2026-06-08T08:51:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7029481)
[2026-06-08T08:51:35] Filtering fragments with small insert size (remaining=7028801)
[2026-06-08T08:51:38] Filtering alignments with long gaps (remaining=7028799)
[2026-06-08T08:51:40] Filtering fragments with both mates in the same gene (remaining=7027933)
[2026-06-08T08:51:43] Filtering fusions arising from hairpin structures (remaining=6708910)
[2026-06-08T08:51:46] Filtering reads with a mismatch p-value <=0.01 (remaining=3210505)
[2026-06-08T08:52:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=1192536)
[2026-06-08T08:52:14] Finding fusions and counting supporting reads (total=830314)
[2026-06-08T08:52:33] Merging adjacent fusion breakpoints (remaining=819267)
[2026-06-08T08:52:35] Filtering multi-mapping fusions by alignment score and read support (remaining=488253)
[2026-06-08T08:53:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:53:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=486149)
[2026-06-08T08:53:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=308066)
[2026-06-08T08:53:24] Filtering fusions with <2 supporting reads (remaining=45563)
[2026-06-08T08:53:25] Filtering fusions with an e-value >=0.3 (remaining=14102)
[2026-06-08T08:53:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14154)
[2026-06-08T08:53:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14010)
[2026-06-08T08:53:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14010)
[2026-06-08T08:53:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8175)
[2026-06-08T08:53:39] Searching for fusions with spliced split reads (remaining=8311)
[2026-06-08T08:53:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=5107)
[2026-06-08T08:53:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5073)
[2026-06-08T08:53:48] Searching for fusions with >=4 spliced events (remaining=6233)
[2026-06-08T08:53:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2437)
[2026-06-08T08:54:07] Filtering fusions with anchors <=23nt (remaining=2036)
[2026-06-08T08:54:08] Filtering end-to-end fusions with low support (remaining=1982)
[2026-06-08T08:54:09] Filtering fusions with no coverage around the breakpoints (remaining=1948)
[2026-06-08T08:54:10] Indexing gene sequences 
[2026-06-08T08:54:17] Filtering genes with >=30% identity (remaining=595)
[2026-06-08T08:54:21] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=251)
[2026-06-08T08:54:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=237)
[2026-06-08T08:54:26] Searching for additional isoforms (remaining=334)
[2026-06-08T08:54:27] Assigning confidence scores to events 
[2026-06-08T08:54:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:54:31] Writing fusions to file 'aih-tih-sc-7c6c07-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:54:34] Writing discarded fusions to file 'aih-tih-sc-7c6c07-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:55:05] Freeing resources
[2026-06-08T08:55:24] Done (elapsed time=00:12:17, CPU time=00:12:15, peak memory=17.2gb)