[2026-06-08T08:56:26] Launching Arriba 2.4.0
[2026-06-08T08:56:26] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:56:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:56:49] Reading chimeric alignments from 'aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10294822)
[2026-06-08T09:06:12] Marking multi-mapping alignments (marked=6620108)
[2026-06-08T09:06:16] Detecting strandedness (reverse)
[2026-06-08T09:06:16] Assigning strands to alignments 
[2026-06-08T09:06:18] Annotating alignments 
[2026-06-08T09:06:49] Filtering duplicates (remaining=7345245)
[2026-06-08T09:06:57] 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=7031251)
[2026-06-08T09:06:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7031251)
[2026-06-08T09:07:00] Filtering viral contigs with expression lower than the top 5 (remaining=7031251)
[2026-06-08T09:07:05] Filtering viral contigs with less than 5% coverage (remaining=7031251)
[2026-06-08T09:07:07] Estimating fragment length (mate gap mean=-84.0673, mate gap stddev=31.1305, read length mean=134.484)
[2026-06-08T09:07:07] Filtering read-through fragments with a distance <=10000bp (remaining=6672877)
[2026-06-08T09:07:09] Filtering inconsistently clipped mates (remaining=6550124)
[2026-06-08T09:07:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6366745)
[2026-06-08T09:07:15] Filtering fragments with small insert size (remaining=6366061)
[2026-06-08T09:07:17] Filtering alignments with long gaps (remaining=6366061)
[2026-06-08T09:07:19] Filtering fragments with both mates in the same gene (remaining=6364742)
[2026-06-08T09:07:21] Filtering fusions arising from hairpin structures (remaining=5964352)
[2026-06-08T09:07:23] Filtering reads with a mismatch p-value <=0.01 (remaining=2762386)
[2026-06-08T09:07:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=1234515)
[2026-06-08T09:07:52] Finding fusions and counting supporting reads (total=910484)
[2026-06-08T09:08:08] Merging adjacent fusion breakpoints (remaining=903303)
[2026-06-08T09:08:10] Filtering multi-mapping fusions by alignment score and read support (remaining=597249)
[2026-06-08T09:08:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=594263)
[2026-06-08T09:08:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=351957)
[2026-06-08T09:08:50] Filtering fusions with <2 supporting reads (remaining=44557)
[2026-06-08T09:08:51] Filtering fusions with an e-value >=0.3 (remaining=14275)
[2026-06-08T09:08:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=14328)
[2026-06-08T09:08:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=14241)
[2026-06-08T09:08:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=14241)
[2026-06-08T09:08:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10005)
[2026-06-08T09:09:03] Searching for fusions with spliced split reads (remaining=10038)
[2026-06-08T09:09:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=4840)
[2026-06-08T09:09:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4778)
[2026-06-08T09:09:10] Searching for fusions with >=4 spliced events (remaining=5891)
[2026-06-08T09:09:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2232)
[2026-06-08T09:09:32] Filtering fusions with anchors <=23nt (remaining=1749)
[2026-06-08T09:09:33] Filtering end-to-end fusions with low support (remaining=1706)
[2026-06-08T09:09:33] Filtering fusions with no coverage around the breakpoints (remaining=1672)
[2026-06-08T09:09:34] Indexing gene sequences 
[2026-06-08T09:09:41] Filtering genes with >=30% identity (remaining=486)
[2026-06-08T09:09:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=220)
[2026-06-08T09:09:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=184)
[2026-06-08T09:09:52] Searching for additional isoforms (remaining=252)
[2026-06-08T09:09:53] Assigning confidence scores to events 
[2026-06-08T09:09:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:57] Writing fusions to file 'aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:00] Writing discarded fusions to file 'aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:33] Freeing resources
[2026-06-08T09:10:50] Done (elapsed time=00:14:24, CPU time=00:14:22, peak memory=15gb)