[2026-06-08T08:24:50] Launching Arriba 2.4.0
[2026-06-08T08:24:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:09] Reading chimeric alignments from 'aih-tih-sc-c55577-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=13120242)
[2026-06-08T08:31:34] Marking multi-mapping alignments (marked=10067270)
[2026-06-08T08:31:39] Detecting strandedness (no)
[2026-06-08T08:31:39] Annotating alignments 
[2026-06-08T08:32:25] Filtering duplicates (remaining=3706403)
[2026-06-08T08:32:31] 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=3310957)
[2026-06-08T08:32:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3310957)
[2026-06-08T08:32:36] Filtering viral contigs with expression lower than the top 5 (remaining=3310957)
[2026-06-08T08:32:42] Filtering viral contigs with less than 5% coverage (remaining=3310957)
[2026-06-08T08:32:44] Estimating fragment length (mate gap mean=-84.4374, mate gap stddev=28.5302, read length mean=122.337)
[2026-06-08T08:32:44] Filtering read-through fragments with a distance <=10000bp (remaining=3176197)
[2026-06-08T08:32:47] Filtering inconsistently clipped mates (remaining=3109113)
[2026-06-08T08:32:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3022121)
[2026-06-08T08:32:53] Filtering fragments with small insert size (remaining=3021525)
[2026-06-08T08:32:56] Filtering alignments with long gaps (remaining=3021525)
[2026-06-08T08:32:58] Filtering fragments with both mates in the same gene (remaining=3020816)
[2026-06-08T08:33:01] Filtering fusions arising from hairpin structures (remaining=2853945)
[2026-06-08T08:33:04] Filtering reads with a mismatch p-value <=0.01 (remaining=1171585)
[2026-06-08T08:33:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=295294)
[2026-06-08T08:33:20] Finding fusions and counting supporting reads (total=217524)
[2026-06-08T08:33:35] Merging adjacent fusion breakpoints (remaining=214092)
[2026-06-08T08:33:35] Filtering multi-mapping fusions by alignment score and read support (remaining=112286)
[2026-06-08T08:34:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:15] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=111462)
[2026-06-08T08:34:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=62935)
[2026-06-08T08:34:16] Filtering fusions with <2 supporting reads (remaining=7054)
[2026-06-08T08:34:16] Filtering fusions with an e-value >=0.3 (remaining=1897)
[2026-06-08T08:34:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1943)
[2026-06-08T08:34:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1856)
[2026-06-08T08:34:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1856)
[2026-06-08T08:34:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1824)
[2026-06-08T08:34:25] Searching for fusions with spliced split reads (remaining=1908)
[2026-06-08T08:34:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=1426)
[2026-06-08T08:34:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1415)
[2026-06-08T08:34:31] Searching for fusions with >=4 spliced events (remaining=1502)
[2026-06-08T08:34:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=394)
[2026-06-08T08:34:48] Filtering fusions with anchors <=23nt (remaining=285)
[2026-06-08T08:34:49] Filtering end-to-end fusions with low support (remaining=277)
[2026-06-08T08:34:49] Filtering fusions with no coverage around the breakpoints (remaining=270)
[2026-06-08T08:34:49] Indexing gene sequences 
[2026-06-08T08:34:51] Filtering genes with >=30% identity (remaining=74)
[2026-06-08T08:34:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=38)
[2026-06-08T08:34:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=35)
[2026-06-08T08:34:54] Searching for additional isoforms (remaining=44)
[2026-06-08T08:34:55] Assigning confidence scores to events 
[2026-06-08T08:34:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:57] Writing fusions to file 'aih-tih-sc-c55577-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:34:57] Writing discarded fusions to file 'aih-tih-sc-c55577-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:35:13] Freeing resources
[2026-06-08T08:35:33] Done (elapsed time=00:10:43, CPU time=00:10:42, peak memory=17.3gb)