[2026-06-08T08:45:06] Launching Arriba 2.4.0
[2026-06-08T08:45:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:20] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:25] Reading chimeric alignments from 'aih-tih-sc-c5cb90-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=17081723)
[2026-06-08T08:52:59] Marking multi-mapping alignments (marked=12260866)
[2026-06-08T08:53:06] Detecting strandedness (reverse)
[2026-06-08T08:53:06] Assigning strands to alignments 
[2026-06-08T08:53:09] Annotating alignments 
[2026-06-08T08:53:55] Filtering duplicates (remaining=6189228)
[2026-06-08T08:54:04] 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=5759542)
[2026-06-08T08:54:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5759542)
[2026-06-08T08:54:10] Filtering viral contigs with expression lower than the top 5 (remaining=5759542)
[2026-06-08T08:54:17] Filtering viral contigs with less than 5% coverage (remaining=5759542)
[2026-06-08T08:54:20] Estimating fragment length (mate gap mean=-83.8699, mate gap stddev=27.0483, read length mean=122.696)
[2026-06-08T08:54:20] Filtering read-through fragments with a distance <=10000bp (remaining=5469889)
[2026-06-08T08:54:23] Filtering inconsistently clipped mates (remaining=5372497)
[2026-06-08T08:54:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5220743)
[2026-06-08T08:54:31] Filtering fragments with small insert size (remaining=5219829)
[2026-06-08T08:54:35] Filtering alignments with long gaps (remaining=5219829)
[2026-06-08T08:54:38] Filtering fragments with both mates in the same gene (remaining=5218818)
[2026-06-08T08:54:41] Filtering fusions arising from hairpin structures (remaining=4988958)
[2026-06-08T08:54:44] Filtering reads with a mismatch p-value <=0.01 (remaining=2038847)
[2026-06-08T08:54:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=686978)
[2026-06-08T08:55:07] Finding fusions and counting supporting reads (total=524649)
[2026-06-08T08:55:26] Merging adjacent fusion breakpoints (remaining=517736)
[2026-06-08T08:55:28] Filtering multi-mapping fusions by alignment score and read support (remaining=266553)
[2026-06-08T08:56:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=265576)
[2026-06-08T08:56:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=159389)
[2026-06-08T08:56:19] Filtering fusions with <2 supporting reads (remaining=19018)
[2026-06-08T08:56:20] Filtering fusions with an e-value >=0.3 (remaining=4427)
[2026-06-08T08:56:20] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4477)
[2026-06-08T08:56:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4389)
[2026-06-08T08:56:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4389)
[2026-06-08T08:56:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4357)
[2026-06-08T08:56:32] Searching for fusions with spliced split reads (remaining=4395)
[2026-06-08T08:56:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=2968)
[2026-06-08T08:56:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2950)
[2026-06-08T08:56:41] Searching for fusions with >=4 spliced events (remaining=3374)
[2026-06-08T08:56:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1220)
[2026-06-08T08:56:58] Filtering fusions with anchors <=23nt (remaining=1006)
[2026-06-08T08:56:59] Filtering end-to-end fusions with low support (remaining=977)
[2026-06-08T08:57:00] Filtering fusions with no coverage around the breakpoints (remaining=956)
[2026-06-08T08:57:00] Indexing gene sequences 
[2026-06-08T08:57:04] Filtering genes with >=30% identity (remaining=279)
[2026-06-08T08:57:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=68)
[2026-06-08T08:57:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=68)
[2026-06-08T08:57:08] Searching for additional isoforms (remaining=82)
[2026-06-08T08:57:09] Assigning confidence scores to events 
[2026-06-08T08:57:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:12] Writing fusions to file 'aih-tih-sc-c5cb90-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:13] Writing discarded fusions to file 'aih-tih-sc-c5cb90-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:36] Freeing resources
[2026-06-08T08:58:00] Done (elapsed time=00:12:54, CPU time=00:12:52, peak memory=21.2gb)