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Hey Martin,

I have added dropped amplicon information to the truth vcfs I am using to evaluate viridian assemblies but keep getting the error below. Is there a bug or am I doing something wrong?

[2022-04-08T11:30:13 cte INFO] Load runs from file cte_viridian_output/ART_assemblies/manifest.tsv [2022-04-08T11:30:13 cte INFO] ============================================================ [2022-04-08T11:30:13 cte INFO] Start processing run 1/10: 0_a [2022-04-08T11:30:13 cte INFO] Start evaluating viridian_assemblies/ART_assemblies/0_a/consensus.fa [2022-04-08T11:30:13 cte INFO] Using reference FASTA: /usr/local/lib/python3.8/dist-packages/cte/data/MN908947.fasta [2022-04-08T11:30:13 cte INFO] Using truth VCF: truth_vcfs/0_a/04.truth_dropped.vcf [2022-04-08T11:30:13 cte INFO] Loading primers from file /usr/local/lib/python3.8/dist-packages/cte/data/covid-artic-v4.vwf.tsv [2022-04-08T11:30:13 cte INFO] Making multiple sequence alignment (ref vs truth vs seq to evaluate) [2022-04-08T11:30:13 cte INFO] Run command: mafft --anysymbol --nuc --quiet --maxiterate 1000 --thread 1 cte_viridian_output/ART_assemblies/OUT/Processing/0_a/MSA/to_align.fa > cte_viridian_output/ART_assemblies/OUT/Processing/0_a/MSA/msa.fasta [2022-04-08T11:30:17 cte INFO] Return code = 0 from: mafft --anysymbol --nuc --quiet --maxiterate 1000 --thread 1 cte_viridian_output/ART_assemblies/OUT/Processing/0_a/MSA/to_align.fa > cte_viridian_output/ART_assemblies/OUT/Processing/0_a/MSA/msa.fasta [2022-04-08T11:30:17 cte INFO] Gathering stats from MSA Traceback (most recent call last): File "/usr/local/bin/cte", line 8, in <module> sys.exit(main()) File "/usr/local/lib/python3.8/dist-packages/cte/__main__.py", line 98, in main args.func(args) File "/usr/local/lib/python3.8/dist-packages/cte/tasks/eval_runs.py", line 13, in run multi_run_evaluator.evaluate_runs( File "/usr/local/lib/python3.8/dist-packages/cte/multi_run_evaluator.py", line 48, in evaluate_runs new_results = one_run_evaluator.eval_one_fasta( File "/usr/local/lib/python3.8/dist-packages/cte/one_run_evaluator.py", line 44, in eval_one_fasta multi_aln.gather_stats(amp_scheme, per_pos_tsv=per_position_tsv_out) File "/usr/local/lib/python3.8/dist-packages/cte/msa.py", line 335, in gather_stats self.stats = stats_from_three_way_aln( File "/usr/local/lib/python3.8/dist-packages/cte/msa.py", line 223, in stats_from_three_way_aln row, col = aln_bases_to_stats_row_and_col(ref_base, truth_base, eval_base) File "/usr/local/lib/python3.8/dist-packages/cte/msa.py", line 199, in aln_bases_to_stats_row_and_col raise NotImplementedError( NotImplementedError: Case not found for ref,truth,cons bases: A,Z,G

Have attached the failed vcf.

Thanks!
Daniel
04.truth_dropped.vcf.gz