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zjshi / Maast

Microbial agile accurate SNP Typer
MIT License
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KeyError: ? #20

Open liushuqing506 opened 7 months ago

liushuqing506 commented 7 months ago

''' 1398/GCA_017353475.1_ASM1735347v1_genomic.fna Running mummer4; start reference genome path: 1398/GCA_017353475.1_ASM1735347v1_genomic.fna

GCA_017353475.1_ASM1735347v1_genomic - GCA_021764685.1_ASM2176468v1_genomic
GCA_017353475.1_ASM1735347v1_genomic - GCA_003184245.1_ASM318424v1_genomic
GCA_017353475.1_ASM1735347v1_genomic - GCA_017353475.1_ASM1735347v1_genomic
GCA_017353475.1_ASM1735347v1_genomic - GCA_000482605.1_ASM48260v1_genomic
GCA_017353475.1_ASM1735347v1_genomic - GCA_902796085.1_Rumen_uncultured_genome_RUG14133_genomic
GCA_017353475.1_ASM1735347v1_genomic - GCA_026104335.1_ASM2610433v1_genomic

Reading reference genome count contigs: 82 count sites: 3060890 Initializing alignments count genomes: 13 Reading alignment blocks Traceback (most recent call last): File "/home/liusq/miniconda3/envs/maast/share/maast-1.0.8-0/bin/maast.py", line 1395, in main() File "/home/liusq/miniconda3/envs/maast/share/maast-1.0.8-0/bin/maast.py", line 1382, in main call_snps_main(args) File "/home/liusq/miniconda3/envs/maast/share/maast-1.0.8-0/bin/maast.py", line 1187, in call_snps_main run_mummer4(args) File "/home/liusq/miniconda3/envs/maast/share/maast-1.0.8-0/bin/maast.py", line 516, in run_mummer4 msa_path = gen_msa.build_msa(indir=args['mummer4_dir'], overwrite=True, subset=args["subset_map"]) File "/home/liusq/miniconda3/envs/maast/share/maast-1.0.8-0/snps_io/gen_msa.py", line 97, in build_msa genomes[genome_id][r['c1']][r['s1']-1:r['e1']] = ref[r['c1']][r['s1']-1:r['e1']] KeyError: 'CP110483.1' '''

zjshi commented 6 months ago

Hi liushuqing506, thanks for trying maast. Could you please let me know how you ran your analysis?