snippy-multi ERROR: Can't open --ref BZ100/ref.fa

[makerer5]

Hi, I have a question for you about snippy-multi: I tried to run snippy-multi. I first generated a label file (input.tab) as follows: BZ93 /home/disk/project/G20240703/genome_analysis/geome/BZ93.fsa BZ_48_8 /home/disk/project/G20240703/genome_analysis/geome/BZ_48_8.fsa BZ107 /home/disk/project/G20240703/genome_analysis/geome/BZ107.fsa BZ85 /home/disk/project/G20240703/genome_analysis/geome/BZ85.fsa BZ77 /home/disk/project/G20240703/genome_analysis/geome/BZ77.fsa BZ67 /home/disk/project/G20240703/genome_analysis/geome/BZ67.fsa BZ79 /home/disk/project/G20240703/genome_analysis/geome/BZ79.fsa BZ98 /home/disk/project/G20240703/genome_analysis/geome/BZ98.fsa

When I run the following command, I get the following error: snippy-multi input.tab --ref sequence.fasta --cpus 16 --outdir mysnippy > multi.sh sh multi.sh ERROR: Can't open --ref BZ100/ref.fa

I tried to find the answer in the github issue, and the #463 issue is exactly the same as my current situation. But he solved the problem by replacing the GBK file with a fasta file, but my reference genome is a fasta file. Why does "ERROR: Can't open --ref BZ100/ref.fa" still appear now?

[lanroad-tiger]

can you try 'less multi.sh' and show your result? Maybe I can help u after seeing that

[makerer5]

Thank you very much for helping me solve this error. Below is my input file (input.txt) and error message (snippy38583.log), as well as the information generated by the "less multi.sh" command (less_multi.log) less_multi.log input.txt snippy38583.log

[lanroad-tiger]

Please confirm: Whether a series of folders (such as ‘BZ_63’) have been generated in the ‘mysnippy’ path? In your question, you mentioned that your ref file is in fasta format instead of gbk, but in ‘multi.sh’, it shows ‘--ref MW2.gb’. Please double check your reference genome and confirm whether it contains sequences. If none of the above works, you can try running a single line command in ‘mult.sh’ to see if it is effective (e.g., snippy --outdir ‘BZ_63’ --R1 ‘/public/home/xxluo/metagenome/project/G20240703/genome_analysis/genome_RawData/BZ_63_R1.fq.gz’ --R2 ‘/public/home/xxluo/metagenome/project/G20240703/genome_analysis/genome_RawData/BZ_63_R2.fq.gz’ --ref MW2.gb --cpus 16 --outdir mysnippy).

[makerer5]

Sorry, I made a mistake in the previous statement. 1) There are no BZ_63...BZ_100 folders in the mysnippy directory. 2) I tried setting the reference genome to .gb and .fasta format files, but neither worked (serialtest38593.log). 3) I ran the single-line command you mentioned and did not receive any error message (serialtest38595.log). serialtest38595.log serialtest38593.log

[fanvanf]

make sure the output path changed to an absolute path