snippy-multi can't open --ref

[a14578]

I'm trying to run snippy-multi for a few assembled genomes.

I've generated a tab file (input.tab) as follows:

isolate12 /msa/12_PROKKA_06152021.fna isolate2 /msa/2_PROKKA_06162021.fna isolate25 /msa/25_PROKKA_06162021.fna isolate87 /msa/87_PROKKA_06162021.fna isolate3 /msa/3_PROKKA_06152021.fna isolate32 /msa/32_PROKKA_06162021.fna isolate82 /msa/82_PROKKA_06152021.fna isolate38 /msa/38_PROKKA_06162021.fna isolate98 /msa/98_PROKKA_06162021.fna isolate1 /msa/1_PROKKA_06162021.fna

When i run the below commands I get the below error: snippy-multi input.tab --ref K12MG1655_sequence.gbk --cpus 16 > runme.sh sh ./runme.sh

ERROR: Can't open --ref isolate12/ref.fa 


In the snps.log file I also get the errors:

samtools faidx reference/ref.fa

[faidx] Could not build fai index reference/ref.fa.fai

Do you have any advice please?

[andersgs]

@anna1457 a common gotcha with GBK files is that they sometimes do not include the sequence data, just the annotations. Can you open the GBK file in a text editor and confirm the sequence is present?

When downloading from NCBI, make sure to select the Genbank (Full) option.

[andersgs]

We need to add a test for sequence data being present in GBK files.

[a14578]

Thanks for your help. I actually just finished the run using the fasta file instead of the GenBank file, and this has worked. I just checked the GenBank file and as you said, there was no fasta sequence present in it! Thanks again!

[andersgs]

No worries, best of luck.

[springinging]

How did you solve this trouble? I also met this problem,.

ERROR: Can't open --ref 772sequence/ref.fa

The form of my input.tab was : isolate1 /path/to/seq1.fasta isolate2 /path/to/seq2.fasta

Regards!

[woguta]

ERROR: Can't open --ref ./genome_ref/ASM676v1.fasta