SNIPPY-CORE ERROR: Could not extract base XX_Referenece.1:134 for isolate XXX_out

[gilmahu]

Dear Tseemann,

We got this unusual error when running snippy-core on the snippy output folders where it says: " ERROR: Could not extract base NZ_CP084351.1:134 for isolate AD_SRR13280317_1.fastq_out" (with NZ_CP084351 being the reference genome and AD_SRR13280317_1.fastq_out, the output folder of one of the samples. We have tested different troubleshooting including excluding the sample that encountered the problem but the same error occurred again with another sample and this kept going on as we exclude more samples.

There was no error with the initial snippy run. Is this a reference issue? or what is causing this problem as this has stopped the run and we could not reach the final steps of obtaining the full.aln file.

Any suggestions?

[Chris091089]

Hi could you show your list of tabulated files please.

Maybe I can help you.

Regards

From Christhian Franco (Mexico)

[gilmahu]

Hi Christian, Thanks for your feedback. The .tab files are not directly supported here by GitHub so I have uploaded them to my figshare account and you can use the link here to access them directly: https://figshare.com/s/f4510372607e3ef1e56e I look forward to your suggestions.

Best regards Gildas

[Chris091089]

Which version of Samtools do you have?

[DDDDimi]

hello，I had the same issue, was your problem solved