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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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Using one of the samples as reference.gbk #214

Closed manuss11 closed 4 years ago

manuss11 commented 5 years ago

Hello, I'm running Nullarbor2 and I want to use one of our annotated strains (by a previous nullarbor run) as reference, but I found the following error:

--------------------- WARNING --------------------- MSG: Bad LOCUS name? Changing [NODE_1_length_1250606_cov_31.5067721250606] to 'unknown' and length to 'NODE_1_length_1250606_cov_31.5067721250606

Duplicate sequence unknown in /home/qiime2/Isolate_k53/contigs.gbk

It seems that the contigs.gbk file obtained by nullarbor did not work for snippy analysis Which file from the nullarbor output should be used to employ as reference in a subsequent nullarbor analysis? I see that the file contigs.fa works, but then snippy analysis doesn't include genes info.

Thanks a lot

tseemann commented 5 years ago

The contig names produced by Spades are too long. Genbank requires contig IDs to be < 37 characters long. Try manually running prokka with --compliant mode on the contigs you want to use as a reference.

manuss11 commented 5 years ago

Thanks a lot, it works fine!