Make.sra mimark file problem

Commands in mothur
1

Hi everyone,

I’m new with submitting Illumina (MiSeq) sequences to the NCBI. A colleague suggested me to try the command make.sra as it is super easy to use.
However, I’m struggling with my mimark file at the moment… I filled the template as described on the Wiki page… but I get an error message I run the make.sra command :
[ERROR]: MIMarks file is missing group 16S_BGR_B1, please correct.
[ERROR]: MIMarks file is missing group 16S_BGR_B2, please correct.
[ERROR]: MIMarks file is missing group 16S_BGR_B3, please correct.
[ERROR]: MIMarks file is missing group 16S_BGR_S1, please correct.
… (for all the samples) - as you can guess, 16S_BGR… are the sample ID (were the same in the oligos file, and in the fastq containing file).

I don’t understand which information is missing in the mimark file because I filled all the required (*) fields for each sample…

Thank you!

Alice

2

Did you run the get.mimarkspackage, https://mothur.org/wiki/Get.mimarkspackage, command?

3

Yes, I did use the get.mimarkspackage command to get my mimark template.

Finally, I just solved my problem. Apparently, the problem was in the first column (sample_name) generated by mothur itself using the oligos file. The sample_name were XXXX_forwardbarcode.reversebarcode. So i just removed the two barcodes in the name, and then the make.sra worked fine. No more error message… I now have my submission.xml file.

However, do you think it is a bug? Is there gonna be problem with my sequences downstream in the submission procedure? And just for you to know, the barcodes have been already removed of the sequences by the staff at the GENOMICS ANALYSIS PLATFORM.

I am using Mothur 1.39.0.

Thank you!

Alice