Question: SRA submission Error
0
gravatar for suren04
6 months ago by
suren040
USA
suren040 wrote:

Hi all, I was trying to submit my RNA seq data to NCBI. I am getting this error for some samples. Please help troubleshoot the problem.

Error: Your table upload failed because multiple BioSamples cannot have identical attributes. You should have one BioSample for each specimen, and each of your BioSamples must have differentiating information (excluding sample name, title, bioproject accession and description). This check was implemented to encourage submitters to include distinguishing information in their samples. If the distinguishing information is in the sample name, title or description, please recode it into an appropriate attribute, either one of the predefined attributes or a custom attribute you define. If it is necessary to represent true biological replicates as separate BioSamples, you might add an 'aliquot' or 'replicate' attribute, e.g., 'replicate = biological replicate 1', as appropriate. Note that multiple assay types, e.g., RNA-seq and ChIP-seq data may reference the same BioSample if appropriate.
Sample name
MN1806CN_treatment_Aphid_30d_R1
MN1806CN_treatment_Aphid_30d_R2
MN1806CN_treatment_Aphid_30d_R3
MN1806CN_treatment_control_30d_R1
MN1806CN_treatment_control_30d_R2
MN1806CN_treatment_SCN_30d_R1
MN1806CN_treatment_SCN_30d_R2
MN1806CN_treatment_SCN_30d_R3
MN1806CN_treatment_SCNAphid_30d_R1
MN1806CN_treatment_SCNAphid_30d_R2
MN1806CN_treatment_SCNAphid_30d_R3
PI518671_treatment_Aphid_30d_R1
PI518671_treatment_Aphid_30d_R2
PI518671_treatment_Aphid_30d_R3
PI518671_treatment_control_30d_R1
PI518671_treatment_control_30d_R2
PI518671_treatment_control_30d_R3
PI518671_treatment_SCN_30d_R1
PI518671_treatment_SCN_30d_R2
PI518671_treatment_SCN_30d_R3
PI518671_treatment_SCNAphid_30d_R1
PI518671_treatment_SCNAphid_30d_R2
PI518671_treatment_SCNAphid_30d_R3

My tables for submission looks like this:

enter image description here

sra • 608 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by suren040

Did you try contacting NCBI?

Contact sra@ncbi.nlm.nih.gov with any question or concern about your data or submission.

ADD REPLYlink written 6 months ago by h.mon26k

First of all, you should put sample name only once (e.g. MN1806CN_treatment_Aphid_30d).

Then at the end of the file (excel or txt) there are columns like Filename filename2 filename3.

This is where you put your full fastq name :

MN1806CN_treatment_Aphid_30d_R1.fastq MN1806CN_treatment_Aphid_30d_R2.fastq MN1806CN_treatment_Aphid_30d_R3.fastq (or fastq.gz)

Then, in Library ID column add a random number for every sample (I normally put 1 to as many files I have).

That s it!

The error you get occurs because all your files have identical attributes (all columns same information). Adding ID column will solve the problem.

Do NOT forget to submit sample name only once

ADD REPLYlink modified 6 months ago by RamRS22k • written 6 months ago by 2nelly160

Hi Nelly,
Thanks for the quick response. The columns like Filename filename2 filename3 are in the SRA METADATA section. Before that, there is a template file for BIOSAMPLE ATTRIBUTES where we put the information attached above. It gave error to the samples of 30th day (e.g.MN1806CN_treatment_Aphid_30d_R1...) and NOT for samples of 5th day (e.g. MN1806CN_treatment_Aphid_5d_R1). What could be the reason?

ADD REPLYlink modified 6 months ago by RamRS22k • written 6 months ago by suren040

The error should probably be due to the same name. First be sure that the name are different. For example in biosample add sample only once (no replicates) Then at the end add an ID column like in metadata. The in metadata, for every sample you can upload different replicates like i told you ( filename, filename1...) for instance

biosample:

name        col1    col2   col3   col4   ID
sample1     ----     ----     ----     -----   01
sample2     ----     ----     ----     -----   02
sample3     ----     ----     ----     -----   03

metadata:

name        col1    col2   col3   col4   ID     filename         filename2         filename3
sample1     ----     ----     ----     -----   01    sample1_R1   sample1_R2      sample1_R3
sample2     ----     ----     ----     -----   02    sample2_R1   sample2_R2      sample2_R3
sample3     ----     ----     ----     -----   03    sample3_R1   sample3_R2      sample3_R3

I hope that helps

ADD REPLYlink modified 6 months ago by RamRS22k • written 6 months ago by 2nelly160

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink written 6 months ago by RamRS22k

my bad!! sorry for that

ADD REPLYlink written 6 months ago by 2nelly160

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

code_formatting

ADD REPLYlink written 6 months ago by RamRS22k

perhaps only slightly helpful but the EBI interface to submit RNAseq data (Annotare) is quite straightforward and easy to use I feel.

ADD REPLYlink written 6 months ago by lieven.sterck5.5k
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