Problems of run abort with QIIME Visualizations apps on Illumina BaseSpace

[SantoshThapa1]

Hello,

I ran the QIIME Visualizations apps available on Illumina BaseSpace to analyze 16SV4 sequence data generated by MiSeq platform. I successfully ran the "QIIME Preprocessing" app in the BaseSpace. However, my run aborted several times while running the "QIIME Visualization app". The reason of aborting the operation reads "File "/usr/local/lib/python2.7/dist-packages/qiime/parse.py", line 138, in parse_mapping_file raise QiimeParseError("No data found in mapping file.") qiime.parse.QiimeParseError: No data found in mapping file."

I am new to work with sequence data analysis. However, I have created a QIIME mapping file and stored in Google Drive and validated with Keemai. Can I generate the mapping file without BarCodesequence, the LinkerPrimersequence? I prepared my mapping file as follows:

SampleID (first column)

BarcodeSequence (i put 5′ Illumina adapter sequence in 2nd column)

LinkerPrimerSequence (I put forward primer sequence in 3rd column)

ReversePrimerSequence (I put 806r modified illumina in 4th column)

Description (I put sample description in last column)

Could you please suggest me is there anything wrong with my mapping file set up in Google spreadsheet.

Thank you. Santosh

[ElDeveloper]

Does the mapping file pass the validation with Keemai? How many samples do you have listed in your mapping file?

In general we use the QIIME forum to provide support, would you mind sending in a post to the forum with your question, I'll follow-up there, you can find the forum here: https://groups.google.com/forum/#!forum/qiime-forum

[SantoshThapa1]

Yes, the mapping file passed the validation with Keemai. There are 3 samples listed in my mapping file.

I tried to post in the QIIME forum, but could not. No idea (will try it again !) !

Thanks,

Santosh

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From: Yoshiki Vázquez Baeza notifications@github.com Sent: Thursday, March 24, 2016 1:37 PM To: biocore/qiime Cc: Santosh Thapa Subject: Re: [qiime] Problems of run abort with QIIME Visualizations apps on Illumina BaseSpace (#2138)

Does the mapping file pass the validation with Keemai? How many samples do you have listed in your mapping file?

In general we use the QIIME forum to provide support, would you mind sending in a post to the forum with your question, I'll follow-up there, you can find the forum here: https://groups.google.com/forum/#!forum/qiime-forum

You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/biocore/qiime/issues/2138#issuecomment-200963169

[ElDeveloper]

@SantoshThapa1, if at all possible can you copy and past the contents of your mapping file here, or at least a subset of them?

[SantoshThapa1]

AFS_Nymphs_data.xlsx This is my mapping file. Thank you.

[ElDeveloper]

@SantoshThapa1, thanks for sending that, the problem is that your sample names all start with the # sign, and lines starting with a # sign are understood as comments, if you change that, this should work just fine. For more information about the format, see this link.

[SantoshThapa1]

Thank you S much @EIDeveloper