Problems with manifest file

User Support
1

Hi,
I am having problems with my manifest file. I have check that there are no extra columns or spaces.
I have also checked that my path to the files is correct.
Here is my command line:

nesbocam@silicon:/nfs/groups/edwards/For_Ivy/QIIME2_analyses$ qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path subset_torsten_manifest.csv --output-path torstensubset.qza --source-format PairedEndFastqManifestPhred33
There was a problem importing subset_torsten_manifest.csv:

subset_torsten_manifest.csv is not a(n) PairedEndFastqManifestPhred33 file

My manifest file looks like this:
sample-id,absolute-filepath,direction
MW_AHD1_170124,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M00833_0592.001.FLD0257.MW_AHD1_170124_R1.fastq,forward
MW_AHD1_170124,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M00833_0592.001.FLD0257.MW_AHD1_170124_R2.fastq,reverse
MW_AHD1_R1_161201,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M00833_0592.001.FLD0241.MW_AHD1_R1_161201_R1.fastq,forward
MW_AHD1_R1_161201,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M00833_0592.001.FLD0241.MW_AHD1_R1_161201_R2.fastq,reverse
MW_AHD2_161201,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M00833_0592.001.FLD0281.MW_AHD2_161201_R1.fastq,forward
MW_AHD2_161201,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M00833_0592.001.FLD0281.MW_AHD2_161201_R2.fastq,reverse
MW_AHD3_170124_2,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M03992_0261.001.FLD0160.MW_AHD3_170124_1_R1.fastq,forward
MW_AHD3_170124_2,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M03992_0261.001.FLD0160.MW_AHD3_170124_1_R2.fastq,reverse
Tem_R1_170422_1,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M03992_0261.001.FLD0205.Tem_R1_170422_1_R1.fastq,forward
Tem_R1_170422_1,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M03992_0261.001.FLD0205.Tem_R1_170422_1_R2.fastq,reverse
WF_170328_1,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M03992_0261.001.FLD0137.WF_170328_1_R1.fastq,forward
WF_170328_1,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M03992_0261.001.FLD0137.WF_170328_1_R2.fastq,reverse
WF_R1_170612,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M00833_0592.001.FLD0226.WF_R1_170612_R1.fastq,forward
WF_R1_170612,/nfs/groups/edwards/For_Ivy/Torsten_all/MI.M00833_0592.001.FLD0226.WF_R1_170612_R2.fastq,reverse

I would appreciate any help with this. (I also apologize if I posted this twice.)

Camilla

3

Hey there @camillaln!
Can you please attach your CSV manifest for us, instead of copying-and-pasting? That will let us check the file exactly as you have provided to QIIME 2. Thanks!

No, @camillaln is correct --- the manifest contains an internal mapping to the files themselves. Please see the importing tutorial for more details. Thanks!

1 Like
4

Heia,
I just found my error by reading all the posts about this. Apologies for not doing this yesterday - I stopped reading after looking for extra spaces etc.

My error was saving as
csv format (Saving as CSV UTF-8 (comma delimited) (.csv) not CSV (comma separated values) (.csv).
Sorry again!
Camilla

1 Like
5

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