Manifest Errors Issues

[DanielAgVal (Daniel Agudelo-Valencia)]

Hello Guys,

I am having the same problem here, as the tool keep continuing saying that I have an error in the manifest:

pe-33-manifest is not a(n) PairedEndFastqManifestPhred33V2 file:

Filepath on line 10 and column "forward-absolute-filepath" could not be found (/shared/data/DBs/lab_salud/metagenomas/Hernan/1-20_Parejas/II010-10-16S_R1_001.fastq.gz /shared/data/DBs/lab_salud/metagenomas/Hernan/1-20_Parejas/II010-10-16S_R2_001.fastq.gz) for sample "II010".

And this is what the manifest looks like

What is the error in the file?

Thanks

[DanielAgVal (Daniel Agudelo-Valencia)]

This is the command that I am using:

module load bioinformatics/qiime2-2019.10

qiime tools import
–type SampleData[PairedEndSequencesWithQuality]
–input-path pe-33-manifest_v2.tsv
–output-path 33-paired-end.qza
–input-format PairedEndFastqManifestPhred33V2

[thermokarst]

Hi @DanielAgVal, the main part of the error message can be seen here:

@DanielAgVal

Filepath on line 10 and column “forward-absolute-filepath” could not be found (/shared/data/DBs/lab_salud/metagenomas/Hernan/1-20_Parejas/II010-10-16S_R1_001.fastq.gz /shared/data/DBs/lab_salud/metagenomas/Hernan/1-20_Parejas/II010-10-16S_R2_001.fastq.gz) for sample “II010”.

Read this very carefully, you will notice that on line 10 you have two filepaths in the forward-absolute-filepath column (there should only be one filepath). It looks to me like you have a space ( ) between the forward and reverse column, instead of a tab, on this line.

Good luck!

[DanielAgVal (Daniel Agudelo-Valencia)]

Hi, @thermokarst, thank you for your help. Sadly, the error is still present. I created the manifest with the tabulation in Excel and save it with as a text with tabs. Then, I changed the extension to be .tsv.
Is there another way to make this manifest in the command line or another tool that can help to ensure the tabs?

Best,

[thermokarst]

@DanielAgVal

I created the manifest with the tabulation in Excel and save it with as a text with tabs

I would double-check the Excel file first, make sure that you don't have multiple filepaths in a single column.

[DanielAgVal (Daniel Agudelo-Valencia)]

Hello @thermokarst I’ve already done this procedure and it was ok before I started to try qiime command

[Francisco (Francisco Cárdenas)]

if u are using linux try creating the manifest with vim.

Example: vim manifest1.tsv or .txt

to separate the columns use key “Tab”, also you can verify your file with keemei (https://keemei.qiime2.org/)

[thermokarst]

Hi @DanielAgVal - the error message is quite clear in this case - one of your columns has two filepaths listed. You will need to carefully review the original file and check it for mistakes in formatting.

[DanielAgVal (Daniel Agudelo-Valencia)]

Thank you @thermokarst and @Francisco for your tips and help. I’ll look at the manifest and see what I can do.