data import error (manifest format)

Hello sir,

If run this commandline "qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path se-33-manifest --output-path single-end-demux.qza --input-format SingleEndFastqManifestPhred33V2" means, I was getting error like your se-33-manifest is not in proper format. But I ran this same commandline without V2 letter means, I am not getting error.

What does that last letter v2 represent? To me, se-33-manifest was in proper format. If you find any mistake, please let me know sir.

Hi @Asha1,
It looks as though your manifest file is in a .csv (comma separated values) format, whereas the expected format in V2 is a .tsv (tab separated values) format as outlined here.

As for your second question:

This is referring to “Version 2” of the manifest formats and corresponds to the format displayed in the link above. This is what your manifest file would look like using this V2 format:

sample-id     forward-absolute-filepath       reverse-absolute-filepath
sample-1      $PWD/some/filepath/sample0_R1.fastq.gz  $PWD/some/filepath/sample1_R2.fastq.gz
sample-2      $PWD/some/filepath/sample2_R1.fastq.gz  $PWD/some/filepath/sample2_R2.fastq.gz
sample-3      $PWD/some/filepath/sample3_R1.fastq.gz  $PWD/some/filepath/sample3_R2.fastq.gz
sample-4      $PWD/some/filepath/sample4_R1.fastq.gz  $PWD/some/filepath/sample4_R2.fastq.gz

This format makes it possible to combine your manifest and sample metadata file together and is super convenient. However, before this format was implemented as the ‘recommended’ type, another manifest format was available which is the format I believe you are using. I’m not sure at which QIIME 2 version this change over but if you look at say the 2018.6 documentation for importing (https://docs.qiime2.org/2018.6/tutorials/importing/#fastq-manifest-formats) you can see that the previous manifest format was a .csv and was set up like so:

sample-id,absolute-filepath,direction
sample-1,$PWD/some/filepath/sample1_R1.fastq,forward
sample-1,$PWD/some/filepath/sample1_R2.fastq,reverse

As to maintain backward compatibility, both formats are still kept with the newest one now being referred to as V2.

tl;dr directing QIIME 2 to use the original manifest file format by removing the V2 from your command should fix your issue.

2 Likes

Thanks a lot for your reply sir. I will look in to it.

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.