Manifest file not a directory

Technical Support
#1

Dear Qiimers,

After using Qiime for some time, I feel ready to take the big stepa nd move to Qiime2 :slight_smile:

As I normally start my pipeline with demultiplexed paired-end files, I am tryng to import such files into Qiime2. here's my command line:

qiime tools import \
    --type 'SampleData[PairedEndSequencesWithQuality]' \
    --input-format CasavaOneEightSingleLanePerSampleDirFmt \
    --input-path manifest.2.txt \
    --output-path ./demux.pe.qza

Unfortunately I receive the following error message:

There was a problem importing manifest.2.txt:

manifest.2.txt is not a directory.

Can you please advice?

Thank you, and wish you Happy Holidays
Max

#2

Hello Max,

According to this tutorial, the --input-path should be the folder holding your fastq files. Other --input-formats will use a manifest file, but not --input-format CasavaOneEightSingleLanePerSampleDirFmt.

Let me know if that works for you and keep on following those tutorials!

Colin

2 Likes
#3

Hi, Colin,

Thank you for your kind answer. I replaced the manifest file with the folder holding my fastq, and the program run successfully.
I am a bit confused at this point; how does Qiime2 know which file to use as manifest? Does it check all the text files in the working directory?

Thanks again for your help,
Max

#4

Hi Max,

Ok great! I’m glad that ran.

Nope. Qiime 2 only cares about the files you pass as input, and the location of the output.

I think the confusion is coming from all the different --input-formats that Qiime supports, and how it handles them differently. Take these two formats as examples:

  1. --input-format CasavaOneEightSingleLanePerSampleDirFmt
    This format opens up the --input-path folder, then it looks for fastq files inside that folder and makes one sample for each fastq file.
  2. --input-format SingleEndFastqManifestPhred33
    This format opens up the --input-path file, then it looks for fastq files listed in that file and makes one sample for each fastq file.

Does that make sense?

Colin

According to the documentation:

The manifest file is a comma-separated (i.e., .csv ) text file.

…So why don’t the examples on the website end with .csv? Looks like I missed that discussion. @thermokarst @mortonjt

3 Likes
#5

Oh, I see, I understand now.

I have just tried to run the command from a different folder, without the manifest file, and it worked as well.

So, no need for manifest file when using

--input-format CasavaOneEightSingleLanePerSampleDirFmt

I had missed that. Thank you for your explanation, I appreciate it.

Best,
Max

2 Likes
#6
#7

Thanks @colinbrislawn!

Extensions are just a convention, you could have a comma-separated-values file that was called my-data.colinbrislawn and it would still technically be a CSV!

1 Like
#8
#9

hello mr colinbrinslawn and mstaglimonte, pls i have the same issue i dont get what do you mean by the manifest file. i gather all the fastq gz file in one folder but i cant find it when i run "ls" to put it as input path

#10

Hi, @Amine_taouil ,

If you cannot find the files with ls, you are either in the wrong directory or you copied the files to a different directory than you intended.

Good luck with the long journey of learning command line and bioinformatics :slightly_smiling_face: :+1:

1 Like
#11