Importing fastq, demultiplexed paired end data

[venkar]

Hi,
This is my first time using qiime2 and I am having questions about the import. I have my Fastq files in a directory and I am trying to execute the following command in a directory where I have the manifest file. I built the manifest file in excel and saved it as a csv file and when I do a head this is how it looks.

sample-id,absolute-filepath,direction
DS-28538,/home/Data_Analysis/DS-28538_1.fastq.gz,forward
DS-28538,/home/Data_Analysis/DS-28538_2.fastq.gz,reverse
DS-28542,/home/Data_Analysis/DS-28542_1.fastq.gz,forward
DS-28542,/home/Data_Analysis/DS-28542_2.fastq.gz,reverse

and so on. I save these file as pe-33manifest.csv
The command is as follows - (I am in the working directory as the manifest file)

qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path pe-33-manifest.csv \
--output-path paired-end-demux.qza \
--source-format PairedEndFastqManifestPhred33

After trying out different inputs, now I get the following error - I am working on a SGE cluster and submitting this command interactively.

OSError: [Errno 28] No space left on device

An unexpected error has occurred:

[Errno 28] No space left on device

See above for debug info.
(qiime2-2018.2)

I am working on qiime2-2018.2 version.

I am not sure what is going on or where I could have made mistake. I very much appreciate the response.

EDIT - Per Matthew’s input, I checked with my lab to see that they are Phred33 sequences and have added the the code. Thanks for the suggestion!

Thanks,
Raghavee

[thermokarst]

Hi @venkar - can you please copy and paste the exact command you ran, inside of a code fence (triple backticks in a row):

```
my code here
```

This will make sure it gets formatted like code when posting on the forum.

I can’t be too sure until I see exactly what you ran, but, it looks like you might have an unescaped line return in your command, which caused it to execute too soon, so you could try formatting your command like this, instead:

qiime tools import \
   --type SampleData[PairedEndSequencesWithQuality] \
   --input-path pe-64-manifest \
   --output-path paired-end-demux.qza \
   --source-format PairedEndFastqManifestPhred64

Just curious though, are your reads actually Phred 64? We don’t see that very often anymore - I suspect you might actually have Phred 33 reads. Let us know how it goes!

[venkar]

Hi Matthew,
I have changed my question and added the edits, I now get a different error though.
I really appreciate your suggestions, and they are indeed Phred33.

Thanks,
Raghavee

[Nicholas_Bokulich]

@venkar

After trying out different inputs, now I get the following error - I am working on a SGE cluster and submitting this command interactively.

OSError: [Errno 28] No space left on device

Could you share your complete error message? Based on what you've shared, it sounds like you might be having the same issue as this topic. This is probably an issue with permissions on your SGE cluster. Please try the suggestions made in that post and get back to us (with the full error message) if you are still having trouble.

@venkar

I have changed my question and added the edits, I now get a different error though.

In the future, you should post a new forum topic instead of editing the original post. This will make it easier for users to search in the future who have the same problem as your original problem. It will also make tracking and answering these questions easier. Thanks in advance for helping!