Plugin Error: list index out of range for qiime demux summarize

User Support
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1

I am trying to summarize the information in my samples after importing data using the Casava 1.8 paired-end demultiplexed fastq format. I successfully obtain a demux-paired-end.qza file, but when I run the following I receive an error message:

> qiime demux summarize \
  --i-data demux-paired-end.qza \
  --o-visualization demux-paired-end.qzv

Error Message: Plugin error from demux: list index out of range

What should I be doing differently?

3

Hi @emmo1! Can you please provide the following information so that we can help you?

  1. What version of QIIME 2 are you running? Run qiime info to find that info.
  2. Can you provide the verbose debug output for the error message? Depending on your version of QIIME 2, there’ll be a path displayed at the end of your error message showing you where the debug log is. If you don’t see that message, or the debug log file no longer exists, you can rerun your command with --verbose to get the detailed error message.
  3. How many samples do you have in your demultiplexed data?

Thanks!

5

Hi @jairideout,

In response to your questions:

  1. What version of QIIME 2 are you running? Run qiime info to find that info.

QIIME 2 version: 2017.7.0

  1. Can you provide the verbose debug output for the error message? Depending on your version of QIIME 2, there’ll be a path displayed at the end of your error message showing you where the debug log is. If you don’t see that message, or the debug log file no longer exists, you can rerun your command with --verbose to get the detailed error message.

Traceback (most recent call last):
File "/data/home/aemmons/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packag$ results = action(**arguments)
File "", line 2, in summarize
File "/data/home/aemmons/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packag$ output_types, provenance)
File "/data/home/aemmons/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packag$ ret_val = callable(output_dir=temp_dir, **view_args)
File "/data/home/aemmons/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packag$ for file in link]
File "/data/home/aemmons/miniconda3/envs/qiime2-2017.7/lib/python3.5/site-packag$ for file in link]
IndexError: list index out of range

  1. How many samples do you have in your demultiplexed data?
    159 Samples

Thanks for the help!

7

Thanks for the details @emmo1! I’m not sure what’s going wrong here – my hunch is that during import of your sequence data there is somehow a forward reads sample that doesn’t have corresponding reverse reads, and the import step isn’t detecting the problem. This is just a hunch though!

Would you be able to share your demux-paired-end.qza file with me (e.g. using Dropbox, Google Drive, or some other file hosting service)? A direct message through the forum is fine if you don’t want to post the link here. That’d speed up the debugging process. If you’re not able to share the data, let me know and I’ll follow up with some steps we can take to keep debugging. Thanks!

10

(@emmo1 shared demux-paired-end.qza with me and I debugged this locally.)

After exporting the data with qiime tools export, there are 313 fastq files. With paired-end data there must by exactly two fastq files for each sample. Since you have 159 samples, there would need to be 159x2=318 files to have everything matched up. Can you verify that there are exactly two fastq files per sample and then try re-importing that data? I suspect demux summarize will complete successfully after resolving this issue.

The error message raised by demux summarize isn’t too helpful. I submitted an issue so we can detect unpaired samples when you’re importing data, that way the issue is detected earlier in the analysis. We’ll follow up here when that fix is in a QIIME 2 release!

1 Like
12

@jairideout

Thanks for taking the time to figure out what was going on! Yes, it seems there were reverse reads missing, and it worked after re-importing.

2 Likes
14

QIIME 2 2017.9 now validates that both forward and reverse reads are present for every sample when importing!

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