Cannot merge rep-seqs.qza files from different samples with "qiime feature-table merge-seq-data"

Hello, I am new to Qiime 2 and even do not have any bioinformatics background. I learn everything from the online tutorial and the forum. I really appreciate all these information that I can use to training myself.

I tried to use Casava 1.8 to import my paired-end demultiplexed fastq files and follow the “Atacama soil microbiome” tutorial to continue my analysis. However, as addressed by others, I got similar issues with data2 to analyze my paired end demultiplexed data (2 fastq files per sample for 7 samples in total ).

After searching on the forum, I decided to do the analysis individually. For now, I have got 7 table.qza files and 7 rep-seqs.qza files. I can merge those table.qza files successfully by following the “Merging denoised data” in the Fecal microbiota transplant (FMT) study. However, I keep getting error message when I try to merge those rep-seqs.qza files.

Here is what I did:

$ qiime feature-table merge-seq-data \
>   --i-data1 EUFsoil-01-dada2-rep-seqs.qza \
>   --i-data2 EUFsoil-02-dada2-rep-seqs.qza \
>   --o-merged-data merged-rep-seqs.qza

Here are messages that I got:

Traceback (most recent call last):
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/commands.py", line 185, in __call__
    arguments, missing_in, verbose, quiet = self.handle_in_params(kwargs)
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/commands.py", line 257, in handle_in_params
    kwargs, fallback=cmd_fallback
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/q2cli/handlers.py", line 302, in get_value
    return qiime2.Artifact.load(path)
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/sdk/result.py", line 64, in load
    archiver = archive.Archiver.load(filepath)
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 290, in load
    archive = cls.get_archive(filepath)
  File "/home/sue0210/miniconda3/envs/qiime2-2017.10/lib/python3.5/site-packages/qiime2/core/archive/archiver.py", line 250, in get_archive
    raise ValueError("%s does not exist." % filepath)
ValueError: EUFsoil-01-dada2-rep-seqs.qza does not exist.

I have double check the file is in the folder.
The version that I use is qiime2-2017.10.

Could anyone can help with this issue?

Thank you very much.

Hi @andia0210!

I am not quite following what you are referring to here - do you think you could link to a few of the forum posts you are referencing? Generally speaking, you should be able to import your paired-end sequences all at once, not on a per-sample basis (but, I might be missing something here, so please correct me if I misunderstood!). The one caveat here is that if you are planning on running DADA2 for quality control and read joining, DADA2 expects you to provide your data on a per-run basis (but it seems unlikely that you would have one sample per run…). Anyway, just wanted to make sure we were squared away here, first.

The error message (ValueError: EUFsoil-01-dada2-rep-seqs.qza does not exist.) means QIIME 2 wasn’t able to find the file named EUFsoil-01-dada2-rep-seqs.qza — is it possible you forgot to change directories to your analysis directory before running that command? Another option is to provide the absolute path to the QZA when running the command. If that isn’t the case, can you please run ls from within that directory, and provide the results here? Thanks! :t_rex:

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