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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
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Step 3 Fatal error: Files compressed with gzip are not supported #389

Closed lz41 closed 4 years ago

lz41 commented 4 years ago

Hey all,

I was running step 3 in ipyrad and it gave out this error:

"Step 3: Clustering/Mapping reads within samples [####################] 100% 0:03:01 | dereplicating

Encountered an Error. Message: IPyradError:

Fatal error: Files compressed with gzip are not supported

Use debug flag (-d) for full code traceback."

After i used debug flag, it gave the error in detail: ---------------------------------------------------------------------------IPyradError Traceback (most recent call last) in /projects/spe1/software/miniconda3/lib/python3.7/site-packages/ipyrad/assemble/clustmap.py in dereplicate(data, sample, nthreads) 760 errmsg = proc.communicate()[0] 761 if proc.returncode: --> 762 raise IPyradError(errmsg.decode()) 763 764 IPyradError:

Fatal error: Files compressed with gzip are not supported

What i don't understand is that all the files i use are in .gz and step 1, step 2 went just fine.

Anyone has insights on what's going on and how to fix it?

Thanks!

isaacovercast commented 4 years ago

Looks like a stale conda environment. Try this:

conda install -c bioconda vsearch -f

I bet that'll fix it. You might have other problems though. did you install ipyrad in a clean conda environment? Maybe you updated ipyrad and it didn't update all the dependencies? Try installing in a clean environment as well, that's guaranteed to work.

On Tue, Jan 28, 2020 at 5:37 PM lz41 notifications@github.com wrote:

Hey all,

I was running step 3 in ipyrad and it gave out this error:

"Step 3: Clustering/Mapping reads within samples [####################] 100% 0:03:01 | dereplicating

Encountered an Error. Message: IPyradError:

Fatal error: Files compressed with gzip are not supported

Use debug flag (-d) for full code traceback."

After i used debug flag, it gave the error in detail: ---------------------------------------------------------------------------IPyradError Traceback (most recent call last) in /projects/spe1/software/miniconda3/lib/python3.7/site-packages/ipyrad/assemble/clustmap.py in dereplicate(data, sample, nthreads) 760 errmsg = proc.communicate()[0] 761 if proc.returncode: --> 762 raise IPyradError(errmsg.decode()) 763 764 IPyradError:

Fatal error: Files compressed with gzip are not supported

What i don't understand is that all the files i use are in .gz and step 1, step 2 went just fine.

Anyone has insights on what's going on and how to fix it?

Thanks!

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isaacovercast commented 4 years ago

All good? Reopen and comment if not.

eaton-lab commented 4 years ago

@lz41 Our conda recipe on bioconda now includes zlib (even though it is available by default on many systems), which when available will allow vsearch to read zipped files. So updating ipyrad should fix the problem if the directions above do not work.

lz41 commented 4 years ago

Thanks! I tried to reinstall the conda environment and it looks like it works now!