Need help to run Picrust in linux

[M_sha]

Hello,

I am trying to run the tutorial found here https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.3.0-beta)#minimum-requirements-to-run-full-tutorial

If it runs okay then I will go with my real data to determine KEGG pathway profile for microbiomes.

However I am facing the attached error when I run the following command

place_seqs.py -s ../seqs.fna -o out.tre -p 8 --intermediate intermediate/place_seqs 

Can anyone please help me out?

Thanks in advance.

Sincerely,

M_sha

[Gavin Douglas]

Hey there,

I don't actually see any attached error - would you mind re-sending it?

Also, how much RAM do you have? Often the problem when running that command is that users run out of memory.

Cheers,

Gavin

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[M_sha]

Hi Gavin,

Please see the attached images.

This time I ran my data and found the attached errors.

FYI, I installed picrust2 (version, 2.3.0_b) from bioconda in conda environment (anaconda3) in linux. The RAM is 16 GB.

Please help me out to resolve these issues.

Thanks.

Regards,

Shahin

[Gavin Douglas]

Hey again,

I would recommend running the step separately with “place_seqs.py” (see tutorial) with only one thread and see if that works.

Cheers,

Gavin

To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/8c4f5235-92bf-470a-98da-cfeab00df2a8n%40googlegroups.com.
<New, 2.PNG><New, 1.PNG><New, 3.PNG>

[M_sha]

Hi Dr. Gavin,

As per your recommendation, I ran "place_seqs.py" using 1 thread, but there is no output file (out.tre) produced in the directory.

Please advise me.

Thanks

Shahin

[Gavin Douglas]

Hey Shahin,

You can try placing the reads with SEPP instead, as described here: https://github.com/picrust/picrust2/wiki/Swapping-in-SEPP-for-read-placement-with-q2-picrust2

To get the stratified output you will need to follow that page up to running sepp fragment-insertion and then export the QIIME 2 tree QZA to newick format. You can then run “hsp.py” with this tree with placed ASVs. The advantage of running SEPP is that it takes much less RAM.

Cheers,

Gavin

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[M_sha]

Hi Dr. Gavin,

I got your idea. But I need to clarify that I have installed the latest Qiime2 (version qiime2-2020.11).

Would this qiime2 version support picrust plugin?

If not how I can proceed with my target?

Thanks. 

[Gavin Douglas]

Hey again,

Yes that should work because you don't need to use the picrust2 plugin - the fragment insertion command is actually just part of the default QIIME 2 installation.

Cheers,

Gavin

To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/c861692a-f3b2-4b83-ac47-86be16d9381bn%40googlegroups.com.

[M_sha]

Hi Dr. Gavin,

I ran fragment insertion option but it shows the following error reports:

Plugin error from fragment-insertion:                                                                                                                                                                                               Command '['run-sepp.sh', '/tmp/qiime2-archive-288_xayh/cf2085d8-d4f4-430c-bfdf-0b1e5dcdb10c/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '1', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-1b64b58t/2028ee20-c65b-470e-9cf5-80e2b4e28d0d/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-1b64b58t/2028ee20-c65b-470e-9cf5-80e2b4e28d0d/data/tree.nwk', '-r', '/tmp/qiime2-archive-1b64b58t/2028ee20-c65b-470e-9cf5-80e2b4e28d0d/data/raxml-info.txt']' returned non-zero exit status 1.                                                                           

Debug info has been saved to /tmp/qiime2-q2cli-err-y5awp7ws.log 

How can resolve all the issues and get my analysis done to predict KEGG pathway abundances?

Please advise.

Thanks.

Shahin

[Gavin Douglas]

Hey Shahin,

What was the exact command you ran?

Thanks,

Gavin

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[M_sha]

Hi Dr. Gavin,

I actually ran the following commands from the SEPP tutorial...

wget http://kronos.pharmacology.dal.ca/public_files/tutorial_datasets/picrust2_tutorial_files/picrust2_default_sepp_ref.qza \ -O picrust2_default_sepp_ref.qza 

qiime fragment-insertion sepp --i-representative-sequences mammal_seqs.qza \ --p-threads 1 \ --i-reference-database picrust2_default_sepp_ref.qza \ --output-dir tutorial_placed_out

[Gavin Douglas]

Oh that’s odd - is there any information in the log file regarding what the problem was?

Sometimes with QIIME 2 commands you get more informative errors if you run the commands directly (as in the “run-sepp.sh” command that it is wrapping), so that would be another way to further troubleshoot this.

Cheers,

Gavin

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