gavinmdouglas / q2-picrust2 Goto Github PK

Hi!

Thanks for the great plugin on the qiime2 platform. I've heard that it is now possible to run picrust2 for ITS data, but was wondering how I can do this in qiime2 using the qiime picrust2 full-pipeline command? Thanks in advance!

Hi,
Is there any information on when will q2-picrust2 plugin be officially part of QIIME2? I mean be part of qiime2 docker image?

Thank you!

Alex

Hi Gavin,

I am having problems with the q2-picrust2 plugin, version 0.0.3 on a new qiime2-2019.4 environment. After the install (which, by the way removes a lot of necessary plugins, such as q2-DADA2), I get again a similar error as picrust/picrust2#44 when trying to run the following (with the test tables):

qiime picrust2 full-pipeline --i-table mammal_biom.qza \ --i-seq mammal_seqs.qza \ --output-dir q2-picrust2_output \ --p-threads 20 \ --p-hsp-method pic \ --p-max-nsti 2

Which throws the error:

`Plugin error from picrust2:

[Errno 39] Directory not empty: blabla/users/andy/tmp/tmpd89n2chr'

Debug info has been saved to blabla/users/andy/tmp/qiime2-q2cli-err-3fvp9dj4.log`

I solved it again by adding a pass at line 482 of shutil.py (in anaconda3/envs/qiime2-2019.4/lib/python3.6/shutil.py) as I did previously. It worked and produced the output, but I would like to transfer the fix you applied couple of months ago in the full picrust2 pipeline, can you help?

Best,

Hi! I'm using the script hsp.py to output the nearest-sequenced taxon index (NSTI) values for each ASV, to correspond to the nearest 16S sequence and I am running into this error:
Error running this command:
Rscript /home/nish89/miniconda3/envs/MoMent/lib/python3.6/site-packages/picrust2/Rscripts/castor_hsp.R out.tre /tmp/tmpqhzcmb7m/subset_tab_0 mp 0.5 FALSE FALSE /tmp/tmpk9tvxgsd/predicted_counts.txt /tmp/tmpk9tvxgsd/predicted_ci.txt 100

Standard error of the above failed command:
Error:
Error - at least one trait in the prediction table was entirely missing values.
Execution halted

I am new to metagenome inference and have been closely following the PICRUSt2 Tutorial. I am confused as to why there are missing values from out.tre, my output from placing my study ASVs into a reference tree.

Any help is greatly appreciated!

Running with the following error
qiime picrust2 custom-tree-pipeline --i-table /home/qiime2/picrust2-2.0.3-b/mine/table.qza \

                                --i-tree /home/qiime2/picrust2-2.0.3-b/mine/picrust_setup/tree.qza \
                                --output-dir /home/qiime2/picrust2-2.0.3-b/mine/output

Error running this command:
hsp.py -i KO -t /tmp/tmp6khk89rc/placed_seqs.tre -p 1 -o /tmp/tmp6khk89rc/picrust2_out/KO_predicted -m mp
(qiime2-2018.11)

Any thoughts on how to fix this issue?

I've seen some closed issue on ths topic, but is the only solution to actually go into some code and adapt it myself? Isn't there a real/permanent fix for this yet? I wouldn't mind fixing it through adaptation of the code, but it will make it a bit more difficult for me when multiple users on our system eventually install and try out this plugin out, since I would have to first adapt it for every user, which is obviously not ideal.

So, any other ideas or fixes would be welcome! Thanks!

I'm on CentOS7 and trying to run this command:

qiime picrust2 full-pipeline --i-table 02-output-dada2-pe-unfiltered/00-table-repseqs/table.qza --i-seq 02-output-dada2-pe-unfiltered/00-table-repseqs/repseqs.qza --output-dir q2-picrust2_output --p-placement-tool sepp --p-threads 4 --p-hsp-method mp --p-max-nsti 2 --verbose

Thanks for developing this, by the way! I would much prefer this plugin over the stand-alone version (if it ends up working fine).

hello,

I run qiime picrust2 full-pipeline successfully yesterday.
But I run into the the Directory not empty errors:

Traceback (most recent call last):
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "<path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-211>", line 2, in full_pipeline
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_picrust2/_full_pipeline.py", line 70, in full_pipeline
verbose=highly_verbose)
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/pipeline.py", line 203, in full_pipeline
print_stdout=verbose, print_stderr=True)
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/util.py", line 265, in system_call_check
print(stderr_log, file=sys.stderr)
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/util.py", line 789, in exit
self.cleanup()
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/util.py", line 798, in cleanup
_shutil.rmtree(self.name)
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/shutil.py", line 484, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "path/00.conda/envs/qiime2-2019.10/lib/python3.6/shutil.py", line 482, in rmtree
os.rmdir(path)
OSError: [Errno 39] Directory not empty: 'path/tmp/tmpr2r8zwcx'

Plugin error from picrust2:

[Errno 39] Directory not empty: 'path/tmp/tmpr2r8zwcx'

Best

I followed the q2-picrust2 tutorial with both the tutorial files and my own. I believe my execution was successful – resulted in all four output files which matched the data shown in the tutorial (no errors). The predicted functions currently seem to be aggregated for all samples by function, specifically looking at the KEGG Orthlog output file. Is there a way to split that so it displays predicted functions for each respective sample?

Thanks.

Hi,
I have tried to install q2-picrust2 in the most recent q2-2022.8 environment, but the install command (conda install q2-picrust2=2021.11 -c conda-forge -c bioconda -c gavinmdouglas) did not complete.

You placed on the q2 Library site the following note: "Note that the plugin version for qiime2-2021.11 is specified."
Will the q2-picrust2=2021.11 work together with the latest q2 release?

Thanks

I recently came across this publication at github #9 and it resonated with some queries I've had in mind.
I'd truly appreciate it if you could spare some time to address a few questions related to the topic. I believe your perspective and knowledge could greatly benefit my understanding.

For thr prediction of functional analysis on ITS. As far as I understood we can use picrust2. In the github repo you gave the demonstration/explanation for 16s rRNA what I should change in the command lines in order to make it applicable on ITS.
thank you in advance