Template filepath does not exist: iMGMC-16SrRNA-alignment.fasta

[elayton13]

Hello,

I am trying to use iMGMC for picrust analysis using the following code:

conda create -n iMGMC-PICRUSt -c bioconda picrust pynast fasttree ./iMGMC-PICRUSt.bash run2_feature.biom run2_sequences.fasta

As detailed in the picrust information page. But it seems I am missing a number of required files such as: iMGMC-CopyNr-16SrRNA.tab iMGMC-KO_traits.tab along with a number of other traits files

I can't seem to find these files as part of the downloads on here - am I supposed to generate these somehow?

Thanks for your advice

[tillrobin]

Dear Elayton, this files are part of this repositorie and you can see on the site: https://github.com/tillrobin/iMGMC/tree/master/PICRUSt

Best Till

[elayton13]

Hi Till

Thanks for the quick reply, sorry I missed that. I am still having some issues with missing files and packages, please see some of the error message below:

./iMGMC-PICRUSt.bash /home/emma/iMGMC/run2_feature.biom /home/emma/iMGMC/run2_sequences.fasta /home/emma/iMGMC mkdir: cannot create directory ‘run2_feature’: File exists Traceback (most recent call last): File "/home/emma/anaconda3/envs/iMGMC-PICRUSt/bin/pynast", line 194, in main() File "/home/emma/anaconda3/envs/iMGMC-PICRUSt/bin/pynast", line 178, in main for seq, status in pynast_iterator: File "/home/emma/anaconda3/envs/iMGMC-PICRUSt/lib/python2.7/site-packages/pynast/util.py", line 651, in ipynast_seqs current_result = pw_alignment_iterator.next() File "/home/emma/anaconda3/envs/iMGMC-PICRUSt/lib/python2.7/site-packages/pynast/pycogent_backports/uclust.py", line 399, in uclust_search_and_align_from_fasta_filepath TmpDir=tmp_dir,HALT_EXEC=HALT_EXEC) File "/home/emma/anaconda3/envs/iMGMC-PICRUSt/lib/python2.7/site-packages/cogent/app/util.py", line 166, in init self._error_on_missing_application(params) File "/home/emma/anaconda3/envs/iMGMC-PICRUSt/lib/python2.7/site-packages/cogent/app/util.py", line 435, in _error_on_missing_application % command cogent.app.util.ApplicationNotFoundError: Cannot find uclust. Is it installed? Is it in your path? cat: iMGC-16S-alignment.fasta: No such file or directory

Is the iMGC-16S-alignment.fasta supposed to be the iMGMC-16SrRNA-alignment.fasta? I have tried downloading uclust from the website, copying it to my directory and making it executable, but it seems there is still an issue with this. Any advice on this would be appreciated

Best wishes Emma

[tillrobin]

Hi Emma, The best would be to clone the full repository or download the full zip. Change to the folder /iMGMC/PICRUSt/. Now all files should be there. Please write again if you have still problems. The pipeline is quite old, sometime new updates in bioconda make problems, but PATH problems should be resolvable.

Best Till

[elayton13]

Hi Till,

I'm still getting the same error message even after cloning the repository. Any ideas on what I could try next? Do you expect the issue is to do with the pynast / uclust installs?

Best wishes Emma

[tillrobin]

Hi Emma, PyNAST was not updated since 2018, that problem is maybe the newer Python version. Try to rebuild the enviroment with old Python 2.7: conda create -n iMGMC-PICRUSt -c bioconda picrust pynast fasttree python=2.7

Hope this will help.

Best Till

[elayton13]

Hi Till,

Tried this but still the same issue, do you have any other suggestions please?

Thanks Emma

[tillrobin]

Dear Emma, I checked again. The problem is the depending of pynast to uclust executable, but it's no longer available, see: executable uclust

Please get in direct contact with me: https://www.helmholtz-hzi.de/en/nc/service/contact/person/till-robin-lesker/

Best Till