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eead-csic-compbio / metagenome_Pfam_score

Protocol for finding informative protein families and then using them to score metagenomic sets.
GNU General Public License v3.0
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Problem Running #6

Open jsevereyn opened 3 years ago

jsevereyn commented 3 years ago

I installed through git clone https://github.com/eead-csic-compbio/metagenome_Pfam_score

I installed HMMER v3.1b2 and all the dependencies through conda numpy matplotlib pandas seaborn

Im on Python 3.6.12 and Perl v5.16.3

I tried to run it, but I have the following error

(MEBS) [jcastros@dylan faa]$ perl /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl -input /datos/jcastros/meta-huasco/meta_prokka/faa -type metagenomic -comp 0

/home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl -input /datos/jcastros/meta-huasco/meta_prokka/faa -type metagenomic -fdr 0.01 -comp 1

Computing Mean Size Length (MSL) ...

H5.faa MSL=141 MSLbin=150

H4.faa MSL=145 MSLbin=150

H3.faa MSL=147 MSLbin=150

H1.faa MSL=118 MSLbin=100

H0.faa MSL=142 MSLbin=150

sulfur  carbon  iron    nitrogen    oxygen

H5.faa Error: File existence/permissions problem in trying to open HMM file cycles/sulfur/my_Pfam.sulfur.hmm. HMM file cycles/sulfur/my_Pfam.sulfur.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H5.faa.sulfur.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/carbon/my_Pfam.carbon.hmm. HMM file cycles/carbon/my_Pfam.carbon.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H5.faa.carbon.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/iron/my_Pfam.iron.hmm. HMM file cycles/iron/my_Pfam.iron.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H5.faa.iron.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm. HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H5.faa.nitrogen.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/oxygen/my_Pfam.oxygen.hmm. HMM file cycles/oxygen/my_Pfam.oxygen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H5.faa.oxygen.hmmsearch.tab

readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. NA H4.faa Error: File existence/permissions problem in trying to open HMM file cycles/sulfur/my_Pfam.sulfur.hmm. HMM file cycles/sulfur/my_Pfam.sulfur.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H4.faa.sulfur.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/carbon/my_Pfam.carbon.hmm. HMM file cycles/carbon/my_Pfam.carbon.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H4.faa.carbon.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/iron/my_Pfam.iron.hmm. HMM file cycles/iron/my_Pfam.iron.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H4.faa.iron.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm. HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H4.faa.nitrogen.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/oxygen/my_Pfam.oxygen.hmm. HMM file cycles/oxygen/my_Pfam.oxygen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H4.faa.oxygen.hmmsearch.tab

readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. NA H3.faa Error: File existence/permissions problem in trying to open HMM file cycles/sulfur/my_Pfam.sulfur.hmm. HMM file cycles/sulfur/my_Pfam.sulfur.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H3.faa.sulfur.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/carbon/my_Pfam.carbon.hmm. HMM file cycles/carbon/my_Pfam.carbon.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H3.faa.carbon.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/iron/my_Pfam.iron.hmm. HMM file cycles/iron/my_Pfam.iron.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H3.faa.iron.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm. HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H3.faa.nitrogen.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/oxygen/my_Pfam.oxygen.hmm. HMM file cycles/oxygen/my_Pfam.oxygen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H3.faa.oxygen.hmmsearch.tab

readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. NA H1.faa Error: File existence/permissions problem in trying to open HMM file cycles/sulfur/my_Pfam.sulfur.hmm. HMM file cycles/sulfur/my_Pfam.sulfur.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H1.faa.sulfur.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/carbon/my_Pfam.carbon.hmm. HMM file cycles/carbon/my_Pfam.carbon.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H1.faa.carbon.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/iron/my_Pfam.iron.hmm. HMM file cycles/iron/my_Pfam.iron.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H1.faa.iron.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm. HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H1.faa.nitrogen.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/oxygen/my_Pfam.oxygen.hmm. HMM file cycles/oxygen/my_Pfam.oxygen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H1.faa.oxygen.hmmsearch.tab

readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. NA H0.faa Error: File existence/permissions problem in trying to open HMM file cycles/sulfur/my_Pfam.sulfur.hmm. HMM file cycles/sulfur/my_Pfam.sulfur.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H0.faa.sulfur.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/carbon/my_Pfam.carbon.hmm. HMM file cycles/carbon/my_Pfam.carbon.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H0.faa.carbon.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/iron/my_Pfam.iron.hmm. HMM file cycles/iron/my_Pfam.iron.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H0.faa.iron.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm. HMM file cycles/nitrogen/my_Pfam.nitrogen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H0.faa.nitrogen.hmmsearch.tab

NA

Error: File existence/permissions problem in trying to open HMM file cycles/oxygen/my_Pfam.oxygen.hmm. HMM file cycles/oxygen/my_Pfam.oxygen.hmm not found (nor an .h3m binary of it)

ERROR: failed to generate /datos/jcastros/meta-huasco/meta_prokka/faa/H0.faa.oxygen.hmmsearch.tab

readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. readline() on closed filehandle COMPL at /home/jcastros/miniconda3/envs/MEBS/metagenome_Pfam_score/mebs.pl line 337. NA (MEBS) [jcastros@dylan faa]$

valdeanda commented 3 years ago

Dear Jsevereyn

Sorry for the confusion we moved MEBS to a new location https://github.com/valdeanda/mebs. The development of eead-csic-compbio/metagenome_Pfam_score as well as any updates and new versions of MEBS will be posted on this new website. Please do git clone https://github.com/valdeanda/mebs.git Let me know if that worked for you. Sorry for any inconvenience. Val

jsevereyn commented 3 years ago

Hi, I did this git clone https://github.com/valdeanda/mebs.git

and I get the exact same error

Maybe is the HMMER version (I tried a lot), but maybe it has todo with the other dependencies or with the fact that Im using conda, I dont know

conda install -c bioconda hmmer this install hmmer v3.3.2 I also tried conda install -c bioconda hmmer=3.2 conda install -c bioconda hmmer=3.1 conda install -c bioconda hmmer=3.1b2 (3.1b1 is not available)

sorry to bother you, Im a bench scientist

valdeanda commented 3 years ago

Hi jsevereyn, you don't have to sorry about anything. Sorry for the delay in response. Are you running the script inside the mebs directory? You have to be inside mebs directory for the main script to find the config.txt file Try running the script again with the example genome files

cd mebs 
perl mebs.pl -input gen_test/ -type genomic -comp  > test.genomes.tsv

Let me know if that worked for you. Val

jsevereyn commented 3 years ago

Yes, it worked perfectly when I moved to the MEBS home folder

thank you very much

valdeanda commented 3 years ago

Awesome!

I will be posting the new readme soon In the meantime, let me know if you have questions about the interpretation Val

El El lun, feb. 15, 2021 a la(s) 1:52 a. m., jsevereyn < notifications@github.com> escribió:

Yes, it worked perfectly when I moved to the MEBS home folder

thank you very much

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jsevereyn commented 3 years ago

Thank you very much

Yes, I just started to read the paper to figure out what the score and asterisks means (I understand that it does not refer to differences between samples).

I have 5 metagenomes and this was the MEBS output: sulfur carbon oxygen iron nitrogen H5.faa 9.409 33.231 6.676 9.273 18.800 H4.faa 9.409 32.793 6.692 9.273 18.318 H3.faa 9.399 37.082 7.157 9.273 20.333 H1.faa 8.837 75.067 6.847 9.391 20.357 H0.faa 9.399 67.304 7.149 9.273 19.177*

valdeanda commented 3 years ago

Hello Juan

You have very interesting data! H1.faa seems that there's lots of methanogenesis happening there, consistently with the low sulfur score in that particular sample. Probably methanogens outcompete sulfate reducers in that sample. But idk

Here is the table of the Entropy Scores of non redundant organisms.

Entropy Score Table

To normalize the values and plot them use the script mebs_vis.py.

python3 mebs_vis.py output.mebs.tsv

Im available for a videocall so I can help you with your output while I finish the mebs workshop and I update the readme.

Best Val

jsevereyn commented 3 years ago

Hi, Valerie

I already plotted the results and made a similar interpretation to the one you mentioned, clearly H1 site and the CH4 cycle are the notable ones.

Thank you so much for your advice