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Problem Running #6
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Dear Jsevereyn Sorry for the confusion we moved MEBS to a new location https://github.com/valdeanda/mebs. |
Hi, I did this 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 sorry to bother you, Im a bench scientist |
Hi jsevereyn, you don't have to sorry about anything.
Let me know if that worked for you. |
Yes, it worked perfectly when I moved to the MEBS home folder thank you very much |
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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Dr. Valerie De Anda
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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: |
Hello Juan You have very interesting data! Here is the table of the Entropy Scores of non redundant organisms. To normalize the values and plot them use the script mebs_vis.py.
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 |
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 |
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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]$
The text was updated successfully, but these errors were encountered: