Would it be possible to modify the visual output scripts to either allow for file format selection, or by default output to PDF or SVG rather than PNG to allow the figures to be edited/scaled/etc.?

Hi,
I'm wondering if there is an easy way to modify the nitrogen pathway to replace or add the amoA gene from the uncultured archaeon by the same gene from the type strain nitrosopumilus maritimus that will much more represent the pathway by archaea
Thanks
Greg

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]$

Dear Sir,

Can you help to figure out the problem? When I input the file *.faa which is download from MG-RAST. The script feedback error.

_[root@ts-rd350 metagenome_Pfam_score]# perl mebsv1.pl -input W1_350genecalling_coding.faa -type metagenomic
mebsv1.pl -input W1_350genecalling_coding.faa -type metagenomic -fdr 0.01 -comp 0

# ERROR: cannot list W1_350genecalling_coding.faa_

By the way, it is the same for the test file:

_[root@ts-rd350 metagenome_Pfam_score]# perl mebsv1.pl -input test_metagenomes/4511045.3_metagenome.faa -type metagenomic
mebsv1.pl -input test_metagenomes/4511045.3_metagenome.faa -type metagenomic -fdr 0.01 -comp 0

ERROR: cannot list test_metagenomes/4511045.3_metagenome.faa_

And this:
_[root@ts-rd350 metagenome_Pfam_score]# perl mebsv1.pl -input test_metagenomes/ -type metagenomic
mebsv1.pl -input test_metagenomes/ -type metagenomic -fdr 0.01 -comp 0

Computing Mean Size Length (MSL) ...
4440966.3_metagenome.faa MSL=175 MSLbin=150 4511045.3_metagenome.faa MSL=32 MSLbin=30

sulfur	carbon	oxygen	iron	nitrogen	

4440966.3_metagenome.faa
Error: Unrecognized format, trying to open hmm file cycles/sulfur/my_Pfam.sulfur.hmm for reading.

#ERROR: failed to generate test_metagenomes//4440966.3_metagenome.faa.sulfur.hmmsearch.tab
NA
Error: Unrecognized format, trying to open hmm file cycles/carbon/my_Pfam.carbon.hmm for reading.

ERROR: failed to generate test_metagenomes//4440966.3_metagenome.faa.carbon.hmmsearch.tab
NA
Error: Unrecognized format, trying to open hmm file cycles/oxygen/my_Pfam.oxygen.hmm for reading.

ERROR: failed to generate test_metagenomes//4440966.3_metagenome.faa.oxygen.hmmsearch.tab
NA
Error: Unrecognized format, trying to open hmm file cycles/iron/my_Pfam.iron.hmm for reading.

ERROR: failed to generate test_metagenomes//4440966.3_metagenome.faa.iron.hmmsearch.tab

NA

Error: Unrecognized format, trying to open hmm file cycles/nitrogen/my_Pfam.nitrogen.hmm for reading.

ERROR: failed to generate test_metagenomes//4440966.3_metagenome.faa.nitrogen.hmmsearch.tab
Use of uninitialized value $path in concatenation (.) or string at mebsv1.pl line 248.
Use of uninitialized value $path in concatenation (.) or string at mebsv1.pl line 249.
NAIncorrect number of command line arguments.
Usage: hmmsearch [options]

where most common options are:
-h : show brief help on version and usage

To see more help on available options, do hmmsearch -h

sh:行1: .hmmsearch.tab: 未找到命令
sh:行2: .hmm: 未找到命令
Unsuccessful stat on filename containing newline at mebsv1.pl line 253.

ERROR: failed to generate test_metagenomes//4440966.3_metagenome.faa.

.hmmsearch.tab
NA
4511045.3_metagenome.faa
Error: Unrecognized format, trying to open hmm file cycles/sulfur/my_Pfam.sulfur.hmm for reading.

ERROR: failed to generate test_metagenomes//4511045.3_metagenome.faa.sulfur.hmmsearch.tab
NA
Error: Unrecognized format, trying to open hmm file cycles/carbon/my_Pfam.carbon.hmm for reading.

ERROR: failed to generate test_metagenomes//4511045.3_metagenome.faa.carbon.hmmsearch.tab
NA
Error: Unrecognized format, trying to open hmm file cycles/oxygen/my_Pfam.oxygen.hmm for reading.

ERROR: failed to generate test_metagenomes//4511045.3_metagenome.faa.oxygen.hmmsearch.tab
NA
Error: Unrecognized format, trying to open hmm file cycles/iron/my_Pfam.iron.hmm for reading.

ERROR: failed to generate test_metagenomes//4511045.3_metagenome.faa.iron.hmmsearch.tab
NA
Error: Unrecognized format, trying to open hmm file cycles/nitrogen/my_Pfam.nitrogen.hmm for reading.

ERROR: failed to generate test_metagenomes//4511045.3_metagenome.faa.nitrogen.hmmsearch.tab
Use of uninitialized value $path in concatenation (.) or string at mebsv1.pl line 248.
Use of uninitialized value $path in concatenation (.) or string at mebsv1.pl line 249.
NAIncorrect number of command line arguments.
Usage: hmmsearch [options]

where most common options are:
-h : show brief help on version and usage

To see more help on available options, do hmmsearch -h

sh:行1: .hmmsearch.tab: 未找到命令
sh:行2: .hmm: 未找到命令
Unsuccessful stat on filename containing newline at mebsv1.pl line 253.

ERROR: failed to generate test_metagenomes//4511045.3_metagenome.faa.

.hmmsearch.tab
NA_

Hello!!
I get the following error when I run the command:

perl mebs.pl -input Proteins/ -type genomic -fdr 0.01 -comp

ERROR: failed to generate Proteins//Proteins_organism_1.faa.sulfur.hmmsearch.tab

NAIncorrect number of command line arguments.

Usage: hmmsearch [options]

where most common options are:
-h : show brief help on version and usage
To see more help on available options, do hmmsearch -h

The same happens with all of the files and all the cycles

Thanks,
Ivana

Dear Valerie,
I would like to ask if it is possible to use one of the scripts reported in this repository to assess the completeness of KEGG modules starting from a list of KEGG codes IDs.
I tried to use MetQy software but I did not obtain successful results. I cannot use MAPLE due to the huge number of genomes to investigate.
Sincerely
Stefano Campanaro
Department of Biology
University of Padova