Error for the input file

[Lily-WL]

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_

[valdeanda]

Hi Lily,
Since we did some recent updates in the algorithm, can you please do
git pull in the mebs directory? Or download the newest version.?
Once you've done that, you need to move your metagenome from MG-RAST in to a new directory.
mebs.pl requires a input directory, not a fasta file.
That should fix the problem.
Please let me know if everything worked well
Val

[Lily-WL]

Dear Valdeanda,

I diid what you said, but the error still came.

[root@ts-rd350 metagenome_Pfam_score]# git pull
Already up-to-date.
[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

[valdeanda]

Hi Lily, I haven't updated the readme, sorry. Try with the mebs.pl script instead of mebsv1.pl
That should fix the problem
Let me know if that works for you
Valerie

[Lily-WL]

[root@ts-rd350 metagenome_Pfam_score]# perl mebs.pl -input test_metagenomes/ -type metagenomic
mebs.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
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
NA

[valdeanda]

HI LILy
I just ran the same comand line and It worked well
perl mebs.pl -input test_metagenomes/ -type metagenomic

 mebs.pl -input test_metagenomes/ -type metagenomic -fdr 0.01 -comp 0

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

sulfur	carbon	oxygen	iron	nitrogen

4511045.3_metagenome.faa -2.295 1.790 5.412 2.745 13.024
4440966.3_metagenome.faa 5.817 8.804 1.178 4.579 11.697

Try the following:
Did you change the config file? That could cause problems because mebs will look for the corresponding files according to the paths in the config file.
To avoid any problems, try the following:

1. Clone the repository again, to make sure that everything is updated (I've already deleted the other script)
2. Cd into the directory and run the command line

perl mebs.pl -input test_metagenomes/ -type metagenomic

Let me know if that worked.

[valdeanda]

Hi Lili,
Here is the updated readme, please let me know if cloning the repository worked well.

https://eead-csic-compbio.github.io/metagenome_Pfam_score/READMEv1.html

[Lily-WL]

Dear Valdeanda,

I downloaded the file and the error are the same. The time is long to get the file in China. My OS is Centos 7.

[root@ts-rd350 metagenome_Pfam_score]# perl mebs.pl -input test_metagenomes/ -type metagenomic
mebs.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.

....................

[valdeanda]

Hi Lyly,
Did you already clone the repository?, The error looks like an error that we already fixed. Please let me know all the steps that you did in order to see what's the problem. You have already installed hmmsearch right?
The -comp option should be empty (without the "0")
Valerie

[Lily-WL]

I just git clone and have the file "metagenome_Pfam_score", then excute the script "perl mebs.pl -input test_metagenomes/ -type metagenomic" in this file.

And the hmmsearch can be called from any place, such as in /opt. You can see the output in the following.

[root@ts-rd350 opt]# hmmsearch -h
hmmsearch :: search profile(s) against a sequence database
HMMER 3.0 (March 2010); http://hmmer.org/
Copyright (C) 2010 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).

Usage: hmmsearch [options]
where basic options are:
-h : show brief help on version and usage

options directing output:
-o : direct output to file , not stdout
-A : save multiple alignment of all hits to file
.........................

[eead-csic-compbio]

Hi Lily-WL,
in case it helps, I just tried it in my system running hmmsearch 3.1b1 and it worked. So it might be that you need to update HMMER to 3.1b. Please try that and let us know how it goes,
Bruno

[eead-csic-compbio]

Hi again, I can confirm that those HMMs are not compatible with HMMER v3.0, since I was able to reproduce your error. So please, update to at least v3.1b1, cheers

[Lily-WL]

Thank you very much! The problem is fixed.