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DallasThomas / SACCHARIS

Improve functional predictions of uncharacterized sequences for any CAZyme or CBM family
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hello. i have some problems #6

Closed byeollee closed 5 years ago

byeollee commented 5 years ago

hello. i have some problem... when i download the dbcan, i can't hmmpress dbcan-fam-HMMs.txt

wget http://csbl.bmb.uga.edu/dbCAN/download.php/dbCAN-fam-HMMs.txt
wget http://csbl.bmb.uga.edu/dbCAN/download.php/hmmscan-parser.sh
hmmpress dbcan-fam-HMMs.txt

Error: File existence/permissions problem in trying to open HMM file dbcan-fam-HMMs.txt. HMM file dbcan-fam-HMMs.txt not found (nor an .h3m binary of it)

this results coming out.

please help me..

thank you

byeollee commented 5 years ago

i don't understand download step... i already all software but Saccharis.pl not working.

thank you :)

DallasThomas commented 5 years ago

Hello byeollee,

So for your first issue - your error is telling you that hmmpress is unable to find the file. In your wget you download

--> dbCAN-fam-HMMs.txt

Yet when you try hmmpress you try calling

--> dbcan-fam-HMMs.txt

Which is not the same filename for what you downloaded. Try

--> hmmpress dbCAN-fam-HMMs.txt

Make sure you are in the same directory this file is located.

For your second comment - I am really going to need more information in order to help you out. You mentioned you already have all of the software. I am assuming you mean you have installed dbCAN, Muscle, HMMER, ProtTest, FastTree and RAxML. Can you test each package to make sure they are all working first? I am then assuming you downloaded (cloned this repository) all of the perl scripts that make up Saccharis. Were the scripts added to a location in your PATH? The scripts will also need to be made executable,

for example --> chmod +x Saccharis.pl

If all of this can be confirmed to have been completed can I ask what it says when you try to run Saccharis?

byeollee commented 5 years ago

I am follow each install step for package. but i am not sure it is right. How can i check the test??

Second one is When i insert code ./Saccharis.pl,

this results coming out

Usage: Saccharis.pl [-Options [--] [Arguments...]]

Arguments: --directory --threads
--group
--family --RAXML : Flag - to choose RAXML over FastTree --raxml
--seqfile </path/filename> --Fragments : Boolean Flag - if added means keep Fragments --help : print Options and Arguments instead of fetching data --man : print complete man page instead of fetching data

Options: --directory | -d 

     : You can set a predefined output directory with this flag, though you
       must give it's path.  Default is Current Working Directory (CWD)

 --threads | -t    <threads>

     : This is basically straightforward.  Some scripts allow the use of
       multi-core processing.  Set a number in here from 1 to > <max_cores>
       The default is set at 2.

 --group | -g      <group_name>

     : This can be a single group or a list of groups to run.  Lists are comma
       delimited in single quotes. They are case-sensitive - lowercase please...

       -> eg. characterized
       -> eg. 'characterized, all, bacteria'

     : Allowable GroupNames

       -> all, archaea, bacteria, eukaryota, unclassified, characterized,
          subfamilies

 --family | -f     <family_name>

     : This is a single family name. 

       -> eg. GH43

       NOTE: You can only run a single family per run...

 --raxml | -r      <version_raxml>

     : There are 3 different raxml programs that you can run, which one you 
       choose will be based off of the age and type of your CPU.

       -> Older/Slower CPU           -- raxml
       -> Somewhat Older/Faster CPU  -- raxmlHPC-PTHREADS-SSE3 (default)
       -> Newest Procesors           -- raxmlHPC-PTHREADS-AVX

 --seqfile | -s    </path/filename>

     : If you would like to add your own sequences to this run - this is your 
       chance.  Sequences MUST be in FASTA FORMAT - if they are not the script
       will fail.  Make sure to include path with filename.
     : Sequence Header lines must start with a uniqure 9 character string with
       the following format:

       -> >U[0-9]{1,8} - That is a >U followed by 8 digits

        ex. U00000001

 --Fragments | -F

     : This is a boolean value flag that by default is set to TRUE, which means
       fragments are left out by default.  If you would like to include fragment
       sequences from CAZY, include this flag in our call

is it right??

THANK YOU.

DallasThomas commented 5 years ago

To test the different packages - each of the programs documentation provides a way to check that their software has been installed properly.

As for Saccharis.pl this is the output you would expect if called the way you called it.

byeollee commented 5 years ago

Thank You so much,

I check each package can run. All run well👌

Could you give the some example?? I am not sure I run well using Saccharis.pl

Oh also, I am still can’t hmmpress dbCAN-fam-HMMs.txt. so I download hmmpress results file. is it fine??

Thank you 😄

byeollee commented 5 years ago

Hello there.

when i run the perl cazy_extract.pl --family CE4 --group all --Fragment false

this results coming out

Attempt to bless into a reference at /usr/local/share/perl/5.26.1/HTML/TagParser.pm line 236.

what can i do?? please help me. i don't know.... what is wrong

thank you

DallasThomas commented 5 years ago

Under the instructions in the Readme there is a heading that deals with this issue. There is a problem with one of the lines in the perl library TagParser.pm that you need to change.

You will need to use an editor and open the file TagParser.pm at the location given in your error then goto line 236 and change the line to the following:

bless $self, ref($package) || $package;