Transdecoder - mkdir error Pipeliner.pm line 123

[Twan K]

Dear ,

I am trying to run TransDecoder for the first time. 

I used the following code:

perl C:\Users\Admin\Desktop\TransDecoder-TransDecoder-v5.5.0\TransDecoder.LongOrfs -t C:\Users\Admin\Desktop\Test.fasta

But, then I got the following error message:

Error, cannot mkdir C:/Users/Admin/C:Users/Admin/Test.fasta.trans.decoder_dir.__checkpoints_longorfs at C:/Users/Admin/Desktop/Transdecoder-TransDecoder-v.5.5.0/PerLib/Pipeliner.pm line 123.

Thus, it appears the Pipeliner.pm code, the working directory is pasted twice. Below I have copied the corresponding code of the Pipeliner.pm.

Do you have suggestions on how to solve this?

        my $checkpoint_file = $cmd->get_checkpoint_file();
        if ($checkpoint_file !~ m|^/|) {
            if (my $checkpoint_dir = $self->get_checkpoint_dir()) {
                $checkpoint_file = "$checkpoint_dir/$checkpoint_file";
                $cmd->reset_checkpoint_file($checkpoint_file);
            }
        }
       

        push (@{$self->{cmd_objs}}, $cmd);
    }
   
    return $self;

}

sub set_checkpoint_dir {
    my $self = shift;
    my ($checkpoint_dir) = @_;
    $checkpoint_dir = &ensure_full_path($checkpoint_dir);
    if (! -d $checkpoint_dir) {
        mkdir($checkpoint_dir) or die "Error, cannot mkdir $checkpoint_dir";
    }
    $self->{checkpoint_dir} = $checkpoint_dir;

[Brian Haas]

Hi,

TransDecoder is meant to run under mac or linux.  I don't have experience with running it under Windows, but you might get it to work if you use cygwin.  Otherwise, best to find a linux server.

best,

~b

--
You received this message because you are subscribed to the Google Groups "TransDecoder-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to transdecoder-us...@googlegroups.com.
To post to this group, send email to transdeco...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/transdecoder-users/64ba1159-c188-47fb-a491-b0d28e8472b8%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Twan K]

Thanks. 

I will try that to see if I can get it to work.

Op dinsdag 19 februari 2019 15:27:52 UTC+1 schreef Brian Haas:

To unsubscribe from this group and stop receiving emails from it, send an email to transdecoder-users+unsub...@googlegroups.com.

To post to this group, send email to transdeco...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/transdecoder-users/64ba1159-c188-47fb-a491-b0d28e8472b8%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.