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Question: Assembler ABySS ERROR RUNNING COMMAND (abyss-3.sam.gz)
0
gravatar for minh.le67
3.4 years ago by
minh.le67 • 0
United States
minh.le67 • 0 wrote:

Galaxy sequence assembler Abyss paired-end

wrapper file path
/home/shed_tools/__/repos/edward-kirton/abyss_toolsuite/__/abyss_toolsuite/abyss/

https://bitbucket.org/Lythimus/parses/src/b3144af13f4f/tools/sr_assembly/abyss/abyss-pe_wrapper.pl 

[abyss-pe_wrapper.pl]
# GET ARGS
my $kmer_size=shift @ARGV;
my $min_num_pairs=shift @ARGV;
my $outdir=shift @ARGV;
my $outfile=shift @ARGV;
my $contigs_outfile=shift @ARGV;
my $sam_outfile=shift @ARGV;
my $hist_outfile=shift @ARGV;

 

Galaxy Abyss paired-end dataset generation

"ERROR RUNNING COMMAND: gunzip /home/galaxy/database/job_working_directory/000/76/dataset_137_files/abyss-3.sam.gz"

"gzip: /home/galaxy/database/job_working_directory/000/76/dataset_137_files/abyss-3.sam.gz: No such file or directory"
??
I'm not sure why the err msg is generated?  it looks like the file "abyss-3.sam.gz" is not created.  I'm using GNU Make 3.81

Thanks so much for your help.  have a pleasant day.
assembly abyss-pe abyss wrapper • 987 views
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modified 3.3 years ago • written 3.4 years ago by minh.le67 • 0
0
gravatar for Dannon Baker
3.4 years ago by
Dannon Baker ♦ 3.7k
United States
Dannon Baker ♦ 3.7k wrote:

I'm not an expert on this one, but the command looks mangled to me:

/home/galaxy/databasejob_working_directory/000/76/dataset_137_files/abyss-3.sam.gz

Should be 

/home/galaxy/database/job_working_directory/000/76/dataset_137_files/abyss-3.sam.gz

 

What revision of Galaxy are you running?
ADD COMMENT • link written 3.4 years ago by Dannon Baker ♦ 3.7k

The directory path in the wrapper is corrrect.

It was a typo error in the posting.  i could not use copy-and-paste because galaxy instance is running on a virtual machine (oracle virtualbox).

ADD REPLY • link written 3.4 years ago by minh.le67 • 0

Ahh, bummer, thought this was going to be an easy one :)

Tangential, but if you install the VirtualBox Extension Pack in your guest operating system you can most likely enable bidirectional clipboard which is super handy for things just like this.

Can you follow up with which version of galaxy you're running?

ADD REPLY • link written 3.4 years ago by Dannon Baker ♦ 3.7k

How would I find which version of galaxy instance is running?  thanks.

ADD REPLY • link written 3.4 years ago by minh.le67 • 0
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