Question: (Closed) abyss-3.sam.gz (GALAXY ERROR RUNNING COMMAND)
0
gravatar for minh.le67
4.2 years ago by
minh.le670
United States
minh.le670 wrote:

Galaxy abyss-pe wrappers.

/home/shed_tools/__/repos/edward-kirton/abyss_toolsuite/__/abyss_toolsuite/abyss/

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

"No such file"
??
I'm not sure why the err msg is generated?

Thanks so much for your help.  have a pleasant day.
 

abyss abyss-pe galaxy • 918 views
ADD COMMENTlink modified 4.2 years ago by karl.stamm3.5k • written 4.2 years ago by minh.le670

There is a dedicated instance of Biostar for Galaxy. You might have better luck there. If you repost this on that site, please let us know.

Thanks and good luck!

ADD REPLYlink written 4.2 years ago by Dan D6.8k

https://biostar.usegalaxy.org/p/13271/

ADD REPLYlink written 4.2 years ago by minh.le670

User posted on the dedicated Galaxy Biostar.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Dan D6.8k
0
gravatar for karl.stamm
4.2 years ago by
karl.stamm3.5k
United States
karl.stamm3.5k wrote:

Try reading the error message.

 

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

"No such file"

 

Okay so there's two files mentions, GUNZIP and ABYSS-3.SAM.GZ

 

One of those two are not present. 

ADD COMMENTlink written 4.2 years ago by karl.stamm3.5k
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