abyss-3.sam.gz (GALAXY ERROR RUNNING COMMAND)
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.
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1 answer
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.
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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!
https://biostar.usegalaxy.org/p/13271/
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!