why I have a velvetg blank script?

leonardo_ca · 04-05-2018, 01:41 PM

Hey there,
I came across this really odd situation and have no idea about what to do. I’ve just installed Velvet-1.2.10 and realized that the “velvetg” script is actually in blank!

~/velvet_1.2.10
more velvet*
::::::::::::::
velvetg
::::::::::::::

******** velveth: Not a text file ********

./velvetg = return nothing
./velveth = return usage/help

I installed velvet following the manual.
I’ve just run the velveth and no error was reported.

./velveth out_name 31 -fastq.gz ~/read_1_PAIRED.fq.gz ~/read_2_PAIRED.fq.gz

But, running the following return “-bash: ./velvetg: Text file busy”

./velvetg out_name -cov_cutoff 4 > ./velvetg out_name -min_contig_lgth 100

Could anyone help me? I believe I am missing something but I could not realize what.
Thanks

mastal · 04-05-2018, 02:23 PM

Are you sure that velveth produced the expected output?
What files did you get in the output directory after velveth ran?

If you think it didn't install properly the first time, you could download it again
and repeat the installation.

After compiling with 'make', you should have a directory named bin, with binary files named velveth and velvetg if make is successful.

leonardo_ca · 04-06-2018, 04:10 AM

Hi mastal, thanks for replying.
velveth produced the correct files: Log Roadmaps Sequences

I am installing it again to see what happens. Interestingly (maybe because of the version) there is no velvet/bin/ directory and the velveth and velvetg are inside velvet/ alongside other files and directories.

leonardo_ca · 04-06-2018, 07:12 AM

Now working!

Cloned from Github Reinstalled and it is working.
git clone https://github.com/dzerbino/velvet.git
cd velvet
make ’CATEGORIES=300’ ’MAXKMERLENGTH=57’ ’OPENMP=1’
./velveth
./velvetg --> both running and binaries as velvetg was empty before. Also no “-bash: ./velvetg: Text file busy” error.

Thanks

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04-05-2018, 01:41 PM	#1
leonardo_ca Junior Member Location: Brasil Join Date: Dec 2017 Posts: 5	why I have a velvetg blank script? Hey there, I came across this really odd situation and have no idea about what to do. I’ve just installed Velvet-1.2.10 and realized that the “velvetg” script is actually in blank! ~/velvet_1.2.10 more velvet* :::::::::::::: velvetg :::::::::::::: ****** velveth: Not a text file ****** ./velvetg = return nothing ./velveth = return usage/help I installed velvet following the manual. I’ve just run the velveth and no error was reported. ./velveth out_name 31 -fastq.gz ~/read_1_PAIRED.fq.gz ~/read_2_PAIRED.fq.gz But, running the following return “-bash: ./velvetg: Text file busy” ./velvetg out_name -cov_cutoff 4 > ./velvetg out_name -min_contig_lgth 100 Could anyone help me? I believe I am missing something but I could not realize what. Thanks Last edited by leonardo_ca; 04-05-2018 at 01:44 PM.

04-05-2018, 02:23 PM	#2
mastal Senior Member Location: uk Join Date: Mar 2009 Posts: 667	Are you sure that velveth produced the expected output? What files did you get in the output directory after velveth ran? If you think it didn't install properly the first time, you could download it again and repeat the installation. After compiling with 'make', you should have a directory named bin, with binary files named velveth and velvetg if make is successful. Last edited by mastal; 04-05-2018 at 02:34 PM.

04-06-2018, 04:10 AM	#3
leonardo_ca Junior Member Location: Brasil Join Date: Dec 2017 Posts: 5	Hi mastal, thanks for replying. velveth produced the correct files: Log Roadmaps Sequences I am installing it again to see what happens. Interestingly (maybe because of the version) there is no velvet/bin/ directory and the velveth and velvetg are inside velvet/ alongside other files and directories.

04-06-2018, 07:12 AM	#4
leonardo_ca Junior Member Location: Brasil Join Date: Dec 2017 Posts: 5	Now working! Cloned from Github Reinstalled and it is working. git clone https://github.com/dzerbino/velvet.git cd velvet make ’CATEGORIES=300’ ’MAXKMERLENGTH=57’ ’OPENMP=1’ ./velveth ./velvetg --> both running and binaries as velvetg was empty before. Also no “-bash: ./velvetg: Text file busy” error. Thanks