Question: wgsim no output
0
gravatar for robinjugas
5 months ago by
robinjugas0
robinjugas0 wrote:

Hi, I run into problems using wgsim. I want to generate simple non erroneous testing reads with specified length and output size. I have installed it the right way from github, cloned it, compiled it. But with many various commands it does not produce any reads. I tried

./wgsim -N10000  -S11 Ecoli_MG1655.fasta ready.fq /dev/null
./wgsim -N 2000 -1 5000 -S11 Ecoli_MG1655.fasta ready.fq /dev/null

and etc. Different fastas produces the same nothing. The output is always the same:

[wgsim] seed = 11
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 0 sequences, total length: 0

So it means it is installed, but there is no output. I have read other topics but they are dealing with different issues. Thanks for any possible hints. RJ

wgsim assembly reads • 254 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by robinjugas0
1

/dev/null generally means send the output to nothing (null device, which is a special device which discards the information written to it). I am not sure why you have that directive at the end of your command lines. Have you tried using a real file name there?

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax34k

Hi, that /dev/null is there because the wgsim usually provides two files output as pair-end reads. So by /dev/null I omit the second file. It is stated at the README file, the description of what does it mean I have found somewhere else. I will try it. Rj

ADD REPLYlink modified 5 months ago • written 5 months ago by robinjugas0
1
gravatar for robinjugas
5 months ago by
robinjugas0
robinjugas0 wrote:

The whole problem was in empty fasta input file. Even I dont know how it is possible since I dont remember deleting it. Thanks for responses.

ADD COMMENTlink written 5 months ago by robinjugas0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 940 users visited in the last hour