wgsim no output

Question

[RJ]

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

[GenoMax]

/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?

[RJ]

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

Answer 1

[RJ]

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.