grep errors for FASTA file (possible glimmer error?)

Question

[oars]

I am using the ‘extract’ program in glimmer to extract sequences for predicted genes. For some reason I keep getting an error with my grep step and cannot figure out why. My command is as follows:

extract -2 assem31.fa glm_assem31.predict | grep -v X > glm_assem31.predict.seq

And I get the following error message:

ERROR:  Skipped following coord line
>assem31

I've also tried piping the grep command as follows:

extract -2 assem31.fa glm_assem31.predict | 'grep -v X' > glm_assem31.predict.seq

And now get an additional error message:

ERROR:  Skipped following coord line
>assem31
grep -v X: command not found

Does anyone see something wrong with my grep option? I do create my output file but noting is in it (0 kb).

Answer 1

[Alex Reynolds]

That error message is from Glimmer, not grep:

$ wget https://ccb.jhu.edu/software/glimmer/glimmer302b.tar.gz
$ tar xvf glimmer302b.tar.gz
...
$ cd glimmer3.02
$ grep -nr "ERROR:  Skipped following coord line" .
./SimpleMake/extract.cc:88:                fprintf (stderr, "ERROR:  Skipped following coord line\n");
./SimpleMake/extract.cc:97:                fprintf (stderr, "ERROR:  Skipped following coord line\n");
...
./src/Util/extract.cc:88:                fprintf (stderr, "ERROR:  Skipped following coord line\n");
./src/Util/extract.cc:97:                fprintf (stderr, "ERROR:  Skipped following coord line\n");

You might look at the Glimmer source code on and before those lines, to see what would cause that error to arise in extract.

[oars]

Thanks - I did email the POC listed in the users manual so maybe he'll have some insight on what is going wrong.

Answer 2

[oars]

I don't know what I did correct but I finally created the output file, even after producing the same errors???