Question: grep errors for FASTA file (possible glimmer error?)
0
gravatar for oars
12 months ago by
oars150
oars150 wrote:

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).

glimmer grep • 379 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by oars150
1
gravatar for Alex Reynolds
12 months ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

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.

ADD COMMENTlink written 12 months ago by Alex Reynolds27k

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

ADD REPLYlink written 12 months ago by oars150
0
gravatar for oars
12 months ago by
oars150
oars150 wrote:

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

ADD COMMENTlink written 12 months ago by oars150
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