Abyss-pe error
Gandhi, Khanjan
I have used ABYSS before for single end assembly, but using abyss-pe for the first time. I have a couple of questions.
1. This seems to be a very small error however, I am not able to find the cause.
abyss-pe k=25 n=10 in='RNJ_s_5_1_CAGATC_sequence (paired) trimmed (paired).fastq' name=RNJ
make: *** No rule to make target `RNJ-contigs.fa', needed by `all'. Stop.
All the executable files are compiled and are present in the PATH as well.
2. One more question I have is, I have paired end data in one file only, and not in separate files. Will that cause a problem?
3. Can Abyss perform a reference assembly?
Thanks,
Kuki
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Shaun Jackman
On Fri, 2010-12-03 at 07:51 -0800, Gandhi, Khanjan wrote:
> Hi all,
>
> I have used ABYSS before for single end assembly, but using abyss-pe for the first time. I have a couple of questions.
>
> 1. This seems to be a very small error however, I am not able to find the cause.
>
> abyss-pe k=25 n=10 in='RNJ_s_5_1_CAGATC_sequence (paired) trimmed (paired).fastq' name=RNJ
> make: *** No rule to make target `RNJ-contigs.fa', needed by `all'. Stop.
> All the executable files are compiled and are present in the PATH as well.
The spaces in your file name may be causing problems. Try renaming your
files to remove the spaces and parentheses. You could use a symlink if
you like.
> 2. One more question I have is, I have paired end data in one file only, and not in separate files. Will that cause a problem?
Having the paired-end data in a single file is fine.
> 3. Can Abyss perform a reference assembly?
No.
Cheers,
Shaun