I tried looking through the manual to figure out if it was possible to resume a run rather than starting all the way at the beginning. It seems to have ~1 week run time on the species I am working on and I would rather not re-start after fixing an error that resulted from an incorrect path to a file. Is it possible to resume after correcting the error in the config file? Thanks!
Katherine
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You need to run the remaining steps manually as expemplified in the
Step_by_Step_script.sh script found in the Sample directory, at least to
complete the last metassembly where metassemble stopped. You'll need to
figure out the last step that finished correctly, the main steps are:
1)computing the CE-statistic for the input assemblies (bowtie2 for
alginments and mateAn for the actual computation), 2) whole genome
alignment (nucmer), 3) merging the assemblies through the WGA (asseMerge),
4) computing the final sequence (meta2fasta). After that you may just use
the output sequence in a new run of metassemble with the reamining input
assemblies.
I tried looking through the manual to figure out if it was possible to
resume a run rather than starting all the way at the beginning. It seems to
have ~1 week run time on the species I am working on and I would rather not
re-start after fixing an error that resulted from an incorrect path to a
file. Is it possible to resume after correcting the error in the config
file? Thanks!
Thanks for the feedback! That's kind of what I gathered (but I was hoping there was an easier way) so I have already started running the individual steps.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
I tried looking through the manual to figure out if it was possible to resume a run rather than starting all the way at the beginning. It seems to have ~1 week run time on the species I am working on and I would rather not re-start after fixing an error that resulted from an incorrect path to a file. Is it possible to resume after correcting the error in the config file? Thanks!
Katherine
Hi,
You need to run the remaining steps manually as expemplified in the
Step_by_Step_script.sh script found in the Sample directory, at least to
complete the last metassembly where metassemble stopped. You'll need to
figure out the last step that finished correctly, the main steps are:
1)computing the CE-statistic for the input assemblies (bowtie2 for
alginments and mateAn for the actual computation), 2) whole genome
alignment (nucmer), 3) merging the assemblies through the WGA (asseMerge),
4) computing the final sequence (meta2fasta). After that you may just use
the output sequence in a new run of metassemble with the reamining input
assemblies.
On Mon, Feb 5, 2018 at 9:17 AM, Katherine Dougan kdougan91@users.sourceforge.net wrote:
Thanks for the feedback! That's kind of what I gathered (but I was hoping there was an easier way) so I have already started running the individual steps.