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Runtime errors while running graph2pro #4
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Hi, Goor, Could you please send us the fastg file that you use to run the graph2pro pipeline ? I can't repeat the error from our fastg file. It seems to me it is a format issue. Please send to [email protected] Thanks much. |
Hi, Goor, I downloaded your fastg file, and tested on my local machine. It turned out it worked just fine. I used the following command: Also could you go to another repository at We have updated version for whole pipeline there. It will be easier to run the whole pipeline. Thanks much. Let me know any other question. |
Hi Sujun,
Thank you for the prompt reply.
Using the program files from the new repository, I was able indeed to
successfully produce peptides list using the DBGraph2Pro command.
Thereafter, I want on and tried to run the entire wrapper script on your
test data, but got the following error message:
*../graph2pro-var.sh: 29: ../graph2pro-var.sh: Syntax error: "(" unexpected*
Could you please advise on that?
Sincerely,
Goor
…On Thu, Aug 23, 2018 at 5:46 PM lisujun ***@***.***> wrote:
Hi, Goor,
I downloaded your fastg file, and tested on my local machine. It turned
out it worked just fine. I used the following command:
DBGraph2Pro -s 10_assembly_graph.fastg -f -k 99 -o
10_assembly_graph.graph2pep
Also could you go to another repository at
https://github.com/COL-IU/graph2pro-var
We have updated version for whole pipeline there. It will be easier to run
the whole pipeline.
Thanks much. Let me know any other question.
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It is very strange. |
also can you go to the graph2pro-var repository to report the issues? We will primarily work on that script. This one focused on the Graph2Pro only. Thanks |
Hi,
I'm trying to run Graph2Pro (cloned July 19th) on the contigs and assembly graph produced by MEGAHIT (v1.0.3) but encounter a run-time error.
My contigs file contains 229,067 contigs (228MB file) and the assembly graph contains 1,114,710 entries in FASTG format (732MB file).
I'm running the analysis on a high power machine (1TB RAM and 80 cores) with Ubuntu 14.04 as the O/S.
I paste down here the output of the command.
Thank you in advance,
Goor
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