Runtime errors while running graph2pro

[goorsa]

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

---

Now read edges from file 10_ge_500bp.contigs.fa
num edge to be allocated: 229067
kmersize 99
edgeseqfile 10_ge_500bp.contigs.fa
229067 edges input
num_vertex 229067
num_vertex 320421
input edge extracted: 229067
vertex created: 320421
*** Error in `/programs/graph2pro/Graph2Pro/DBGraph/DBGraph2Pro': double free or corruption (out): 0x00007f7928bd3010 ***
./run_graph2_pro.cmd: line 1: 51091 Aborted (core dumped) /programs/graph2pro/Graph2Pro/DBGraph/DBGraph2Pro -d 10 -e 10_assembly_graph.fastg -s 10_ge_500bp.contigs.fa -o prot -f -k 99

[lisujun]

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 lisujun@gmail.com

Thanks much.

[lisujun]

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.

[goorsa]

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. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AoMceGHosk2y7uTivL0GmdaMnCB_TJoJks5uTsA4gaJpZM4Vwh95> .

[lisujun]

It is very strange.
I re-ran the script, I can't reproduce your error. What's your shell ?

[lisujun]

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