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petitmingchang / TO-GCN

Pipeline of time-ordered gene coexpression network (TO-GCN) construction from three-dimensional (gene expression, condition, and time) data
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Segmentation fault when running Cutoff program #7

Closed mb47 closed 1 year ago

mb47 commented 4 years ago

Hi, I have successfully run Cutoff on the example data, but it segfaults with no further error message when I run my own data through it. I have checked the format of the input data carefully and it appears to be excactly the same as the example data (and it is a smaller dataset). I have six timepoints and two conditions, i.e. 12 columns in addition to the gene IDs. I have attached the input data. thanks Micha geneLevelTPM.TFs.biorep.1.txt geneLevelTPM.allGenes.biorep.1.txt

petitmingchang commented 4 years ago

Hi Micha,

I just ran the Cutoff with your data and got the result without any error.

Here is the command and the output: ./Cutoff 6 6 geneLevelTPM.TFs.biorep.1.txt geneLevelTPM.allGenes.biorep.1.txt

No. of TFs: 1057 No. of Genes: 30910 No. of samples under Cond.1: 6 No. of samples under Cond.2: 6

Waiting for histogram generation and cutoff values calculation......

Cutoff of postive coexpression for Cond.1 = 0.92 Cutoff of postive coexpression for Cond.2 = 0.93 Cutoff of negative coexpression for Cond.1 = -0.86 Cutoff of negative coexpression for Cond.2 = -0.85

You can just copy and paste the following command to get the GCNs or change parameters by yourself: GCN 6 6 geneLevelTPM.TFs.biorep.1.txt geneLevelTPM.allGenes.biorep.1.txt 0.92 0.93 -0.86 -0.85

mb47 commented 4 years ago

Hi, thanks for getting back to us. I was trying to point the program at input files located in a different directory (providing absolute paths) but that turned out to be the problem -- apparently the input files need to be co-located with the executables. It worked fine when I ran it with the local files. It would be good to change that, or update the documentation to reflect it. thanks Micha

wchluo commented 2 years ago

Hi, @petitmingchang I got a same Segmentation fault as @mb47 . The input data carefully checked, and the every Cutoffs contained in "TO-GCN-master" were used except that in "Windows". Could you like to test my input data? thanks. wchluo 20220328193436

allGene.TPM.txt TF.TPM.txt

petitmingchang commented 2 years ago

Hi, @wchluo

I transform your data into "numbers" by excel and the program works. Please download the attached files and run again.

petitmingchang

allGene.TPM2.txt TF.TPM2.txt

wchluo commented 2 years ago

Hi, @petitmingchang

Thank you for you help, the program work good. Then I transform by myselft, works too. Thanks a lot. PS: Only two decimals were allowed, so strange!

wchluo

mzhoufulai commented 2 years ago

Hi, @petitmingchang I have run Cutoff with example data successfully, but when i ran my own data, got segmentation fault error. I tried to transform my data into "numbers" by excel as you mentioned above, but it still failed. Could you help me to test my input data? Thanks a lot.

Here is my command and output: ./Cutoff 5 5 TF.txt All_genes.txt

No. of TFs: 1380 No. of Genes: 30220 No. of samples under Cond.1: 5 No. of samples under Cond.2: 5

Waiting for histogram generation and cutoff values calculation......

Segmentation fault (core dumped)

Here is my input files:

All_genes.txt TF.txt

petitmingchang commented 2 years ago

Hi @mzhoufulai

I found there are some genes whose ID length greater than 25 characters in All_genes.txt. Since TO-GCN programs only accept gene ID length shorter than 21 characters, I just cut down those gene IDs to shorter ones and solved the issue.

petitmingchang

mzhoufulai commented 2 years ago

Hi @petitmingchang

Thanks for your quick response. It worked fine.

mzhoufulai

Jessica19960620 commented 1 year ago

Hi, I have successfully run Cutoff on the example data, but it segfaults with no further error message when I run my own data through it. I have checked the format of the input data carefully and it appears to be excactly the same as the example data. I have 20 timepoints and two conditions, i.e. 20 columns in addition to the gene IDs. I have attached the input data. thanks Jessica All_genes.txt TFs.txt

petitmingchang commented 1 year ago

Hi @Jessica19960620

I just ran the Cutoff and GCN with your data and found no error. Here are two commands I used:

./Cutoff 10 10 TFs.txt All_genes.txt ./GCN 10 10 TFs.txt All_genes.txt 0.85 0.85 -0.76 -0.69

Can you describe your question more clearly? Thanks!

petitmingchang

Jessica19960620 commented 1 year ago

Hi, petitmingchang

thank you so much.

Jessica

2023年7月12日 17:43，petitmingchang @.***> 写道：

Hi @Jessica19960620 https://github.com/Jessica19960620 I just ran the Cutoff and GCN with your data and found no error. Here are two commands I used:

./Cutoff 10 10 TFs.txt All_genes.txt ./GCN 10 10 TFs.txt All_genes.txt 0.85 0.85 -0.76 -0.69

Can you describe your question more clearly? Thanks!

petitmingchang

— Reply to this email directly, view it on GitHub https://github.com/petitmingchang/TO-GCN/issues/7#issuecomment-1632189883, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUUILV4RERA6M5YDBMIPAGLXPZWV5ANCNFSM4MFRPVNA. You are receiving this because you were mentioned.

Jessica19960620 commented 1 year ago

Hi, I have two question. The first one: I want to calculate the level about C1+C20, but I'm not sure which number can I chose from here(0.91 0.92 -0.95 -0.79). ./TO-GCN 10 10 TO-GCN-S4-10/TF.txt TO-GCN-S4-10/TF.txt 0.91 -0.79 TO-GCN-S4-10/seeds.txt 1 The second: can I use key genes on a biosynthesis pathway as “TF.txt” for TO-GCN? Thank you so much. Jessica

2023年7月12日 17:43，petitmingchang @.***> 写道：

Hi @Jessica19960620 https://github.com/Jessica19960620 I just ran the Cutoff and GCN with your data and found no error. Here are two commands I used:

./Cutoff 10 10 TFs.txt All_genes.txt ./GCN 10 10 TFs.txt All_genes.txt 0.85 0.85 -0.76 -0.69

Can you describe your question more clearly? Thanks!

petitmingchang

— Reply to this email directly, view it on GitHub https://github.com/petitmingchang/TO-GCN/issues/7#issuecomment-1632189883, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUUILV4RERA6M5YDBMIPAGLXPZWV5ANCNFSM4MFRPVNA. You are receiving this because you were mentioned.

petitmingchang commented 1 year ago

Hi @Jessica19960620

For Q1, Please use the command below:

./TO-GCN 10 10 TO-GCN-S4-10/TF.txt TO-GCN-S4-10/TF.txt 0.91 0.92 TO-GCN-S4-10/seeds.txt 1

For Q2, I suggest using the original TF.txt because that provides the complete information of time order in the TO-GCN. Then you can pinpoint which level those key genes locate in the TO-GCN.

petitmingchang

Jessica19960620 commented 1 year ago

okay. I got it. Thank you so much.

Jessica

2023年7月16日 10:01，petitmingchang @.***> 写道：

Hi @Jessica19960620 https://github.com/Jessica19960620 For Q1, Please use the command below:

./TO-GCN 10 10 TO-GCN-S4-10/TF.txt TO-GCN-S4-10/TF.txt 0.91 0.92 TO-GCN-S4-10/seeds.txt 1

For Q2, I suggest using the original TF.txt because that provides the complete information of time order in the TO-GCN. Then you can pinpoint which level those key genes locate in the TO-GCN.

petitmingchang

— Reply to this email directly, view it on GitHub https://github.com/petitmingchang/TO-GCN/issues/7#issuecomment-1636948060, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUUILV27CK5Z4L4XINUMSFLXQNDP5ANCNFSM4MFRPVNA. You are receiving this because you were mentioned.