Not able to see any result

[vivekruhela]

Hello,
I've followed every instruction as it is but in the end I am not able to see any result on the browser. I have pulled the docker successfully. I have run it successfully. After getting machine ip, I am giving http://docker-machine-ip/zika but nothing is there just blank screen. What could be the possible reason.

Note: If I run the docker run command more than once, then it shows an error of docker: Error response from daemon: driver failed programming external connectivity on endpoint brave_tereshkova (48a7b1732b44d80b89dd9be6e3a31ce589c4f13f0965a40ebfc585a322edaa80): Bind for 0.0.0.0:80 failed: port is already allocated. , First time there is no error.

[wangz10]

Hi @vivekruhela , you want to replace docker-machine-ip with the actual IP address of your Docker machine.

The error message you got hints that you already have a docker container running at port 80. You can find the container by running docker ps. Then refer to this SO post to find the IP: https://stackoverflow.com/questions/17157721/how-to-get-a-docker-containers-ip-address-from-the-host.

[vivekruhela]

Thanks. Problem is solved. Now I am running the docker but facing the problem in cell 30 with error message Found array with 0 feature(s) (shape=(8, 0)) while a minimum of 1 is required. in RNA_seq.PCA_plot() . Should I raise another issue or continue here.

[brettvanderwerff]

@vivekruhela I used this pipeline a bit. I don't know if your problem is related to this but just a heads up that the headers for the table gotten from : http://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP070895

are different now than what is hard coded into the script. You will have to change how the pandas df is indexed if you have not already, which is easy. I don't know if this is related to your problem, but this bug occurs the cell above the PCA plot so I wonder.

[vivekruhela]

@brettvanderwerff : Thanks for reply. You may be right but as I trace the error in all previous steps, I found the following results :

1. expr_df file is empty (in cell 33) because of filtration of all non-expressed and lowly-expressed genes

2. The reason of empty expr_df is problem in normalization.R Error in gene.length

I have checked the code for normalization.R and all the files which are used/called internally, the script should run properly and should generate rpkmMatrix_featureCount.txt but actually not generating any such file in folder. I have run the docker and pipeline according to the steps mentioned in their paper and readme file. How to deal with this error.

[wangz10]

Hi @vivekruhela , can you try to replace the normalize.R with this file: https://raw.githubusercontent.com/MaayanLab/Zika-RNAseq-Pipeline/master/normalize.R and run this cell again?

[vivekruhela]

@wangz10 : Sorry for late reply. It worked by using Normalization.R script from github.(Luckily, I didn't checked this message and I found this bug by self by looking at rpkm function in edgeR and confirmed it by cross checking at github repository) Thanks. Everything worked perfectly with all the results and plots except at the last steps when genes affected by Zika infection are checked against MGI memmalian phenotype level 4 and as a result I am getting enrichr_result = []. As I have checked in all the previous steps, there was no sign of error then there must be some genes in enrichr_result but I am getting an error in the line enrichr_result = RNAseq.enrichr_result(d_platform_cd['combined-up'].gmt=gene_set_library) as Lenght Mismatch: Extected axis has 0 element, new value has 7 elements and the reason of this error is RNAseq.enrichr_result() on d_platform_cd with given gene_set_library return nothing/Null ([ ]). Need last suggestion on this pipeline. Thanks for your time.

[wangz10]

@vivekruhela if d_platform_cd is empty, it is likely that you haven't construct the meta_df properly. Solution should be:

@vivekruhela I used this pipeline a bit. I don't know if your problem is related to this but just a heads up that the headers for the table gotten from : http://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP070895

[vivekruhela]

@wangz10 : I've checked that too. Initially, in the docker, all the table.txt index names are with _s (e.g. Run_s,infection_status_s etc) while on the table file header has changed, so I remove _s from all the index names otherwise it was throwing an error of Key error and everything else remains the same. After removing _s, everything in the notebook was working well. Please if you look at the text file, there are no such keys like shown in e.g. above. So I think by this way, meta_df file should be correct according to the commands provided. @brettvanderwerff was also pointing the same.