Has the link expired? I did not find the dbscSNV.zip data file.

[Licko0909]

Hello, I want to reproduce the four models in the kipoi manuscript，but according to the download link, I did not find the dbscSNV.zip data file.

According to the instructions, to reproduce "tf-binding - Figure 2", I need to first enter the "/src/splicing" path and execute "snakemake" to reproduce "splicing - Figure 5", as shown in the following two figures:

Later, I implemented it as required, and finally this problem occurred:

1. After executing snakemake, everything goes well until the dbscSNV.smk part is run. The error is displayed on line 101 in /manuscript/src/splicing/dbscSNV.smk. The zip file cannot be obtained. Does the file ftp://dbnsfp:[email protected]/dbscSNV.zip exist?

You can try it，Wget ftp://dbnsfp:[email protected]/dbscSNV.zip

2. In addition, I found that line 24 in /src/splicing/Snakefile has written "/data".
   

Last question: can I just run src/splicing/download_annotation.smk to download the GFT and FASTA data needed to reproduce "tf binding - Fig2"? How to run the .smk file? Because "snakemake" that executes "splicing - Fig5" now appears above "No such file dbscSNV.zip"

Sincerely hope to get your answer, I look forward to it! thank!

[Avsecz]

1. Try an alternative link for dbscSNV from https://drive.google.com/uc?id=0B60wROKy6OqcZkw2bWt2TGU5NDA&export=download
2. I fixed the data/data line. Thanks for reporting!
3. Yes. You can now just download the annotations now using snakemake download_annotations in the src/splicing folder

[Licko0909]

1. Try an alternative link for dbscSNV from https://drive.google.com/uc?id=0B60wROKy6OqcZkw2bWt2TGU5NDA&export=download
2. I fixed the data/data line. Thanks for reporting!
3. Yes. You can now just download the annotations now using snakemake download_annotations in the src/splicing folder

Thank！I successfully downloaded the dbscSNV.zip file according to the link you gave, and modified the corresponding code of the snakefile to ensure the smooth execution of the code. As I expected, there is no longer any error about dbscSNV, but the problem finally appears，

Based on the error message, I was thinking about whether there was a problem with one of the input files here. But I guarantee that the way these input files are obtained is either executed by snakemake in splicing or obtained by git clone.

[Avsecz]

Try to remove the .fai or .tbi files of the reference genome fasta file and the vcf file(s). Maybe the index files were still present in the shared data and should get re-generated automatically after you'll remove them.

[Licko0909]

Try to remove the .fai or .tbi files of the reference genome fasta file and the vcf file(s). Maybe the index files were still present in the shared data and should get re-generated automatically after you'll remove them.

Wow！It‘s working now!，thank you very much!!!

[Licko0909]

Try to remove the .fai or .tbi files of the reference genome fasta file and the vcf file(s). Maybe the index files were still present in the shared data and should get re-generated automatically after you'll remove them.

Yesterday, according to your prompt, I deleted the 20180429.filtered.vcf.gz.tbi file, and then I can successfully execute snakemake, and generated the following file:

It is running successfully and lasted for 30min

After running for 30 minutes, it stopped at 83% of the location. It reported "no dbscSNV.zip file". But I downloaded it from your link the previous day and stored it in "data/raw/splicing/dbscSNV"

I found that it automatically deleted data/raw/splicing/dbscSNV/dbscSNV.zip and delete the other files obtained by the pressure.

Later I re-downloaded the dbscSVN.zip file and placed it in the specified path.

The result is still an error, the execution log is as follows:

I found that "Job counts" has changed from 12 to 2!

I don't know if it is because of "cd ~/manuscript"

In order to solve the problem, I manually unpack dbscSNV.zip, leaving the required dbscSNV.chr1 and dbscSNV.zip, and executing snakemak into /src/splicing, still reporting the error.