gencode.v19.annotation.gtf.gz - ERROR: No such file or directory: './clustering/gencode.v19.annotation.gtf.gz'

[julianapcmachado]

Hi there.

When I try running your script: worked_out_example.sh it gives me the following error: IOError: [Errno 2] No such file or directory: './clustering/gencode.v19.annotation.gtf.gz'

The file gencode.v19.annotation.gtf.gz doesn´t exist in the folder: clustering nor in any other folder.

Thanks, Juliana

[drevansa]

Hello,

You should have a copy of gencode.v19.annotation.gtf.gz in a sub directory of the directory you did: git clone https://github.com/davidaknowles/leafcutter.

.....your_path_to_leafcutter.../leafcutter/leafcutter/data/gencode.v19.annotation.gtf.gz

So, as a work around, you can edit line 10 of the worked_out_example.sh to point to the appropriate location on your system. The script is located in your ...../leafcutter/example directory.

The bit to amend is ln: -a ../clustering/gencode.v19.annotation.gtf.gz

If the annotation file is missing for some reason, then you can follow steps http://davidaknowles.github.io/leafcutter/articles/Visualization.html Step 0. Generate the annotation files - Annotation and use the download_human_annotation_codes.sh script to download hg19 and hg38 to a directory of your choice.

[julianapcmachado]

Thanks for your instructions!

But just to make sure, I still do not see the file gencode.v19.annotation.gtf.gz in https://github.com/davidaknowles/leafcutter/tree/master/leafcutter/data...

[drevansa]

I did my install in the past month (most recently a couple of days ago) using: git clone https://github.com/davidaknowles/leafcutter which (I think) automatically downloads a copy of gencode.v19.annotation.gtf.gz

But if you can't find a copy of gencode.v19.annotation.gtf.gz you can download a copy by running leafcutter script "download_human_annotation_codes.sh" from the command line.

This script is located in my install in: .....path_to_leafcutter.../leafcutter/leafviz/download_human_annotation_codes.sh

but you can just run the code contained in that script: curl http://web.stanford.edu/~dak33/leafcutter/annotation_codes.zip -o annotation_codes.zip unzip annotation_codes.zip

This will download and unzip a file in your current working directory, the contents of which: gencode_hg19

• gencode_hg19_all_exons.txt.gz
• gencode_hg19_all_introns.bed.gz
• gencode_hg19_fiveprime.bed.gz gencode_hg19_threeprime.bed.gz
• gencode_hg38
• gencode_hg38_all_exons.txt.gz
• gencode_hg38_all_introns.bed.gz
• gencode_hg38_fiveprime.bed.gz
• gencode_hg38_threeprime.bed.gz

Hope that helps.

[gkumar09]

Hi, I am trying to install the annotation_codes.zip using ./download_human_annotation_codes.sh but getting following error: curl: (56) Recv failure: Connection reset by peer

[gkumar09]

Ok, I resolved it- this had something to do with firewall of my institute- re-tried from home, and was able to get the zip file.

[davidaknowles]

This was a combination of issues. I've split the worked_example in to two versions:

1. python_wrappers.sh which uses the Python one line wrappers (run_ds.py and run_sQTL.py) which downloads gencode.v19.annotation.gtf.gz.
2. worked_example.sh which uses the original bash code (although somewhat cleaned up) and doesn't require gencode.v19.annotation.gtf.gz.