Ega download bam files error

To view and download files for which you have been granted access, pyEGA3 requires your EGA username email address and password saved to a credentials file. Please note that htsget can only be used with files that have corresponding index files in EGA.

First, please ensure you are using the most recent version of pyEGA3 by following instructions in the "Installation and update" section for updating pyEGA3. Please ensure that your credentials are formatted correctly. Email addresses usernames are case-sensitive. If you have an EGA submission account, these credentials are different from your data access credentials. Please ensure you are using your data access credentials with pyEGA3.

Download speed can be optimized using the --connections parameter which will parallelize download at the file level. Using a very high number of connections will introduce overhead that can slow the download of the file. It is important to note that files are still downloaded sequentially, so using multiple connections does not mean downloading multiple files in parallel. We recommend trying with 30 connections initially and adjusting from there to get maximum throughput. Please note that when a file is being saved, it goes through two processes.

First, the downloaded file "chunks" are pieced back together to reconstruct the original file. Second, pyEGA3 calculates the checksum of the file to confirm the file downloaded successfully. Larger files will take more time to reconstruct and validate the checksum. The --saveto command-line argument is now called --output-dir and, in contrast with the original --saveto argument, one can only specify now an output directory, but not an output file.

This change was made to improve the user experience and avoid issues caused by supplying a filename where a directory was expected, and vice versa. Interactive use Data transfers must be carried out on Helix. Helix has a direct connection to the internet and transfers do not go through the HPC proxy servers. Sample session using the latest pyega3 to download the test EGA dataset -t flag. Other users do not seem to have this problem! Here's the output when attempting to download the test data:.

As you can see, the connection to the server is established. The metadata are downloaded, however, when it comes to downloading the actual data all child processes exit!

Hi fklirono. Thank you for reporting this issue. As this is an issue related to your specific user account, if you are still experiencing this behavior please email EGA Helpdesk at helpdesk ega-archive. For now, I will close this issue as this is a service issue that the EGA Helpdesk team is best suited to provide further assistance. Hi malloryfreeberg. I think you were too quick to close this issue. I attempted to download the publicly available test data using the pyega3 script and it failed, i.

I gave the following command:. In the meantime, we managed to identify the root cause of the problem. Our machine was running an old phython3.

When we upgraded to python3. Make sure you mention this somewhere, or even better prevent the script from installing unless python3. You are correct. For example, samples. You can also filter your samples depending on their status:. Add a title for your submission. This way you will easily distinguish between different submission in case you are undergoing multiple submission in the same ega-box. You can start a submission in different steps. For example, you can create a submission in the samples if you already have a study registered.

If these mandatory fields are not populated, you will not be able to save the object:. ACTIONS: 1 Validate : by clicking on the green tick, you will request to validate the object 2 Submit : by clicking the blue arrow, you will request to submit the object 3 Edit : by clicking on the yellow pencil, you will request to edit the object 4 Delete : by clicking the red cross, you will request to delete the object.

Each object is linked in a unidirectional way with another object. Map of linkage of objects in a submission:. For example, an study is not directly linked to a dataset. A dataset is linked to runs linkage between samples and files. These linkages are linked to experiments and, these experiments are the ones directly linked to a study. In the EGA we strongly encourage reusing registered objects if needed. How can you do that?

In each tab you can find a click box where all objects in the ega-box will display. For instance, you want to reuse an old study but you need to register a new experiment, in the experiment tab you will find the following checkbox:.