enasequence / ena-ftp-downloader Goto Github PK

Hi!

I've often used the ENA-FTP-Downloader and just wanted to download a new data set today. However, all downloads fail. I also tried the example from the README file of this GitHub-Repo:

java -jar ena-file-downloader.jar --accessions=SAMEA3231268,SAMEA3231287 --format=READS_FASTQ --location=fastq --protocol=FTP

The output log:

[...] 
(Copyright © EMBL 2022)
 version:1.1.5

Welcome to the ENA File Downloader utility!
----------------------------------------------
Provided parameters:
--accessions=SAMEA3231268,SAMEA3231287
--format=READS_FASTQ
--location=fastq
--protocol=FTP
16:07:49.867 [main ] INFO  - Starting download for format: READS_FASTQ at download location:fastq,protocol:FTP, asperaLoc:null, emailId:null, data hub:null
16:07:49.871 [main ] INFO  - Total 2 sample_accession READS_FASTQ records found
Getting file details from ENA Portal API 100% [===================================================================================================================================================================] 1/1 (0:00:00 / 0:00:00) 
16:07:50.638 [main ] INFO  - Downloading 4 files in total

Starting set 2 with 2 files.

Starting set 1 with 2 files.
Failed to download ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR949/ERR949836/ERR949836_1.fastq.gz
Failed to download ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR949/ERR949855/ERR949855_1.fastq.gz
Failed to download ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR949/ERR949836/ERR949836_2.fastq.gz
Failed to download ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR949/ERR949855/ERR949855_2.fastq.gz
Some files failed to download due to possible network issues. Please re-run the same script=/home/silvio/Software/ENA/download_sample-READS_FASTQ.sh to re-attempt to download those files
Automatically retrying failed downloads...

[...]

Using an FTP client directly works smoothly; thus, the issue does not seem to be due to a problem with the FTP server:

ftp ftp.sra.ebi.ac.uk
ftp> cd /vol1/fastq/ERR949/ERR949836/
ftp> get ERR949836_1.fastq.gz
ftp> get ERR949836_2.fastq.gz

Thank you for the help!

This is similar to two already-closed issues, but the solutions offered to them don't apply to me.

I'm running Windows 8.1 and have installed Oracle JDK 12.0.1. After downloading the .jar file, double-clicking it does nothing, and if I try to run via the command line, I get the same message as reported in earlier issues: Error: Could not find or load main class uk.ac.ebi.ena.downloader.gui.Main

The .jar file in the .zip with runtime also does not run when it is double-clicked.

I keep getting this error when I try to run the JAR.

I suspect I am doing somethign wrong, but I followed the instructions.

% java -showversion
openjdk version "1.8.0_131"
OpenJDK Runtime Environment (build 1.8.0_131-b12)
OpenJDK 64-Bit Server VM (build 25.131-b12, mixed mode)

% java -jar ena-ftp-downloader-v1.0.jar
Error: Could not find or load main class uk.ac.ebi.ena.ftp.gui.Main

% java -jar $PWD/ena-ftp-downloader-v1.0.jar
Error: Could not find or load main class uk.ac.ebi.ena.ftp.gui.Main

Download the latest release (.zip file) from the Releases section of the GitHub project and extract it to a location of your choice. The archive contains an executable jar which contains all dependencies

I downloaded the zip file but couldn't locate any jar file in it?

Been lots of commits since 1.0

Hi, I am using ena-ftp-downloader to download what I think is a small to medium dataset (~135G). However, it has taken me over 3 days and the download is still not complete! I've downloaded the equivalent dataset from NCBI using command-line sratools in less than 3 hours, with minimum hands-on interaction time. I know it is not an issue with my internet upload or download speed. Any suggestions on improving this?

CLI is really weird, when I do:

java -jar ena-file-downloader.jar --help 

to learn supported parameters it asks me choice-questions that is totally opposite to expected CLI experience.

I am having the same issue as the previously closed issue.

I have java-8-oracle installed and also did sudo apt-get install openjfx, but am receiving this same error.

"Downloading stopped due to an error" and there is a red "X" mark in the column of md5. And the downloading stops

Hi!

When I pass `--location=/some/path', this is not used and the files are written to my current work directory.

Could you have a look?