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sanger-bentley-group / gps-pipeline

Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)
GNU General Public License v3.0
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Cannot download seroBA database #95

Closed fugunokaraage closed 5 months ago

fugunokaraage commented 5 months ago

When I do "./run_pipeline --init", the following erorr messages was displayed. What should I do?

ERROR ~ Error executing process > 'INIT:GET_SEROBA_DB'

Caused by: Process INIT:GET_SEROBA_DB terminated with an error exit status (4)

Command executed:

DB_REMOTE="https://github.com/sanger-bentley-group/seroba/archive/refs/tags/v1.0.7.tar.gz" DB_LOCAL="databases/seroba" KMER="71" JSON_FILE="done_seroba.json"

source check-create_seroba_db.sh

Command exit status: 4

Command output: (empty)

Command error: Retrying.

--2024-03-29 06:58:21-- (try: 9) https://github.com/sanger-bentley-group/seroba/archive/refs/tags/v1.0.7.tar.gz Connecting to github.com (github.com)|20.27.177.113|:443... failed: Connection timed out. Retrying.

////

Work dir: Path_to/gps-pipeline/work/f9/9a442f870c02dd24788dc35af570b4

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details

HarryHung commented 5 months ago

Connecting to github.com (github.com)|20.27.177.113|:443... failed: Connection timed out.

It seems the SeroBA Docker container has trouble connecting to GitHub server. Please check your Docker network configuration.