search

CDCgov / seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
https://cdcgov.github.io/seqsender/
Apache License 2.0
32 stars 10 forks source link

can't check status #48

Closed SeanSierra-Patev closed 2 months ago

SeanSierra-Patev commented 6 months ago

I'm having another issue, which I suspect may be the result of my limited experience with docker...

When I try and check the status of a submission, I get this

`docker exec -it seqsender bash seqsender-kickoff check_submission_status --submission_dir ./ --submission_name sub_1 --organism FLU

Error: Submission name: sub_1 for FLU production-data is not found in the submission log file.

Error: Either a submission has not been made or an entry has been moved. `

but the submission log file does exist right where I'm pointing, and contains that submission name

cat submission_log.csv Submission_Name,Organism,Database,Submission_Position,Submission_Type,Submission_Date,Submission_Status,Submission_Directory,Config_File,Table2asn,GFF_File,Update_Date sub_1,FLU,BIOSAMPLE,1,Production,2024-04-02,pending;submitted,/data,/data/sub_1/config.yaml,False,,2024-04-02 sub_1,FLU,SRA,1,Production,2024-04-02,pending;submitted,/data,/data/sub_1/config.yaml,False,,2024-04-02 sub_1,FLU,GENBANK,1,Production,2024-04-02,---;---,/data,/data/sub_1/config.yaml,False,,2024-04-02

dthoward96 commented 6 months ago

Hey @SeanSierra-Patev,

There seemed to have been a typo in the docker image that was causing that. I've update the docker image so that should resolve it. I also corrected your other issue with "isolate" and "strain" names per your email. Let me know if this resolves it for you.