Question: cufflinks on Rna -seq data not working
0
gravatar for istiaqarif
17 months ago by
istiaqarif0
istiaqarif0 wrote:

every time i am trying .. processing doesn't go along it stops.. After several time refreshing it gives an error

{ "userAgent": "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0", "onLine": true, "version": "17.05", "xhr": { "readyState": 4, "responseText": "{\"err_msg\": \"Malformed id ( null ) specified, unable to decode\", \"id\": \"null\", \"err_code\": 400009}", "responseJSON": { "err_msg": "Malformed id ( null ) specified, unable to decode", "id": "null", "err_code": 400009 }, "status": 400, "statusText": "Bad Request" }, "options": { "parse": true, "keys": "type_id,element_count", "filters": { "history_content_type": "dataset_collection" }, "remove": false, "traditional": true, "data": { "keys": "type_id,element_count", "order": "hid", "v": "dev", "q": [ "history_content_type", "deleted", "purged", "visible" ], "qv": [ "dataset_collection", "False", "False", "True" ] }, "emulateHTTP": false, "emulateJSON": false, "textStatus": "error", "errorThrown": "Bad Request" }, "url": "https://usegalaxy.org/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcufflinks%2Fcufflinks%2F2.2.1.0&version=2.2.1.0&__identifer=5y8v84r2qm/api/histories/7d5953d5c45b7a9a/contents?limit=500&offset=0&details=bbd44e69cb8906b559f4d397af3c1b30&order=hid&v=dev&q=deleted&q=purged&q=visible&qv=False&qv=False&qv=True", "model": [], "user": { "id": "14df33f546144a3e", "username": "arif_istiaq", "total_disk_usage": 3010736876, "nice_total_disk_usage": "2.8 GB", "quota_percent": 1, "is_admin": false, "preferences": {}, "tags_used": [ "CpGislands", "exons" ], "deleted": false, "purged": false, "quota": "250.0 GB" } }

cufflinks • 580 views
ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson25k • written 17 months ago by istiaqarif0
1

Describe your steps in more detail. I had other problems with cufflinks like producing FPKMs all zero, but at least it ran.

ADD REPLYlink written 17 months ago by apozhitkov60

It takes a fair bit of time, but at least for me cufflinks jobs do start on usegalaxy.org

ADD REPLYlink written 17 months ago by Devon Ryan1.9k
0
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There were some recent cluster issues. Please rerun the job now. It may queue for a bit due to many others also having job delays (this is what a "gray" job indicates - a job is queued and should be allowed to stay queued until processed). Please see this answer for more about queued data: https://biostar.usegalaxy.org/p/23464/#23599

If errors continue (red result dataset), please see this answer for how to diagnose input problems and get more help if needed: https://biostar.usegalaxy.org/p/23584/

Reporting tool problems with a bug report (after inputs are confirmed to be OK) is also a way for us to learn about corner case tool issues. However, please check your data and rerun first. When reporting a bug (true for everyone), be sure to leave all inputs and outputs undeleted and include a link to the related Biostars post if one has been made.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 17 months ago by Jennifer Hillman Jackson25k
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