Question: Workflow Input data not recognizing the data set
0
gravatar for sjn
2.0 years ago by
sjn10
sjn10 wrote:

I have extracted workflow for ChIPseq analysis from my work history. When I call this workflow to run another data set input data is not recognizing the fastq file. Any idea what is going on?

galaxy • 664 views
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson23k • written 2.0 years ago by sjn10
1
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Double check that the datatype "fastqsanger" has been assigned and is appropriate ("groom" as needed).

Here is how to do both: https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson23k

Thanks for the suggestion. It worked when the data was groomed fastqsanger format. However, it is still puzzling why the original data was not recognized. I used the same data set in Galaxy to do analysis and it worked. All I did was copy the data set to a new history and then called a different work flow. Does copying alter the data structure?

ADD REPLYlink written 2.0 years ago by sjn10

Hello. The datatype fastqsanger must be assigned in order for many tools to recognise inputs (either directly or by using Fastq Groomer).

Was the dataset assigned fastqsanger datatype then that switched to simply fastq after the copy between histories? Very odd. I will run a quick test to see if I can reproduce. Possibly an artefact of the data storage issues that occurred late December (for about a day), but it is worth making sure this not an active problem. If it is, we can report the issue and get some eyes on it for a fix.

Thanks! Jen

ADD REPLYlink written 2.0 years ago by Jennifer Hillman Jackson23k

The original data was in fastqsanger format, which I downloaded from GEO and the analysis was fine. But data was not recognized after copying to a new history. In the new history, I first attempted to switch the data type to fastqsanger (it was showing fastq) but did not work. I had to groom the data to be recognized.

ADD REPLYlink written 2.0 years ago by sjn10

Hi - We would like to do some testing using your exact histories. Would you have time to share link to both? If possible, note the before and after datasets (I can tell within the history inheritance data to a certain degree in the user interface, but this becomes tricker if the datasets were renamed. Plus, most importantly, I want to be absolutely certain we are examining the same problematic data when attempting to reproduce the problem. 

How to share a history: https://wiki.galaxyproject.org/Learn/Share

Send the email to galaxy-bugs@lists.galaxyproject.org. Please make sure all datasets involved are undeleted, include a link to this post, and add in anything else you feel is relevant. Once we make a copy of the data, I'll reply by email and you can perm delete to recover space. I'll watch for your email so this goes quickly.

Thanks again for help with troubleshooting. This is the first time a copy problem of this exact nature has been reported in a very long time (years). If there a problem with the function, we definitely want to correct it!!

Take care, Jen

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Jennifer Hillman Jackson23k
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