Question: Trinity still not working 05-05-2017
0
gravatar for bcking2
13 months ago by
bcking220
bcking220 wrote:

See?!? Its still not working.

Not working, help! I have emailed you this several times and your last post on 4-28-2017 assured me it would be fine. See the screen shot. It is not fine. Cant check version number error.

Brian

trinity errors • 300 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson25k • written 13 months ago by bcking220

Hi Brian, We are rerunning more test runs (all test runs passed last Thursday). I cannot see your graphic, but have found your account and am reviewing it. From the first look, the input fastq reads do not look to be of high-quality and the error indicates that there were no assembly results prior to the stage that failed. I am running FastQC on the inputs to see what is going on. You could do the same (and should be doing this for any dataset, for any workflow, that you haven't already screened/prepped).

How to interpret FastQC reports: https://galaxyproject.org/tutorials/ngs/#fastq-manipulation-and-quality-control

NGS read QC/QC training tutorial: http://galaxyproject.github.io/training-material/NGS-QC/

So you know, the message -ERROR: couldn't run the network check to confirm latest Trinity software version. is just a warning message now, it will not trigger a failed run by itself.

We apologize for the problems with the connection (the prior problem). This is mostly out of our control but improvements have been made (and is why the tool is still labeled as "beta"). We definitely appreciate the feedback about problems. The tuning we'll do to promote the tool off of beta: fix any issues server side, include more usage help on the tool form (input problems are contributing to failures and many do not know how to interpret the log), plus create a training tutorial that includes assembly with Trinity to provide examples/sample data.

Thanks - feedback soon. Jen, Galaxy team

ADD REPLYlink modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson25k
2
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Brian,

The problem is with the inputs. Run FastQC and you'll see the sequence problems. The data has extremely high ambiguous base calls (NNNs) for all 6 inputs in the working history.

In short, there is not enough non-ambiguous base calling content have anything to assemble. This also means that trimming will not be enough to produce a successful assembly. Reads on average only have about 8-10 non-ambiguous bases of content. It is unique content, but very short.

Note: FastQC checks just the first 200k sequences (a sample of the data). So, I also ran it on the last 100k sequences just to make sure there wasn't a problem at the start of the sequencing run (not uncommon with certain technologies). But, that data also produced the same type of QC results.

Hopefully, this helps to explain the current problems (empty results).

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson25k
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