Question: Constant error when mapping reads with LastZ
1
gravatar for simon.schiml
3.2 years ago by
simon.schiml10
Germany
simon.schiml10 wrote:

Hey,

I am not an expert on (bio)informatics and would not consider myself to be one on NGS data analysis. I only managed to find a way to handle the data I have that works fine for me.

However, for 2 days now, I constantly receive the following error message when I try to map my 454 amplicon deep sequencing data to the reference file (both .fasta format):

Traceback (most recent call last): File "/scratch/03166/xcgalaxy/main/staging//10372961/tool_files/lastz_wrapper.py", line 38, in <module> from galaxy import eggs ImportError: cannot import name eggs

Using different datasets from the same experiment or a different reference does not seem to make a difference, nor does changing the job parameters.

Does anyone here know, what I have to do? Or is this a problem on the server's side?

software error • 956 views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by simon.schiml10
0
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Simon,

I just replied to your bug report sent in Saturday. The lines in the target Custom reference genome must be wrapped before using the fasta file with tools. 

Please also see a related post if interested: Lastz Error Comparing FASTA to Text File

Best, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

Thank you for your help and please apologize my impatience.

Unfortunately I am still unable to succeed. How exactly should it be wrapped? I have done this analysis before and I can not remember that I had to wrap anything. I tried setting width to 60 (same as read dataset) but still got the same error.

ADD REPLYlink written 3.2 years ago by simon.schiml10
0
gravatar for simon.schiml
3.2 years ago by
simon.schiml10
Germany
simon.schiml10 wrote:

I am sorry, but this error is still present. No matter if I set line width for the reference and/or the data or not, and even when I try to map my reads to TAIR10 (so no custom reference genome) I still have that same error.

Am I doing something completely wrong?

ADD COMMENTlink written 3.2 years ago by simon.schiml10

Hi Simon,

When I tested your analysis earlier, the job executed with an input custom reference genome that was wrapped. Standard fasta format has wrapped lines, so this is always a good idea: https://wiki.galaxyproject.org/Learn/Datatypes#Fasta

If there are Lastz jobs that are now failing, it is probably from a different cause. Please submit another bug report and we can take a look.

Thanks, Jen, Galaxy team

ADD REPLYlink written 3.2 years ago by Jennifer Hillman Jackson25k
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