Constant error when mapping reads with LastZ

Question: Constant error when mapping reads with LastZ

3.2 years ago by

Germany

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 COMMENT • link •

modified 3.2 years ago • written 3.2 years ago by simon.schiml • 10

3.2 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 3.2 years ago by simon.schiml • 10

3.2 years ago by

simon.schiml • 10

Germany

simon.schiml • 10 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 COMMENT • link written 3.2 years ago by simon.schiml • 10

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 REPLY • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »