IGGalaxy: problem with IMGT Loader

Question: IGGalaxy: problem with IMGT Loader

3.7 years ago by

Italy

Hi all!

From some days I've been trying to use IGGalaxy but I got stuck when I tried to use IMGT Loader using a .txt coming from the merge (done from terminal with the "paste -d" command) of three files outputs from IMGT/HighV-QUEST. These three files are the ones mentioned in the IMGT Loader workbench, the "1_Summary, 5_AA-sequence and 6_Junction files". Basically I have merged horizontally these files into a single, tab separated, file that I saved as a txt file. Then I load it and when I tried to use it within IMGT Loader I got this error "

Traceback (most recent call last):
  File "/home/galaxy/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/davidvanzessen/imgt_loader_igg/f8ba6ab5514b/imgt_loader_igg/imgtconvert.py", line 48, in <module>
    fSummary = pd.read_csv(triplets[0][0], sep="\t")
IndexError: list index out of range "

Need some help!!

Thank you very much.

Margherita Squillario

iggalaxy tool error local testtoolshed • 1.1k views

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modified 3.7 years ago • written 3.7 years ago by margherita.squillario • 0

3.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is a generic error often associated with an untrapped memory problem (the job exceed the available memory dedicated to job execution). This particular tool is in the Test tool shed only and seems to be missing some key repository content (functional tests, etc.) and may be difficult to troubleshoot on your own.

Working with the tool author (contact through the Tool Shed UI, once logged in) and/or the authors of the IGGalaxy platform will help you to find out more.
http://bioinformatics.erasmusmc.nl/wiki/index.php/Immunoglobulin_Galaxy

Hopefully this leads to a solution, Jen, Galaxy team

ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

3.7 years ago by

margherita.squillario • 0

Italy

margherita.squillario • 0 wrote:

Hi!

I have received the answear I was waiting for and it was related to the output of IMGT.

The point was that I had to choose "NO" for the option "Include individual result file and it worked, I was able to upload the IMGT .zip file to IMGT Loader tool. With the Experimenatal Design tool I got no problem while with the last tool "ReportRepertoire" I got the same errors despite the different choice I could make. I just sent an email about this to the author of the tool. I will update my status ASAP.

Thank you Jennifer!

Margherita

ADD COMMENT • link written 3.7 years ago by margherita.squillario • 0

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