AssertionError

[XYZuo]

Hello,
When I run from my sequence file,there will be an AssertionError like this:

I am new in python.Could you please tell me where is the problem?Thank you very much!

-Zuo Xinyi

[phbradley]

Sorry about that! Did you already run "python setup.py" from the tcr-dist-master/ directory? If so did it give any errors? And is this python 2 rather than python 3? Maybe you could tail the output of the logfiles created in those commands above:

tail tcrdist/human_pairseqs_v1*tsv.err

and post that?

[XYZuo]

Sorry about that! Did you already run "python setup.py" from the tcr-dist-master/ directory? If so did it give any errors? And is this python 2 rather than python 3? Maybe you could tail the output of the logfiles created in those commands above:

tail tcrdist/human_pairseqs_v1*tsv.err

and post that?

Hi,
Thanks for your reply.Yes,I already run "python setup.py" from the tcr-dist-master/ directory.There were errors about tar:

tar -xzf tcrdist_extras_v1.tgz
tar: Skipping to next header
tar: Archive base-256 value is out of off_t range

gzip: stdin: invalid compressed data--crc error

gzip: stdin: invalid compressed data--length error
tar: Child returned status 1
tar: Error is not recoverable: exiting now
mv tcrdist_extras_v1/external/* .
mv: cannot stat 'tcrdist_extras_v1/external/*': No such file or directory
mv tcrdist_extras_v1/db ../
mv: cannot stat 'tcrdist_extras_v1/db': No such file or directory
mv tcrdist_extras_v1/datasets ../
mv: cannot stat 'tcrdist_extras_v1/datasets': No such file or directory
mv tcrdist_extras_v1/testing_ref ../

But after several attempts,I finally installed it:

And I used python2.
Here are the human_pairseqs_v1*tsv.err files:
human_pairseqs_v1 tsv.err.zip

Thank you very much!

[phbradley]

Thanks for posting those error files. It looks like the software is not able to open the database files, so I think there must have been a problem downloading and/or unpacking the tcrdist database.

Oh, wait, now I see that it is talking about tcrdist_extras_v1.tgz, which is the old version of the database file. Can you make sure you are running an up-to-date version of the code on github? For example by downloading again? setup.py should be trying to download tcrdist_extras_v2.tgz...

-Phil

[XYZuo]

Thank you very much!We can run it successfully.
However,I still have a question:If I got the results of a sequencing of VDJ clonotypes,could I predict the corresponding epitope through TCRdist?Because the input file need the epitope(The name of the epitope to which the TCR binds).
Thank you again!