Comments (4)
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?
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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!
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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
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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!
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Related Issues (20)
- Add universal newline support HOT 2
- Feature request: save PCs from kPCA to log HOT 1
- Track the clonality of out of frame CDR3s HOT 2
- Limitations in detecting out of frame TCRs HOT 3
- Single Chain parsed_seq Input Generating Blank Output File HOT 1
- Validation Data Missing Epitope Label HOT 2
- Amino Acid sequence inputs HOT 7
- How to use tcr-dist with only V gene-level information? HOT 6
- How to pair the alpha and beta chain reads from one TCR
- make_really_tall_trees.py script always running HOT 1
- text format cluster output for make_tall_trees.py HOT 2
- make_10x_clones_file.py issue HOT 2
- Bad CPU type HOT 4
- Estimation of TCRdiv HOT 8
- setup_gammadelta_db.py issue HOT 2
- usage with mixcr files HOT 8
- Issue with run_basic_analysis
- Losing Clones
- Apply tcr-dist on amino acid sequences HOT 1
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