output is a 3 column file

Question

output is a 3 column file

Closed this issue a year ago · 6 comments

Hi,
When I run the code to generate the initial scores, I get a file with only the first three columns mentioned in the readme.
Shouldn't I get a file with seven columns? Is there any additional step I should do? I'm running TCRMatch in unbuntu.
Many thanks,
Cristina

Answer 1 · 2023-03-15T02:21:52.000Z

Hi Cristina,
Are you passing in your own database with -d? Currently the additional annotations for matches is only supported if you are using the default IEDB database. Please post the command you ran, if possible

Answer 2 · 2023-03-15T08:12:45.000Z

Hi,
Thank you for your answer. I'm using the default IEDB database and the command:
./tcrmatch -i myinputfile -t num_threads [-s threshold] [-d /path/to/database] [-a] > output_file
TCRMatch version was 0.1.1. I tried also with version 1.0.3 but this one didn't work at all.

Answer 3 · 2023-03-15T18:44:44.000Z

For version 1.0.3 what exactly happens when you run it? Here is my output running the test sequences:

I would suggest just running it as
./tcrmatch -i input.txt -t num_threads > output_file just to verify that it is working correctly. The other parameters are optional

Answer 4 · 2023-03-16T08:53:42.000Z

When I run version 1.0.3, it doesn't do anything, it just says:
terminate called after throwing an instance of 'std::invalid_argument'
what(): stoi
Aborted

With version 0.1.1, I tried the command you suggested (./tcrmatch -i input.txt -t num_threads > output_file), and again, the output file only contains the first three columns.
Can you think of anything else I can try? Thanks

Answer 5 · 2023-03-16T17:22:07.000Z

I believe version 0.1.1 does not support the full output. Can you please copy and paste the exact command you ran? stoi() is only called when parsing the number of threads. An example command would be:
tcrmatch -i input.txt -t 15 > output.txt. It sounds like you are passing a string instead of an integer for number of threads? In this case I am specifying 15 as my CPU has 16 cores available. I apologize if the documentation is unclear about this, I will update to make it more apparent

Answer 6 · 2023-03-17T08:57:20.000Z

It finally worked! You were right, I wasn't specifying a number for -t.
Thanks so much for your help!