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jason-weirather / hla-polysolver

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Failure in test for difference between orig.winners.hla.txt and winners.hla.txt #8

Open ysbioinfo opened 6 years ago

ysbioinfo commented 6 years ago

Hi, I want to use polysolver for HLA-typing, thank you very much for developing the conda version of polysolver! (I am not root user so cannot install it using docker as suggested by Broad Institute). I install the polysolver following your guide, all steps seems working well. But when I test on test.bam, there is difference between my output and the standard output. (polysolver) [shiyang@statcomp hla-polysolver-master]$ diff output/winners.hla.txt test/orig.winners.hla.txt 2,3c2,3 < HLA-B hla_b_39_01_01_02l hla_b_39_01_01_03 < HLA-C hla_c_07_01_05 hla_c_07_01_05 --- > HLA-B hla_b_39_01_01_02l hla_b_39_01_01_02l > HLA-C hla_c_07_01_05 hla_c_06_02_01_01 And below is a section of my standard output that seems wrong when I run test script: [samopen] SAM header is present: 6597 sequences. Tue Jul 10 22:05:17 CST 2018 get first winners Tue Jul 10 22:05:17 CST 2018 rm: cannot remove 'output/counts1.R0k6': No such file or directory Tue Jul 10 22:05:26 CST 2018 calculating lik2 winners1 hla_a_24_02_01_01 hla_b_39_01_01_02l hla_c_07_01_05 Tue Jul 10 22:05:28 CST 2018 get second winners rm: cannot remove 'output/counts2.R0k6': No such file or directory winners1 hla_a_24_02_01_01 hla_b_39_01_01_02l hla_c_07_01_05 winners2 hla_a_24_02_01_01 hla_b_39_01_01_03 hla_c_07_01_05 cleanup Do you know which cause this discrepancy? Could you be kind to give me some advice? Thanks!

Yang

xhy1219 commented 4 years ago

same question here. Did you solve it?

ysbioinfo commented 4 years ago

It doesn't matter. Perhaps the version of some packages it use are different from the original POLYSOLVER. I just ignore this discrepancy and run the following steps.

jason-weirather commented 4 years ago

Hello, sorry for the slow reply to the issue. Thank you for catching this, and it has been discussed in the issues before.

https://github.com/jason-weirather/hla-polysolver/issues/7#issuecomment-389284159

I apologize because I don't have a true resolution to this. The best I could do was draw a prominent attention to it on the front page readme, and provide the usual caveats, that this is an implementation of the original source code for HLA polysolver that was released. Since that time the author has been updating a docker, but not the source. I recommend using Sachet's docker if it's at all possible.

https://hub.docker.com/r/sachet/polysolver/tags

v4 is the last I've used, and it worked fine.

This repo was made because we had a project where we needed to run polysolver, and we couldn't move it into an environment where docker would run.

xhy1219 commented 4 years ago

Thanks! I can not use docker, so I manually installed it using original source code(v1.0) as well. The typing result was same with the one from your implementation. So it probably because of the dependencies versions.