the program seems stucked

[yilunhuangyue]

Thank you very much for develping the program. It is very useful for my project. However, I met an problem when running it.
The command i used was: resistify nlr round4.all.prot.fa
Then I got the log file like this:
[15:21:08] INFO Welcome to Resistify version 0.6.2!
WARNING Sequence
augustus_masked-Chr_02_nlr_25-processed-gene-0.0-mRNA-1 is
less than 28 codons - skipping this sequence...
WARNING Sequence
augustus_masked-Chr_08_nlr_26-processed-gene-0.2-mRNA-1 is
less than 28 codons - skipping this sequence...
WARNING Sequence
augustus_masked-ptg000046l_nlr_3-processed-gene-0.3-mRNA-1
is less than 28 codons - skipping this sequence...
INFO Searching for NLRs...
INFO Running hmmsearch...
[15:21:10] INFO 321 NLRs identified...
[15:21:11] INFO Running NLRexpress - this could take a while...
[15:23:53] ERROR * is not a float.
augustus_masked-Chr_08_nlr_10-processed-gene-0.5-mRNA-1
/tmp/tmplz84cb2z/seq.fa.out-1.hmm
[15:24:04] ERROR * is not a float.
snap_masked-Chr_08_nlr_29-processed-gene-0.0-mRNA-1
/tmp/tmpc3ooh1md/seq.fa.out-1.hmm

The program is running for more than one day and I can see multiple thread named "pt_main_thread" in the backend of server as "Sleeping" status. I am not sure what is the problem. Thank you very much for any help.

[SwiftSeal]

Hi @yilunhuangyue

That seems like a bug to me - could you post the sequences of augustus_masked-Chr_08_nlr_10-processed-gene-0.5-mRNA-1 and snap_masked-Chr_08_nlr_29-processed-gene-0.0-mRNA-1? They might have some characters which are causing issues - I'll test them on my end

[yilunhuangyue]

Thanks for your quick reply. I have solved the issue. I used gffread to extract protein sequences and the stop coden was indicated by the charactor '.'. I remove the charactor and the program was successfully finished.

[SwiftSeal]

Ahh I didn't think of that! I have released v0.6.3 to fix this. Thanks for letting me know :)