The result is only sequence information without tree files and computation results

[wang shuyue]

  Hello, I use the window version paml, running will flash back, the figure is the running result, only sequence recognition, but there is no calculation result behind the tree file, I would like to ask you, the tree file is attached to the file hope you can give me some advice, or other scholars give me some advice, thank you very much

[Sandra AC]

Hi there,

I am not sure which test you are trying to run with CODEML as you have not provided the control file you are using. The tree file that you mention is an input file, so nothing would be appended to this file. Is there any error/warning message that you see displayed on the screen or in one of the output files? 

You can try to run this same analysis with a smaller data subset to check whether there is something wrong with your input data and/or control settings -- perhaps the analysis you are running is still performing the calculations as you may have a big alignment file with lots of taxa and they have not yet finished/been printed out. Once this test has finished, please let us know whether there was an error/warning or things ran smoothly with the small data subset and the same settings that you have specified in the control file you are currently using. If you are still experiencing problems with the data subset, please attach the control file and any other relevant information we can use to further troubleshoot this problem.

Hope this helps!
S.

[wang shuyue]

  Thank you very much for your answer. The attachment is my control file, which works normally when I change it to small data, but it won't work if I change it to this one. I have changed A method to recalculate the tree, that is, Attachment A can run, but the tree uploaded before can't, that is, Attachment B would like to know the reason, because I prefer to use the tree of Attachment B, thank you very much非常感谢您的回答。附件是我的控制文件，当我将其更改为小数据时，它正常工作，但是如果我将其更改为此文件，它将不起作用。我改了A的方法来重新计算树，也就是附件A可以运行，但是之前上传的树不能，也就是附件B想知道原因，因为我更喜欢用附件B的树，非常感谢

[Sandra AC]

Hi there,

I have just had time to look at the files you attached and have run some tests. Unfortunately, I have not been able to reproduce your error -- everything ran with both your input tree files. There are some things you may want to take a look at:

1. I extracted your input sequence file from your `mlc` output file (attached in the first message). You may want to check whether you aligned your sequences correctly before running CODEML as it seems there are some out of frame gaps.

2. I used your input sequence file (see above) and then both `A.txt` and `B.txt` files as your input tree files and had no problems when running CODEML (PAML v4.10.7). I just had to change the path to the input sequence and tree files in options `seqfile` and `treefile` in your `codeml.ctl` file, which I believe still has the name of other input files -- if I am not wrong, the input files for the one of the example datasets.

I am not sure why you are getting the error you posted in your first message, so you may want to make sure that the control file you are using is the correct one (i.e., the path to the input files and other settings are correctly specified). Make sure that you have also aligned your sequences correctly.

Hope this helps!
S.

[Sandra AC]

P.S.: I checked again the original input files and I just realised that I managed to run your analysis without problems because some of checks automatically fixed the problem with your input file: your tree in file `A.txt` was not working because the Newick format was wrong. You need to have a semicolon (`;`) at the end of the tree but, instead, you had a colon (`:`). If you fix this, you shall be able to run your analysis! :)

All the best,
S.