For some families get Error in family : Cannot read alignment file (file exists but is invalid)

Evan Cribbie

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Jul 11, 2022, 12:55:18 PM7/11/22

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Dear Benoit,

I am now running on a different dataset than previously and ran into a problem I was hoping you could help with. I tried running Generax and for some of the families I got the error: Error in family ____: Cannot read alignment file (file exists but is invalid). I was wondering if you could let me know why this may be or what I am missing.

I tried rerunning Generax on a subset of the problematic families and all of them reproduce the same issue. I have attached a link to the log file as well as all of the files that should be needed to run Generax on a subset of the problematic files in case that helps.

Thanks in advance for all your help, it is always greatly appreciated.

https://drive.google.com/drive/folders/1933H5mtfsANVHQQdlNEecll2G4gnTCHR?usp=sharing

Best,

Evan

Benoit Morel

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Jul 12, 2022, 5:40:13 AM7/12/22

to Evan Cribbie, GeneRax

Dear Evan,

Some of your alignments contain the character ! which is not supported (we use the same parser as raxml-ng). If they represent gaps or undecided characters (could be A,C,G,orT), you can safely replace them with "-".

I'll see if we can get a better error message.

Best,

Benoit

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Evan Cribbie

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Jul 12, 2022, 10:30:16 AM7/12/22

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Dear Benoit,

Thank you very much!

Best,

Evan

Claire Jordan

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Aug 9, 2022, 12:27:23 PM8/9/22

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Hello! I've been having the same error as Evan although unfortunately I am getting this error message for all my files, not just a selection. I searched for possible characters which are not supported, but I was unable to find any. Could there be another reason for this error that I am overlooking?

Here is a subset of my starting alignment files.

https://drive.google.com/drive/folders/1p2R6Qo2goFkzY67ytiacJripjZ6yyU1Y

Thank you in advance for your time!

Benoit Morel

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Aug 9, 2022, 4:20:37 PM8/9/22

to Claire Jordan, GeneRax

Dear Claire,

Thanks for your post. The problem is that the sequences are not aligned (they have different lengths). There are many programs that can align your sequences (PRANK, mafft, MUSCLE etc.) but I am not expert enough to tell you which one is the best choice...