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stephaneguindon / phyml

PhyML -- Phylogenetic estimation using (Maximum) Likelihood
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Err.: Problem with species VACV's sequence #120

Open stgoldst opened 4 years ago

stgoldst commented 4 years ago

I am getting the above error about the first sequence in my phylip alignment, and when i remove it the same error occurs about the (new) first sequence. I cannot find any gaps/spaces etc in the sequences, so do not know what the problem could be.

stephaneguindon commented 4 years ago

It probably has to do with weird carriage return character or something similar. Would you mind sending me the sequence file?

stgoldst commented 4 years ago

Stephane,

Thanks for the response and yes for sure, attached is the phylip file that is generating an error (K3Lnoindel-alignment). This was manually curated from the second (larger) file, by removing all gaps. With the original file I had no problem generating a result in PhyML, but the manually curated one I am getting the error message. If you can help solve this that would be wonderful! I hope to generate trees from some additionally manually curated alignments, so this will be extremely useful to me going forward. Thanks!

Stephen

From: Stephane Guindon notifications@github.com Sent: Friday, February 7, 2020 1:31:13 AM To: stephaneguindon/phyml Cc: Stephen Goldstein; Author Subject: Re: [stephaneguindon/phyml] Err.: Problem with species VACV's sequence (#120)

It probably has to do with weird carriage return character or something similar. Would you mind sending me the sequence file?

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stgoldst commented 4 years ago

I'm not sure if the files attached, so I'm attaching them here. For making the alignment I have them as .phylip, but that won't upload here.

K3L-alignment copy.txt

K3LnoIndel-alignment copy.txt

stephaneguindon commented 4 years ago

There seems to be a problem with the noIndel alignment around line 216.

stgoldst commented 4 years ago

Thanks, I should have spotted that. I am having issues with another alignment now getting the below error

/data/http/www/binaries/phyml/../sms/sms/sms.sh: ligne315: /data/http/www/binaries/phyml/../sms/sms/criterion.sh: Aucun fichier ou dossier de ce type /data/http/www/binaries/phyml/../sms/sms/strategy.sh: ligne121: computeLK : commande introuvable cp: impossible d'évaluer « /data/http/www/exec/20200212-185941_Xr81/sms/sms.phy_phyml_tree_LG-lr.txt »: Aucun fichier ou dossier de ce type 48FKYW2F212-alignment.txt