Open stgoldst opened 4 years ago
It probably has to do with weird carriage return character or something similar. Would you mind sending me the sequence file?
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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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.
There seems to be a problem with the noIndel alignment around line 216.
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
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.