search

drostlab / orthologr

Genome wide orthology inference and dNdS estimation
https://drostlab.github.io/orthologr/
GNU General Public License v2.0
88 stars 27 forks source link

File blastresult_AllColdShockProteins.fasta.csv could not be read correctly. #26

Closed yasamanrezvani closed 2 years ago

yasamanrezvani commented 3 years ago

Hi, Thanks for the nice package.

I usually use the blast function giving two Genome file of 2 organism in fasta format and run the command. Here is the command:

blast(query_file = "/path/to/Bdivergens1802A_Genome.fasta", subject_file = "/path/to/BmicrotiATCC30222_Genome.fasta", delete_corrupt_cds = T, seq_type = "protein", format = "fasta", blast_algorithm = "blastp")

So far I was able to get the output without any issue. What I am trying to do now is find the orthologs of couple of protein sequences in a single species. I have the proteins sequences in fasta format as well as the subject file. here is my command:

orthlg <- orthologs( query_file = "/path/to/AllColdShockProteins.fasta", subject_files = "/path/to/BmicrotiATCC30222_Genome.fasta", seq_type = "protein", format = "fasta", eval = 0.0001)

I am not sure if i am doing something wrong!! I am getting the following error:

Error in value[3L] : File blastresult_AllColdShockProteins.fasta.csv could not be read correctly. Please check the correct path to blastresult_AllColdShockProteins.fasta.csv or whether BLAST did write the resulting hit table correctly.

Any Idea on how to fix it is so appreciated. Thanks

HajkD commented 3 years ago

Hi @yasamanrezvani

Many thanks for contacting me. Would it be possible to give me a bit more information so that I can try to help resolving the issue?

Could you first try to restart the R session and rerun this function. Maybe some file was still present in the tempdir() that was overwritten or wrongly parsed.

If it still doesn't work, would it be possible to show me some example sequences and header files from the AllColdShockProteins.fasta and BmicrotiATCC30222_Genome.fasta files?

Does the function orthologr::blast_rec() work with the files you use for orthologr::orthologs()

I hope we can resolve this fairly swiftly!

Many thanks, Hajk

HajkD commented 2 years ago

Hi @yasamanrezvani,

Does this still remain an issue or can I close this discussion?

Many thanks, Hajk

yasamanrezvani commented 2 years ago

Hello,

Thanks for your follow up. I have been using your package and it's working fine now.

Thanks, Yasaman

On Mon, 8 Nov 2021 at 12:06, Hajk-Georg Drost @.***> wrote:

Hi @yasamanrezvani https://github.com/yasamanrezvani,

Does this still remain an issue or can I close this discussion?

Many thanks, Hajk

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/drostlab/orthologr/issues/26#issuecomment-963372145, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJSDCLMWVKJ7KF7LMMUOWS3UK77TBANCNFSM46BHONDQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.