Empty output file

[Kata-Pa]

Hello,

I tried to use CASPER with a draft genome assembly consisting of around 1029 contigs (named contig_1, contig_2 etc).
I initially had a problem with the bioservices package. I did installed it but when I was running Run_CASPER.py I was still getting an error that there is no module named 'bioservices'.
However, since I was using the specific region and not the KEGG code, I decided to edit CASPERQuick file and remove lines 27-29 and line 65. After these, the script run but I got no sequences in my "sequences" output folder while in a file named sequencesquickresults.txt I only get the position that I entered in the Run_CASPER.py file (1008,46300,46800).
By looking the script, I am assuming that the problem is the naming of the contigs or something like that, is that right? Could I have any help on that matter please?

Thank you in advance.
/Katerina

[bdoze90]

Hi Katerina, What operating system are you using? If you are using Windows, I would recommend using the GUI release that is located at https://github.com/TrinhLab/CASPERapp/releases. We have made modifications to the code and are working out of this new repository, and slowly deprecated the original repository. If you need a Linux or Mac release, I can expedite this to you but it may be a bit buggy until I can get my software engineer to validate it. Best, Brian Mendoza

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On Thu, Jan 23, 2020 at 10:56 AM Kata-Pa ***@***.***> wrote: Hello, I tried to use CASPER with a draft genome assembly consisting of around 1029 contigs (named contig_1, contig_2 etc). I initially had a problem with the bioservices package. I did installed it but when I was running Run_CASPER.py I was still getting an error that there is no module named 'bioservices'. However, since I was using the specific region and not the KEGG code, I decided to edit CASPERQuick file and remove lines 27-29 and line 65. After these, the script run but I got no sequences in my "sequences" output folder while in a file named sequencesquickresults.txt I only get the position that I entered in the Run_CASPER.py file (1008,46300,46800). By looking the script, I am assuming that the problem is the naming of the contigs or something like that, is that right? Could I have any help on that matter please? Thank you in advance. /Katerina — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AED3A4DNMAK2CXAMDUKONBTQ7G42RA5CNFSM4KKYX2J2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IIJELWQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AED3A4FT3LVBJO3BNA3Y2UDQ7G42RANCNFSM4KKYX2JQ> .

-- Brian Mendoza PhD Candidate, University of Tennessee, Knoxville Graduate Research Associate - Trinh Lab