s looking into the code to see if there was a simple way to
> speed it up, but unfortunately this doesn't seem to be the case. Is there
> any way you can reduce the number of titin entries in your database? Have
> you considered using PEFF?
>
> Thanks,
> -David
>
>
er to know
what to look for. Any thoughts?
On Friday, October 23, 2020 at 3:45:08 PM UTC-4 Emily Kawaler wrote:
> Okay - When I ran the working set of spectra with the database that
> failed, it seems to have failed; when I ran the set of spectra that failed
> with a database
, 2020 at 1:56:18 AM UTC-4 Emily Kawaler wrote:
> While those tests are still running, I pulled out all 185 of the proteins
> that are in the 10OV pepXMLs but not in 01-09OV, figuring that maybe one of
> those is causing the error. I've uploaded that to the same folder
> eve
d I don't see the issue anymore. Perhaps
> this was a decompression issue.
>
> Thanks for checking.
>
> -David
>
> On Thu, Oct 22, 2020 at 12:19 PM Emily Kawaler wrote:
>
>> Hello,
>> Thanks so much for taking a look! I think the selenocysteines ("U"
omewhat. Let me know what you find on your end.
>
> Cheers,
> -David
>
> On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler wrote:
>
>> Sure! The spectra are from the CPTAC2 ovarian propective dataset, though
>> I removed all scans that matched to a standard reference data
omewhat. Let me know what you find on your end.
>
> Cheers,
> -David
>
> On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler wrote:
>
>> Sure! The spectra are from the CPTAC2 ovarian propective dataset, though
>> I removed all scans that matched to a standard reference data
is. Can you please describe those steps?
>
> Thank you,
> -David
>
> On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler wrote:
>
>> I've uploaded the pepXML files, the parameters I used, and the database
>> here.
>> <https://drive.google.com/drive/folders/1gJoi
e the dataset including the pepXML file and the
>> database I can try to replicate the issue here and try to troubleshoot the
>> sticking point.
>>
>> Thanks,
>> -David
>>
>> On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler wrote:
>>
>>> Hello,
tabase I can try to replicate the issue here and try to troubleshoot the
> sticking point.
>
> Thanks,
> -David
>
> On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler wrote:
>
>> Hello, and thank you for your response! It doesn't look like the process
>> is using to
itor the memory usage of the
> machine when you run this dataset, and/or try on one with more memory?
>
> Hope this helps,
> --Luis
>
>
> On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler wrote:
>
>> Hello! I've been running ProteinProphet as part of the Philosopher
>> pipe
Hello! I've been running ProteinProphet as part of the Philosopher pipeline
for a while now with no problems. However, one of my datasets seems to be
getting stuck in the middle of this function. It doesn't throw an error or
anything - just stops advancing (the last
line of the output is
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