Hello,
Thanks so much for taking a look! I think the selenocysteines ("U") are
likely not the problem, since I've got those in all of my databases,
including the ones that run correctly. I'm looking at
03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML and I don't see
anything odd in line 171821 ("<search_score name="nextscore"
value="11.532"/>"), so I think our line numberings might not match up -
what does your problematic line contain?
When I try to run it on my end, it always sticks somewhere in the
10CPTAC_OV files. Right now I'm running a working set of spectra with a
database that didn't work and vice versa, so hopefully that'll help me pin
down whether it's a problem with my spectra or my database - will let you
know how that turns out!
Emily
On Thursday, October 22, 2020 at 3:09:29 PM UTC-4 David Shteynberg wrote:
> Hi Emily,
>
> I analyzed the search results that you sent and I am seeing some strange
> things in at least one of the files you gave me. This may be causing some
> of the problems you saw.
> In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line
> 171821 there are some strange characters (possibly binary) that are
> tripping up the TPP. I think these might be caused by a bug in an analysis
> tool upstream of the TPP. Not sure if there are other mistakes of this
> sort. Also I found some 'U' amino acids in the database which the TPP
> complains about having a mass of 0.
>
> I hope this helps you somewhat. Let me know what you find on your end.
>
> Cheers,
> -David
>
> On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler <e.ka...@gmail.com> wrote:
>
>> Sure! The spectra are from the CPTAC2 ovarian propective dataset, though
>> I removed all scans that matched to a standard reference database (I don't
>> think the scan removal is the issue, since I'm also having this problem on
>> a different dataset without removing any scans; I also checked with xmllint
>> and it looks like the mzML pepXML files are valid). I've been running it
>> with the philosopher pipeline, so the pepXML files were generated with
>> MSFragger as part of that pipeline. The database is a customized variant
>> database with contaminants and decoys added by philosopher's database tool.
>> Are there any other specifics you'd like? I can upload my full
>> philosopher.yml file if that would be helpful.
>>
>> On Tuesday, October 20, 2020 at 1:30:44 AM UTC-4 David Shteynberg wrote:
>>
>>> Hi Emily,
>>>
>>> I got the data and now I am trying to understand how you are running the
>>> analysis. Can you please describe those steps?
>>>
>>> Thank you,
>>> -David
>>>
>>> On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler <e.ka...@gmail.com>
>>> wrote:
>>>
>>>> I've uploaded the pepXML files, the parameters I used, and the database
>>>> here.
>>>> <https://drive.google.com/drive/folders/1gJoi9fqsmIYg_0tl_2Ur-n04MJyuotyc?usp=sharing>
>>>> Please let me know if I should be uploading anything else! Thank you!
>>>>
>>>> On Saturday, October 17, 2020 at 12:04:21 AM UTC-4 Emily Kawaler wrote:
>>>>
>>>>> Thank you! I'm working on getting it transferred to Drive, so it might
>>>>> take a little while, but I'll be in touch!
>>>>>
>>>>> On Tuesday, October 13, 2020 at 3:08:44 PM UTC-4 David Shteynberg
>>>>> wrote:
>>>>>
>>>>>> Hello Emily,
>>>>>>
>>>>>> If you are able to share 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 <e.ka...@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello, and thank you for your response! It doesn't look like the
>>>>>>> process is using too much memory (I've allocated 300 GB and it's maxing
>>>>>>> out
>>>>>>> around 10), and I've kicked up the minprob parameter - it's still
>>>>>>> getting
>>>>>>> stuck, unfortunately.
>>>>>>> Emily
>>>>>>>
>>>>>>> On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote:
>>>>>>>
>>>>>>>> Hello Emily,
>>>>>>>>
>>>>>>>> This is not a problem that we have seen much of. Do you know which
>>>>>>>> version of ProteinProphet / TPP you are using?
>>>>>>>>
>>>>>>>> One potential issue is the large number of proteins (and peptides)
>>>>>>>> that it is trying to process -- can you either monitor 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 <e.ka...@gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> 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 "Computing degenerate peptides for 69919
>>>>>>>>> proteins: 0%...10%...20%...30%...40%...50%"). Has anyone run into
>>>>>>>>> this
>>>>>>>>> problem before?
>>>>>>>>>
>>>>>>>>> --
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