I just re extracted that file and 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 <e.kawa...@gmail.com> wrote:
> 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 ("</modification_info>"), 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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