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
everything else is in (it's called 10OV_uniq.fasta) - I don't see anything
that jumps out immediately. (There are no individual characters unique to
either the headers or the sequences in 10OV, so I don't think there's an
individual character messing things up.)
On Thursday, October 22, 2020 at 3:49:18 PM UTC-4 David Shteynberg wrote:
> 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.ka...@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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