Re: [spctools-discuss] Error running xinteract on Kojak results using latest Docker image

2022-11-14 Thread Michael Riffle 
Worked like a charm, thanks David!

Mike

On Monday, November 14, 2022 at 5:32:29 PM UTC-8 David Shteynberg wrote:

> Hi Mike,
>
> With Kojak data the peptide length is meaningless and recorded as zero in 
> the pepXML.  The default parameters of xinteract use min peptide length of 
> 7 which invalidates all results in this file.  You have to run with min 
> peptide length of zero when processing Kojak data: xinteract -l0
>
> Cheers!
> -David
>
> On Mon, Nov 14, 2022 at 5:06 PM Michael Riffle  wrote:
>
>> Greetings TPP folks,
>>
>> I just pulled the latest Docker image and am trying to run the Kojak then 
>> PeptideProphet. Kojak runs fine, PeptideProphet produces an error. Here is 
>> my output:
>>
>> ```
>> sudo docker run -v `pwd`:/data spctools/tpp xinteract 
>> QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml
>>
>> xinteract (TPP v6.1.0 Parhelion, Build 202206071715-8676 (Linux-x86_64))
>>
>> running: "/usr/local/tpp/bin/InteractParser 'interact.pep.xml' 
>> 'QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml' -L'7'"
>>  file 1: QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml
>>  processed altogether 77134 results
>> INFO: Results written to file: /data/interact.pep.xml
>> command completed in 5 sec
>>
>> running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'"
>> command completed in 1 sec
>>
>> running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml' 
>> '/data/EH217_3pepCnt_plusRev.fasta'"
>> enzyme name is:trypsin
>>   - Building Commentz-Walter keyword tree...
>>   - Searching the tree...
>>   - Linking duplicate entries...
>>   - Printing results...
>>   - Mapped 42490 entries
>>
>> command completed in 3 sec
>>  using MAXEHFX_2019_0510_AZ_034_eh220_comet.pep.xml for PeptideProphet...
>>
>> running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'"
>>  (Kojak)
>> init with Kojak trypsin
>> init Loop model with Kojak trypsin
>> adding XLSecondScoreFraction mixture distribution
>> adding XLTopExpectScore mixture distribution
>> init XL model with Kojak trypsin
>>  PeptideProphet  (TPP v6.1.0 Parhelion, Build 202206071715-8676 
>> (Linux-x86_64)) AKeller@ISB
>>  read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
>>  read in no data
>> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: 
>> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
>>
>> INFO: Processing xl MixtureModel ...
>>
>> command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'" 
>> exited with non-zero exit code: 256
>> QUIT - the job is incomplete
>> ```
>>
>> I suspect the "read no data" line above, towards the end, is the culprit, 
>> but I can't guess what might be causing that. Do you have any ideas?
>>
>> Thanks,
>> Mike Riffle
>>
>>
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>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Error running xinteract on Kojak results using latest Docker image

2022-11-14 Thread 'David Shteynberg' via spctools-discuss 
Hi Mike,

With Kojak data the peptide length is meaningless and recorded as zero in
the pepXML.  The default parameters of xinteract use min peptide length of
7 which invalidates all results in this file.  You have to run with min
peptide length of zero when processing Kojak data: xinteract -l0

Cheers!
-David

On Mon, Nov 14, 2022 at 5:06 PM Michael Riffle  wrote:

> Greetings TPP folks,
>
> I just pulled the latest Docker image and am trying to run the Kojak then
> PeptideProphet. Kojak runs fine, PeptideProphet produces an error. Here is
> my output:
>
> ```
> sudo docker run -v `pwd`:/data spctools/tpp xinteract
> QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml
>
> xinteract (TPP v6.1.0 Parhelion, Build 202206071715-8676 (Linux-x86_64))
>
> running: "/usr/local/tpp/bin/InteractParser 'interact.pep.xml'
> 'QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml' -L'7'"
>  file 1: QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml
>  processed altogether 77134 results
> INFO: Results written to file: /data/interact.pep.xml
> command completed in 5 sec
>
> running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'"
> command completed in 1 sec
>
> running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml'
> '/data/EH217_3pepCnt_plusRev.fasta'"
> enzyme name is:trypsin
>   - Building Commentz-Walter keyword tree...
>   - Searching the tree...
>   - Linking duplicate entries...
>   - Printing results...
>   - Mapped 42490 entries
>
> command completed in 3 sec
>  using MAXEHFX_2019_0510_AZ_034_eh220_comet.pep.xml for PeptideProphet...
>
> running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'"
>  (Kojak)
> init with Kojak trypsin
> init Loop model with Kojak trypsin
> adding XLSecondScoreFraction mixture distribution
> adding XLTopExpectScore mixture distribution
> init XL model with Kojak trypsin
>  PeptideProphet  (TPP v6.1.0 Parhelion, Build 202206071715-8676
> (Linux-x86_64)) AKeller@ISB
>  read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
>  read in no data
> MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
> UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
>
> INFO: Processing xl MixtureModel ...
>
> command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'"
> exited with non-zero exit code: 256
> QUIT - the job is incomplete
> ```
>
> I suspect the "read no data" line above, towards the end, is the culprit,
> but I can't guess what might be causing that. Do you have any ideas?
>
> Thanks,
> Mike Riffle
>
>
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> 
> .
>

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[spctools-discuss] Error running xinteract on Kojak results using latest Docker image

2022-11-14 Thread Michael Riffle 
Greetings TPP folks,

I just pulled the latest Docker image and am trying to run the Kojak then 
PeptideProphet. Kojak runs fine, PeptideProphet produces an error. Here is 
my output:

```
sudo docker run -v `pwd`:/data spctools/tpp xinteract 
QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml

xinteract (TPP v6.1.0 Parhelion, Build 202206071715-8676 (Linux-x86_64))

running: "/usr/local/tpp/bin/InteractParser 'interact.pep.xml' 
'QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml' -L'7'"
 file 1: QEHFX_2019_0510_AZ_034_eh220_comet.pep.xml
 processed altogether 77134 results
INFO: Results written to file: /data/interact.pep.xml
command completed in 5 sec

running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'"
command completed in 1 sec

running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml' 
'/data/EH217_3pepCnt_plusRev.fasta'"
enzyme name is:trypsin
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...
  - Mapped 42490 entries

command completed in 3 sec
 using MAXEHFX_2019_0510_AZ_034_eh220_comet.pep.xml for PeptideProphet...

running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'"
 (Kojak)
init with Kojak trypsin
init Loop model with Kojak trypsin
adding XLSecondScoreFraction mixture distribution
adding XLTopExpectScore mixture distribution
init XL model with Kojak trypsin
 PeptideProphet  (TPP v6.1.0 Parhelion, Build 202206071715-8676 
(Linux-x86_64)) AKeller@ISB
 read in 0 1+, 0 2+, 0 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
 read in no data
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: 
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing xl MixtureModel ...

command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'" exited 
with non-zero exit code: 256
QUIT - the job is incomplete
```

I suspect the "read no data" line above, towards the end, is the culprit, 
but I can't guess what might be causing that. Do you have any ideas?

Thanks,
Mike Riffle


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