Deall All,
I am trying to pass -P options from the xinteract by specifying -P (fix
protein names in OMSSA data) but couldn't get it work. Here is the STDOUT
for OMSSA-TPP pipeline with xinteract which has some issues in writing
output file for InteractParser which lead to failure of the pipeline but
when I run InteractParser with -P options and leaving all the other options
remin same then the OMSSA-TPP pipeline completes.
--------------------------------------------------------------------------------------------------------------------------
[r...@apcf-hn3 DavidTest]# /home/APCF/tpp/bin/xinteract -P
-Ndavidtest.pepprophet.xml -OPd -dDECOY -eT davidtest.pep.xml
/home/APCF/tpp/bin/xinteract (TPP v4.4 JETSTREAM (unstable development
prerelease) rev 0, Build 201007011135 (linux))
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser
'davidtest.pepprophet.xml' 'davidtest.pep.xml' -L'7' -E'trypsin'"
file 1: davidtest.pep.xml
processed altogether 2445 results
results written to file
/mnt/sanfs/APCF/results/tpp/2010-07-19/DavidTest/davidtest.pepprophet.shtml
command completed in 7 sec
running: "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser
'davidtest.pepprophet.xml' NONPARAM DECOYPROBS DECOY=DECOY"
Using Decoy Label "DECOY".
Decoy Probabilities will be reported.
Using non-parametric distributions
(OMSSA)
WARNING!! The discriminant function for OMSSA is not yet complete. It is
presented here to help facilitate trial and discussion. Reliance on this
code for publishable scientific results is not recommended.
init with OMSSA trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) rev
0, Build 201007011135 (linux)) akel...@isb
read in 417 1+, 1290 2+, 361 3+, 54 4+, 3 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 0 Decoys, and 2125 Non-Decoys
WARNING: No decoys with label DECOY were found in this dataset. reverting to
fully unsupervised method.
Iterations: .........10.........20
command "/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser
'davidtest.pepprophet.xml' NONPARAM DECOYPROBS DECOY=DECOY" exited with
non-zero exit code: 11
QUIT - the job is incomplete
[r...@apcf-hn3 DavidTest]# /mnt/sanfs/APCF/APCF_WEB/tpp/bin/InteractParser
'davidtest.pepprophet.xml' 'davidtest.pep.xml' -L'7' -E'trypsin' -P
file 1: davidtest.pep.xml
processed altogether 2445 results
results written to file
/mnt/sanfs/APCF/results/tpp/2010-07-19/DavidTest/davidtest.pepprophet.shtml
[r...@apcf-hn3 DavidTest]#
/mnt/sanfs/APCF/APCF_WEB/tpp/bin/PeptideProphetParser
'davidtest.pepprophet.xml' NONPARAM DECOYPROBS DECOY=DECOY
Using Decoy Label "DECOY".
Decoy Probabilities will be reported.
Using non-parametric distributions
(OMSSA)
WARNING!! The discriminant function for OMSSA is not yet complete. It is
presented here to help facilitate trial and discussion. Reliance on this
code for publishable scientific results is not recommended.
init with OMSSA trypsin
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization:
UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN
PeptideProphet (TPP v4.4 JETSTREAM (unstable development prerelease) rev
0, Build 201007011135 (linux)) akel...@isb
read in 417 1+, 1290 2+, 361 3+, 54 4+, 3 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Found 903 Decoys, and 1222 Non-Decoys
Iterations: .........10.........20......
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 27 iterations
[r...@apcf-hn3 DavidTest]#
---------------------------------------------------------------------------------
I notice the following difference when I run InteractParser with and without
"-P" option.
-------------------------------------------------------
WITHOUT "-P" OPTION
----------------------------------
< <search_hit hit_rank="2" peptide="VTSGTALLFVVTD" peptide_prev_aa="R"
peptide_next_aa="M" protein="24347" num_tot_proteins="1"
num_matched_ions="5" tot_num_ions="24" calc_neutral_pep_mass="1321.712"
massdiff="-0.750000000000011" is_rejected="0" protein_descr="DECOY_Q5VST9
Decoy sequence" num_tol_term="1" num_missed_cleavages="0">
---
WITH "-P" OPTION
----------------------------
> <search_hit hit_rank="2" peptide="VTSGTALLFVVTD" peptide_prev_aa="R"
peptide_next_aa="M" protein="DECOY_Q5VST9" num_tot_proteins="1"
num_matched_ions="5" tot_num_ions="24" calc_neutral_pep_mass="1321.712"
massdiff="-0.750000000000011" is_rejected="0" protein_descr="DECOY_Q5VST9
Decoy sequence" num_tol_term="1" num_missed_cleavages="0">
-------------------------------------------------------
WITHOUT "-P" OPTION
----------------------------------
< <search_hit hit_rank="3" peptide="MITVVYGPDLVN" peptide_prev_aa="R"
peptide_next_aa="I" protein="26762" num_tot_proteins="1"
num_matched_ions="5" tot_num_ions="22" calc_neutral_pep_mass="1319.678"
massdiff="1.283999999999989" is_rejected="0" protein_descr="Q9NQ66
PLCB1_HUMAN 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-1
OS=Homo sapiens GN=PLCB1 PE=1 SV=1" num_tol_term="1"
num_missed_cleavages="0">
-------------------------------------------------------
WITH "-P" OPTION
----------------------------------
> <search_hit hit_rank="3" peptide="MITVVYGPDLVN" peptide_prev_aa="R"
peptide_next_aa="I" protein="Q9NQ66" num_tot_proteins="1"
num_matched_ions="5" tot_num_ions="22" calc_neutral_pep_mass="1319.678"
massdiff="1.283999999999989" is_rejected="0" protein_descr="Q9NQ66
PLCB1_HUMAN 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-1
OS=Homo sapiens GN=PLCB1 PE=1 SV=1" num_tol_term="1"
num_missed_cleavages="0">
------------------------------------------------
Any suggestions please.
with regards,
Dr. Jagan Kommineni
Ludwig Institute for Cancer research
Pakville VIC 3145
Australia.
--
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To post to this group, send email to spctools-disc...@googlegroups.com.
To unsubscribe from this group, send email to
spctools-discuss+unsubscr...@googlegroups.com.
For more options, visit this group at
http://groups.google.com/group/spctools-discuss?hl=en.
