Hi，
Thanks for your answer.
-I can see that "tandem.exe" processes is running by opening the Task
Manager.But there's no .tandem output files.And how to check the
parameters?There's a tandem_params.xml file when I install the TPP in my
computer.And I choose it as my Tandem Parameters Files.And I have loaded in the
attachment.Please help me check it out if it's availiable .Or else is there
any method that I can compile the parameters file?
-I have checked that it's not the case that computer shuts down or goes into
sleep mode before the job is finished.
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JN
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16622080...@163.com
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签名由网易邮箱大师定制
On 11/20/2020 14:18，'Luis Mendoza' via
spctools-discuss<spctools-discuss@googlegroups.com> wrote：
Hello,
This is likely an issue with the webserver not realizing that X!Tandem has
finished running.
Can you see if there are any "tandem.exe" processes running by opening the Task
Manager?
- If you do not see any and if you can see .tandem output files, it means that
the job is done, but the connection to the interface timed out. You can (in
most cases) safely move on to converting this .tandem file to pepXML and then
continue your analysis.
- If Tandem is still running, then check the parameters (are there too many
variable modifications, for example), or try using a more powerful machine.
Furthermore, to tell the interface to consider the job as finished, click on
the Jobs link in Petunia, find the "Running" job and click on "View" under the
Output column. Then, in that page click on the following link: If your
commands have actually completed, or the queue did not work, click here.
Another situation in which this may happen is if the computer shuts down or
goes into sleep mode before the job is finished, so make sure that is not the
case. If so, you will need to re-start the search.
Hope this helps,
--Luis
On Thu, Nov 19, 2020 at 6:32 PM na jiang <16622080...@163.com> wrote:
Hi,
I'm new to TPP.Recently, I intend to use TPP and I have tested my data on
TPP(my operation system is windows.).It seems that TPP is always runing for 2
days and there's only 1 data.I intend to use Tandem Pipeline. What could be the
reason why the TPP never stopped running?
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<?xml version="1.0" encoding="UTF-8"?>
<bioml>
<note> DEFAULT PARAMETERS. The value of "isb_default_input_kscore.xml" is recommended. Change to "isb_default_input_native.xml" for native X!Tandem scoring.</note>
<note type="input" label="list path, default parameters">E:/tpp_data/params/isb_default_input_kscore.xml</note>
<note> FILE LOCATIONS. Replace them with your input (.mzXML) file and output file -- these are REQUIRED. Optionally a log file and a sequence output file of all protein sequences identified in the first-pass can be specified. Use of FULL path (not relative) paths is recommended. </note>
<note type="input" label="spectrum, path">full_mzXML_filepath</note>
<note type="input" label="output, path">full_tandem_output_path</note>
<note type="input" label="output, log path"></note>
<note type="input" label="output, sequence path"></note>
<note> TAXONOMY FILE. This is a file containing references to the sequence databases. Point it to your own taxonomy.xml if needed.</note>
<note type="input" label="list path, taxonomy information">E:/tpp_data/params/taxonomy.xml</note>
<note> PROTEIN SEQUENCE DATABASE. This refers to identifiers in the taxomony.xml, not the .fasta files themselves! Make sure the database you want is present as an entry in the taxonomy.xml referenced above. This is REQUIRED. </note>
<note type="input" label="protein, taxon">protein_database</note>
<note> PRECURSOR MASS TOLERANCES. In the example below, a -2.0 Da to 4.0 Da (monoisotopic mass) window is searched for peptide candidates. Since this is monoisotopic mass, so for non-accurate-mass instruments, for which the precursor is often taken nearer to the isotopically averaged mass, an asymmetric tolerance (-2.0 Da to 4.0 Da) is preferable. This somewhat imitates a (-3.0 Da to 3.0 Da) window for averaged mass (but not exactly)</note>
<note type="input" label="spectrum, parent monoisotopic mass error minus">2.0</note>
<note type="input" label="spectrum, parent monoisotopic mass error plus">4.0</note>
<note type="input" label="spectrum, parent monoisotopic mass error units">Daltons</note>
<note>The value for this parameter may be 'Daltons' or 'ppm': all other values are ignored</note>
<note type="input" label="spectrum, parent monoisotopic mass isotope error">no</note>
<note>This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass. </note>
<note> MODIFICATIONS. In the example below, there is a static (carbamidomethyl) modification on C, and variable modifications on M (oxidation). Multiple modifications can be separated by commas, as in "80.0@S,80.0@T". Peptide terminal modifications can be specified with the symbol '[' for N-terminus and ']' for C-terminus, such as 42.0@[ . </note>
<note type="input" label="residue, modification mass">57.021464@C</note>
<note type="input" label="residue, potential modification mass">15.994915@M</note>
<note type="input" label="residue, potential modification motif"></note>
<note> You can specify a variable modification only when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite). </note>
<note type="input" label="protein, N-terminal residue modification mass"></note>
<note type="input" label="protein, C-terminal residue modification mass"></note>
<note> These are *static* modifications on the PROTEINS' N or C-termini. </note>
<note> SEMI-TRYPTICS AND MISSED CLEAVAGES. In the example below, semitryptic peptides are allowed, and up to 2 missed cleavages are allowed. </note>
<note type="input" label="protein, cleavage semi">yes</note>
<note type="input" label="scoring, maximum missed cleavage sites">2</note>
<note> REFINEMENT. Do not use unless you know what you are doing. Set "refine" to "yes" and specify what you want to search in the refinement. For non-confusing results, repeat the same modifications you set above for the first-pass here.</note>
<note type="input" label="refine">no</note>
<note type="input" label="refine, maximum valid expectation value">0.1</note>
<note type="input" label="refine, modification mass">57.012@C</note>
<note type="input" label="refine, potential modification mass">15.994915@M</note>
<note type="input" label="refine, potential modification motif"></note>
<note type="input" label="refine, cleavage semi">yes</note>
<note type="input" label="refine, unanticipated cleavage">no</note>
<note type="input" label="refine, potential N-terminus modifications"></note>
<note type="input" label="refine, potential C-terminus modifications"></note>
<note type="input" label="refine, point mutations">no</note>
<note type="input" label="refine, use potential modifications for full refinement">no</note>
</bioml>
