Hi,all
Now I excuted the example data in the workflow, but I wonder that if my data is fit for the database. My experiment is about the metabolic mechanism of C. elegans.
Thank you!
As far as I remember the database does definitely not include proteins from C. elegans.
Please download an appropriate database from e.g., Uniprot and configure your database input file node.
You might need to add a DecoyDatabase node to add decoys. The sample data included decoys already.
Ok,now I download the database and there is a error like this.
Error: File not found (the file ‘F:\KNIME_temporary\knime_KNIME_proteomic2645\fs-Decoy_5-12-2649\000\000\DecoyDatabase_0\c.fasta.psq’ could not be found)
Now, you need to either generate a Blast index of your database (see documentation of the OMSSAAdapter node) or use a different search engine adapter (e.g., CometAdapter).
So how to generate a Blast index?
Thank you!
I also try the CometAdapter. This is the error.
The mzML file provided to CometAdapter is not indexed, but comet requires one. We will add an index by writing a temporary file. If you run this analysis more often, consider indexing your mzML in advance!
Standard output: Running: C:/Program Files/KNIME_4.6.1/…/…/Users/leiyuanluo/.eclipse/4491160_win32_win32_x86_64/plugins/de.openms.win32.x86_64_2.7.0.202109131426/payload/bin/Comet/comet.exe -PC:/Users/leiyuanluo/AppData/Local/Temp/20221220_102047_LAPTOP-95OADKP6_41612_1/param.txt -NC:/Users/leiyuanluo/AppData/Local/Temp/20221220_102047_LAPTOP-95OADKP6_41612_1/result C:/Users/leiyuanluo/AppData/Local/Temp/20221220_102048_LAPTOP-95OADKP6_41612_2
Comet version “2019.01 rev. 5”
Standard error: Process ‘C:/Program Files/KNIME_4.6.1/…/…/Users/leiyuanluo/.eclipse/4491160_win32_win32_x86_64/plugins/de.openms.win32.x86_64_2.7.0.202109131426/payload/bin/Comet/comet.exe’ did not finish successfully (exit code: ). Please check the log.
Thank you!
Please run the node with the configuration “debug 10”
I set “debug 10”, There still occur error.
The mzML file provided to CometAdapter is not indexed, but comet requires one. We will add an index by writing a temporary file. If you run this analysis more often, consider indexing your mzML in advance!
File.cpp(80): Keeping temporary files in directory 'C:/Users/leiyuanluo/AppData/Local/Temp/20221220_184714_LAPTOP-95OADKP6_47700_1/
Running: C:/Program Files/KNIME_4.6.1/…/…/Users/leiyuanluo/.eclipse/4491160_win32_win32_x86_64/plugins/de.openms.win32.x86_64_2.7.0.202109131426/payload/bin/Comet/comet.exe -PC:/Users/leiyuanluo/AppData/Local/Temp/20221220_184714_LAPTOP-95OADKP6_47700_1/param.txt -NC:/Users/leiyuanluo/AppData/Local/Temp/20221220_184714_LAPTOP-95OADKP6_47700_1/result C:/Users/leiyuanluo/AppData/Local/Temp/20221220_184714_LAPTOP-95OADKP6_47700_2
Comet version “2019.01 rev. 5”
Process ‘C:/Program Files/KNIME_4.6.1/…/…/Users/leiyuanluo/.eclipse/4491160_win32_win32_x86_64/plugins/de.openms.win32.x86_64_2.7.0.202109131426/payload/bin/Comet/comet.exe’ did not finish successfully (exit code: ). Please check the log.
CometAdapter took 19.36 s (wall), 19.00 s (CPU), 3.61 s (system), 15.39 s (user); Peak Memory Usage: 52 MB.
I’m sorry I can’t enter the link.(http://www.openms.de/doxygen/release/2.7.0/html/TOPP_CometAdapter.html)
I’m sorry I can’t enter the link.(http://www.openms.de/doxygen/release/2.7.0/html/TOPP_CometAdapter.html
Yes, sorry, the webpage is under construction.
https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/2.7.0/html/TOPP_OMSSAAdapter.html
Install makeblastdb and run:
makeblastdb -dbtype prot -in your.fasta .
Regarding Comet: Sorry but this is a problem with the underlying tool. Unfortunately, I cannot see its output here. You need to debug it yourself if you want to use it.
Run the command yourself:
C:/Program Files/KNIME_4.6.1/…/…/Users/leiyuanluo/.eclipse/4491160_win32_win32_x86_64/plugins/de.openms.win32.x86_64_2.7.0.202109131426/payload/bin/Comet/comet.exe -PC:/Users/leiyuanluo/AppData/Local/Temp/20221220_184714_LAPTOP-95OADKP6_47700_1/param.txt -NC:/Users/leiyuanluo/AppData/Local/Temp/20221220_184714_LAPTOP-95OADKP6_47700_1/result C:/Users/leiyuanluo/AppData/Local/Temp/20221220_184714_LAPTOP-95OADKP6_47700_2
Inspect the param file:
C:/Users/leiyuanluo/AppData/Local/Temp/20221220_184714_LAPTOP-95OADKP6_47700_1/param.txt
etc.
Ok，Thank you very much! I opt to use the OMSSAAdapter node. I will focus on it.
@jpfeuffer I’m sorry about that I can’t finish the transfer the format of database. I download the blast+, but I can’t open the makeblastdb bin.
It’s a command line tool. You need to run it from a command line (cmd.exe or PowerShell)
I got it，I have the other format files.