Pipeline for AP-MS data analysis

[Bin-cc]

Hi,

I was trying to analyze AP-MS data by pipeline command of Philosopher. But after executing the command "philosopher pipeline --config philosopher.yml CONTROL_1 CONTROL_2 HDAC1_1 HDAC1_2", it can run until the workspace created, and then an error will appear as follow: "Missing input file. Provide a protein FASTA file or Proteome ID".

However, the FASTA file and mzml files were successfully applied to simple data analysis by Philosopher. I would like to know why such a situation occurs and how to sovle it?

(The files philosopher.yml and comet.params are downloaded from https://github.com/Nesvilab/philosopher/wiki/REPRINT-Analysis)

[sarah-haynes]

Hi, can you check that the path to the FASTA file points to the database you downloaded? In the .yml file, the /path/to/FASTA placeholder needs to be changed.

Sarah

[sarah-haynes]

@prvst reminded me that the pipeline .yml file example was out of date, I updated the pipeline configuration file in the tutorial, hopefully that will work for you. (You can also generate a default .yml file by running philosopher pipeline --print, then edit that one.)

Sarah

[Bin-cc]

Thank you so much for replying my question, it can be able to start searching. But I can only get .pep.xml files, no protein.tsv . Is there something wrong that I haven't noticed?

The run log is as follows:
INFO[17:37:12] Running the validation and inference on C:\Users\18811\Desktop\AP-MS\PRPF31_1
INFO[17:37:12] Executing PeptideProphet on C:\Users\18811\Desktop\AP-MS\PRPF31_1
panic: runtime error: index out of range [0] with length 0

goroutine 1 [running]:
philosopher/lib/ext/peptideprophet.interactParser(0xc001bc63c0, 0x59, 0xc001bc6420, 0x58, 0xc001bc6480, 0x5f, 0xc001bc63c0, 0x59, 0xc001bc6420, 0x58, ...)
/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:218 +0x22a5
philosopher/lib/ext/peptideprophet.PeptideProphet.Execute(0xc001bc63c0, 0x59, 0xc001bc6420, 0x58, 0xc001bc6480, 0x5f, 0xc001bc63c0, 0x59, 0xc001bc6420, 0x58, ...)
/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:125 +0x1f0
philosopher/lib/ext/peptideprophet.Run(0xc00acde180, 0x24, 0xc00acde1b0, 0x25, 0xc00667a320, 0x46, 0xc00a0e4140, 0x34, 0xc00acde1e0, 0x2b, ...)
/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:70 +0x508
philosopher/lib/pip.PeptideProphet(0xc00acde060, 0x24, 0xc01f440820, 0x1c, 0xc00667a0a0, 0x46, 0xc00acde090, 0x2b, 0xc00acde0c0, 0x22, ...)
/workspace/philosopher/lib/pip/pip.go:242 +0x631
philosopher/cmd.glob..func13(0x7867bc0, 0xc000198040, 0x2, 0x4)
/workspace/philosopher/cmd/pipeline.go:81 +0xf25
github.com/spf13/cobra.(*Command).execute(0x7867bc0, 0xc000198000, 0x4, 0x4, 0x7867bc0, 0xc000198000)
/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:844 +0x2c2
github.com/spf13/cobra.(*Command).ExecuteC(0x7868640, 0x0, 0x0, 0x0)
/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:945 +0x336
github.com/spf13/cobra.(*Command).Execute(...)
/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:885
philosopher/cmd.Execute()
/workspace/philosopher/cmd/root.go:35 +0x34
main.main()
/workspace/philosopher/main.go:22 +0x75

[sarah-haynes]

Have both the .pepXML and interact-.pep.xml files been generated successfully? It looks like PeptideProphet fails, which creates the interact-.pep.xml files. Could you share the whole command line log with us and maybe a screenshot/description of how your files are organized?

[Bin-cc]

Hi,

I only got .pep.xml for each .mzml file, neither .pepXML nor interact-.pep.xml. There may be something wrong with comet.params, of course, it may also be PeptideProphet. Because after I chose MSFragger as search engine, with closed_fragger.params, combined_protein.tsv could be generated.

Command line log as follows. Thanks.

C:\Users\18811\Desktop\PRPF31>philosopher pipeline --config C:\Users\18811\Desktop\PRPF31\philosopher_AP-MS.yml C:\Users\18811\Desktop\PRPF31\PRPF31_1 C:\Users\18811\Desktop\PRPF31\PRPF31_2
INFO[10:28:27] Executing Pipeline v3.4.13
INFO[10:28:27] Creating workspace
INFO[10:28:27] Initiating the workspace on C:\Users\18811\Desktop\PRPF31\PRPF31_1
INFO[10:28:27] Creating workspace
INFO[10:28:27] Processing database
INFO[10:28:39] Initiating the workspace on C:\Users\18811\Desktop\PRPF31\PRPF31_2
INFO[10:28:39] Creating workspace
INFO[10:28:39] Processing database
INFO[10:28:51] Running the Database Search on all data
Comet version "2019.01 rev. 1"

Search start: 05/18/2021, 10:28:51 AM

• Input file: C:\Users\18811\Desktop\PRPF31\PRPF31_1\PRPF31_1.mzML
  • Load spectra: 14637
    • Search progress: 100%
    • Post analysis: done
      Search end: 05/18/2021, 10:46:50 AM, 17m:59s

Search start: 05/18/2021, 10:46:51 AM

• Input file: C:\Users\18811\Desktop\PRPF31\PRPF31_2\PRPF31_2.mzML
  • Load spectra: 8332
    • Search progress: 99%
    • Post analysis: done
      Search end: 05/18/2021, 11:02:58 AM, 16m:7s

INFO[11:02:58] Running the validation and inference on C:\Users\18811\Desktop\PRPF31\PRPF31_1
INFO[11:02:58] Executing PeptideProphet on C:\Users\18811\Desktop\PRPF31\PRPF31_1
panic: runtime error: index out of range [0] with length 0

goroutine 1 [running]:
philosopher/lib/ext/peptideprophet.interactParser(0xc001fe43c0, 0x59, 0xc001fe4420, 0x58, 0xc001fe4480, 0x5f, 0xc001fe43c0, 0x59, 0xc001fe4420, 0x58, ...)
/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:218 +0x22a5
philosopher/lib/ext/peptideprophet.PeptideProphet.Execute(0xc001fe43c0, 0x59, 0xc001fe4420, 0x58, 0xc001fe4480, 0x5f, 0xc001fe43c0, 0x59, 0xc001fe4420, 0x58, ...)
/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:125 +0x1f0
philosopher/lib/ext/peptideprophet.Run(0xc00ab76180, 0x24, 0xc00ab761b0, 0x26, 0xc006b9a320, 0x46, 0xc0010c4100, 0x35, 0xc00ab761e0, 0x2c, ...)
/workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:70 +0x508
philosopher/lib/pip.PeptideProphet(0xc00ab76060, 0x24, 0xc00ac22060, 0x1d, 0xc006b9a0f0, 0x46, 0xc00ab76090, 0x2c, 0xc00ab760f0, 0x23, ...)
/workspace/philosopher/lib/pip/pip.go:242 +0x631
philosopher/cmd.glob..func13(0x80c7bc0, 0xc0000940c0, 0x2, 0x4)
/workspace/philosopher/cmd/pipeline.go:81 +0xf25
github.com/spf13/cobra.(*Command).execute(0x80c7bc0, 0xc000094080, 0x4, 0x4, 0x80c7bc0, 0xc000094080)
/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:844 +0x2c2
github.com/spf13/cobra.(*Command).ExecuteC(0x80c8640, 0x0, 0x0, 0x0)
/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:945 +0x336
github.com/spf13/cobra.(*Command).Execute(...)
/home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:885
philosopher/cmd.Execute()
/workspace/philosopher/cmd/root.go:35 +0x34
main.main()
/workspace/philosopher/main.go:22 +0x75

[sarah-haynes]

I see the issue now-- my mistake. I had extension: pepXML in the Peptide Validation section of the pipeline .yml file when it should be extension: pep.xml. Let me know if it still doesn't work when you change that field to pep.xml.

[Bin-cc]

Hi, It indeed works, thank you so much help me a lot. bin liao ***@***.*** 签名由 网易邮箱大师 定制 On 05/19/2021 04:09, Sarah Haynes wrote: I see the issue now-- my mistake. I had extension: pepXML in the Peptide Validation section of the pipeline .yml file when it should be extension: pep.xml. Let me know if it still doesn't work when you change that field to pep.xml. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.