Cannot decode packed binary

[Bin-cc]

Hi,

I follow the LFQ tutorial in this to run my data and everything is well done until the step Filter and estimate FDR. The error is as follows.

INFO[10:50:24] Executing Filter  v4.2.1
INFO[10:50:24] Processing peptide identification files
INFO[10:50:24] Parsing D:\All_for_paper\Microprotein\Search_engine\Philosopher\Philosopher_4.2\interact-dmso_1.pep.xml
FATA[10:50:24] Cannot decode packed binary. XML syntax error on line 21464: expected attribute name in element

I have no idea for this problem. Is there something wrong in my .pep.xml files?

All the best

[Bin-cc]

Hi,

Thank you for your kind replay. This problem seems be solved, but I now encounter a new one. Also in the step Filter and estimate FDR, the error is as follows.

INFO[17:33:03] Post processing identifications
FATA[17:33:03] Cannot read file. open .meta\db.bin: The system cannot find the file specified.

I use the same .mzML file and parameters as FragPipe. And FragPipe can be ran successfully but in Philosopher I encounter the problem above. The process of FragPipe in this and Philosopher in this.

What can I do to resolve it?

All the Best,
Bin

[prvst]

this means you don't have a database annotated in your workspace, you probably skipped the annotation step.

[Bin-cc]

Hi,

Thank you for reminding me. It does work, thank you!

[Bin-cc]

Hi,

Here is the question 2.

I changed the search method into this. But I have another issue. If I follow your advice that setting extension: pepXML into extension: pep.xml in the section Peptide Validation, there is an error like this.

INFO[20:31:34] Running the validation and inference on D:\Philosopher\philosopher\DMSO_1
INFO[20:31:34] Executing PeptideProphet on D:\Philosopher\philosopher\DMSO_1
panic: runtime error: index out of range [0] with length 0

goroutine 1 [running]:
philosopher/lib/ext/peptideprophet.interactParser(0xc0000a6480, 0x59, 0xc0000a6540, 0x58, 0xc0000a6600, 0x5f, 0xc0000a6480, 0x59, 0xc0000a6540, 0x58, ...)
        /workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:179 +0x222c
philosopher/lib/ext/peptideprophet.PeptideProphet.Execute(0xc0000a6480, 0x59, 0xc0000a6540, 0x58, 0xc0000a6600, 0x5f, 0xc0000a6480, 0x59, 0xc0000a6540, 0x58, ...)
        /workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:86 +0x1d2
philosopher/lib/ext/peptideprophet.Run(0xc0000cc090, 0x24, 0xc0000a8320, 0x4a, 0xc0000a8370, 0x46, 0xc0000a6180, 0x59, 0xc0000a83c0, 0x50, ...)
        /workspace/philosopher/lib/ext/peptideprophet/peptideprophet.go:67 +0x4be
philosopher/lib/pip.PeptideProphet(0xc0000cc030, 0x24, 0xc0000a8140, 0x43, 0xc0000a8190, 0x46, 0xc0000a61e0, 0x52, 0xc0000a81e0, 0x49, ...)
        /workspace/philosopher/lib/pip/pip.go:284 +0x5c8
philosopher/cmd.glob..func13(0x2316180, 0xc0001600c0, 0x2, 0x4)
        /workspace/philosopher/cmd/pipeline.go:85 +0x1041
github.com/spf13/cobra.(*Command).execute(0x2316180, 0xc000160080, 0x4, 0x4, 0x2316180, 0xc000160080)
        /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:844 +0x2b1
github.com/spf13/cobra.(*Command).ExecuteC(0x2316c00, 0x456570, 0xc00008df48, 0xc00008df40)
        /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:945 +0x31e
github.com/spf13/cobra.(*Command).Execute(...)
        /home/prvst/go/pkg/mod/github.com/spf13/cobra@v0.0.6/command.go:885
philosopher/cmd.Execute()
        /workspace/philosopher/cmd/root.go:35 +0x34
main.main()
        /workspace/philosopher/main.go:25 +0x83

However, if I still use the parameter extension: pepXML, the error is as follows. But I can attain combined.pep.xml and combined.prot.xml.

INFO[20:44:51] Protein inference results                     decoy=186 target=6871
INFO[20:44:51] Converged to 1.02 % FDR with 2356 Proteins    decoy=24 threshold=0.9748 total=2380
2022/04/20 20:44:52 RemoveAll .: invalid argument

My philosopher.yml and closed_fragger.params are attached.
philosopher.yml
closed_fragger.params.txt

Best regards,
Bin

[prvst]

@Bin-cc the file extension change is only necessary if you run Comet because the extension is named differently from MSFragger.

[Bin-cc]

Hi,

How can I resolve the problem. I have used the annotated database, but I still encounter such problem. What should I do?
BTW, I use the same parameter file and database in FragPipe, and it runs successfully. And Philosopher can also run until last step (FDR Filtering).

INFO[20:44:51] Protein inference results                     decoy=186 target=6871
INFO[20:44:51] Converged to 1.02 % FDR with 2356 Proteins    decoy=24 threshold=0.9748 total=2380
2022/04/20 20:44:52 RemoveAll .: invalid argument

Best,
Bin

[prvst]

Are you using the pipeline?

[Bin-cc]

Hi,

Are there any solution to resolve this problem? I have no idea about this.

INFO[21:03:09] Protein inference results                     decoy=34 target=629
INFO[21:03:09] Converged to 1.09 % FDR with 458 Proteins     decoy=5 threshold=0.9765 total=463
2022/05/10 21:03:09 RemoveAll .: invalid argument

I used the latest version of Philosopher and MSFragger, and also followed the guidence in this with reviewd Uniprot database. But I still encounter the problem above. What do I need to do next? Thank you for your patience.

All the best,
Bin

[Bin-cc]

Yeach. I use the latest version of Philosopher and follow the guidance .yml as you advised. bin liao ***@***.*** 签名由 网易邮箱大师 定制 On 04/27/2022 21:44, Felipe da Veiga Leprevost wrote: Are you using the pipeline? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>