Pipeline fails when asked to create mzid output

[ohickl]

Hi,

I am running Philosopher using the pipeline command on some test metaproteomics data. It seems to run fine, but when I set mzID: true under Individual Reports: it fails with:

...
time="16:43:14" level=info msg="Creating reports"
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x70 pc=0x87c32a]

goroutine 1 [running]:
philosopher/lib/rep.Evidence.MzIdentMLReport({0x0, {{0x0, 0x0}, {0x0, 0x0}, {0x0, 0x0}, {0x0, 0x0}, {0x0, ...}, ...}, ...}, ...)
        /workspace/philosopher/lib/rep/mzid.go:909 +0x424a
philosopher/lib/rep.Run({{0xc00537ac60, 0x24}, {0xc0053704b0, 0x48}, {0xc00537ac90, 0x29}, {0xc015aae480, 0x57}, {0xc005370500, 0x4e}, ...})
        /workspace/philosopher/lib/rep/rep.go:534 +0x5b9
philosopher/lib/pip.Report({{0xc0151674d0, 0x24}, {0xc00a9d6460, 0x48}, {0xc015167500, 0x29}, {0xc000c7e120, 0x57}, {0xc00a9d64b0, 0x4e}, ...}, ...)
        /workspace/philosopher/lib/pip/pip.go:711 +0x299
philosopher/cmd.glob..func13(0x260f1e0?, {0xc0001abc00, 0x2, 0x4})
        /workspace/philosopher/cmd/pipeline.go:123 +0xad8
github.com/spf13/cobra.(*Command).execute(0x260f1e0, {0xc0001ab640, 0x4, 0x4})
        /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:920 +0x847
github.com/spf13/cobra.(*Command).ExecuteC(0x260f4c0)
        /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:1044 +0x3bd
github.com/spf13/cobra.(*Command).Execute(...)
        /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:968
philosopher/cmd.Execute()
        /workspace/philosopher/cmd/root.go:35 +0x25
main.main()
        /workspace/philosopher/main.go:25 +0x90

Also, when turning it off it fails at creating the integrated reports:

...
time="18:22:00" level=info msg="Creating reports"
time="18:22:12" level=info msg="Executing abacus"
time="18:22:12" level=info msg="Restoring PSM results"
time="18:22:24" level=error msg="unsupported number of labels"
panic: unsupported number of labels

goroutine 1 [running]:
philosopher/lib/msg.callLogrus({0xc0034e3680, 0x1c}, {0xb379d5, 0x1?})
        /workspace/philosopher/lib/msg/msg.go:319 +0x354
philosopher/lib/msg.Custom({0xca06c0?, 0xc00cdfc030?}, {0xb379d5, 0x5})
        /workspace/philosopher/lib/msg/msg.go:14 +0x6e
philosopher/lib/aba.savePSMAbacusResult({0xc017b2e030?, 0x41a026?}, {0x0, 0x0}, {0xc037c12000, 0x1f24e, 0x0?}, {0xc018e84a00, 0x2, 0x2}, ...)
        /workspace/philosopher/lib/aba/psm.go:147 +0xdc5
philosopher/lib/aba.psmLevelAbacus({{0xc017b2e000, 0x24}, {0xc0059e25a0, 0x48}, {0xc017b2e030, 0x29}, {0xc00a3461e0, 0x57}, {0xc0059e25f0, 0x4e}, ...}, ...)
        /workspace/philosopher/lib/aba/psm.go:111 +0x205
philosopher/lib/aba.Run({{0xc017b2e000, 0x24}, {0xc0059e25a0, 0x48}, {0xc017b2e030, 0x29}, {0xc00a3461e0, 0x57}, {0xc0059e25f0, 0x4e}, ...}, ...)
        /workspace/philosopher/lib/aba/aba.go:17 +0x5f
philosopher/lib/pip.Abacus({{0xc017b2e000, 0x24}, {0xc0059e25a0, 0x48}, {0xc017b2e030, 0x29}, {0xc00a3461e0, 0x57}, {0xc0059e25f0, 0x4e}, ...}, ...)
        /workspace/philosopher/lib/pip/pip.go:741 +0x1cc
philosopher/cmd.glob..func13(0x260f1e0?, {0xc00011fc00, 0x2, 0x4})
        /workspace/philosopher/cmd/pipeline.go:132 +0xc0c
github.com/spf13/cobra.(*Command).execute(0x260f1e0, {0xc00011f640, 0x4, 0x4})
        /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:920 +0x847
github.com/spf13/cobra.(*Command).ExecuteC(0x260f4c0)
        /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:1044 +0x3bd
github.com/spf13/cobra.(*Command).Execute(...)
        /home/prvst/go/pkg/mod/github.com/spf13/[email protected]/command.go:968
philosopher/cmd.Execute()
        /workspace/philosopher/cmd/root.go:35 +0x25
main.main()

Not sure, if I am setting some parameters wrong, it is because of the large data set and database, or an actual bug.
I attached the params and log.

Any guidance would be greatly appreciated.

On a side note, I would be interested in combining the results of open an closed searches, is there built-in functionality to allow this? I found #214, but it was not entirely clear to me if its fully supported:

IF you put all results from both searches in the same folder, they will be combined.

Does that means, it deals with multiple, possibly conflicting assignments for the same spectrum?

Best

Oskar
philosopher_config.txt
phil_pipeline_mzid_fail_shortened.txt
workspace.txt

[anesvi]

MzID functionality is no longer supported (I do not think it actually ever worked). Sorry about that. More importantly, we suggest you use our FragPipe pipeline, which also has an an option to run command line.Finally, running on big databases indeed can crash Philosopher (we are working on fixing it).

[prvst]

Hi @ohickl You can create mzID with Philosopher, but you need to be aware that there are different versions and depending on how you use the files, there might be some conflicts. We had recent changes to improve speed, and it looks like they are not covering the mzID report, I'll talk with my colleague about that.

Regarding the pipeline error, it seems you forgot to pass the plex parameter (which is basically the same as the TMT-kit used, i.e., tmt-10, tmt-11, ett. The plex attribute accepts a number).

[ohickl]

Ok, thanks for the input, running fragpipe now!