NettyChannelProvider not found

[jayieh]

Hi,

I'd like to run CrystalC on MSFragger open search data on a CentOS 7 system, which unfortunately fails.

This is the command executed and the error I get:

java -Dbatmass.io.libs.thermo.dir=/home/j/jeirich/MSFragger-3.2/ext/thermo -Xmx175G -cp /home/j/jeirich/CrystalC/CrystalC-1.3.2.jar crystalc.Run /home/j/jeirich/CrystalC/CrystalC.params my.pepXML Exception in thread "main" java.util.ServiceConfigurationError: io.grpc.ManagedChannelProvider: Provider io.grpc.netty.shaded.io.grpc.netty.NettyChannelProvider not found at java.util.ServiceLoader.fail(ServiceLoader.java:239) at java.util.ServiceLoader.access$300(ServiceLoader.java:185) at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:372) at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404) at java.util.ServiceLoader$1.next(ServiceLoader.java:480) at io.grpc.ServiceProviders.loadAll(ServiceProviders.java:67) at io.grpc.ServiceProviders.load(ServiceProviders.java:42) at io.grpc.ManagedChannelProvider.<clinit>(ManagedChannelProvider.java:37) at io.grpc.ManagedChannelBuilder.forAddress(ManagedChannelBuilder.java:39) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.init(ThermoRawFile.java:214) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.<init>(ThermoRawFile.java:161) at crystalc.p_ReadData.LoadRawFile(p_ReadData.java:166) at crystalc.Run.ProcessPepXML(Run.java:70) at crystalc.Run.main(Run.java:51) I am using

openjdk version "1.8.0_272" OpenJDK Runtime Environment (build 1.8.0_272-b10) OpenJDK 64-Bit Server VM (build 25.272-b10, mixed mode)

Do you have any advice or is there more information I should provide?

Best

Jürgen

[huiyinc]

Hi Jürgen,

Can you please send me your parameter, pepXML and mzML files so I can take a look of it? Thanks.

Huiyin

jayieh @.***> 於 2021年5月3日 下午5:50 寫道：  Hi,

I'd like to run CrystalC on MSFragger open search data on a CentOS 7 system, which unfortunately fails.

This is the command executed and the error I get:

java -Dbatmass.io.libs.thermo.dir=/home/j/jeirich/MSFragger-3.2/ext/thermo -Xmx175G -cp /home/j/jeirich/CrystalC/CrystalC-1.3.2.jar crystalc.Run /home/j/jeirich/CrystalC/CrystalC.params my.pepXML Exception in thread "main" java.util.ServiceConfigurationError: io.grpc.ManagedChannelProvider: Provider io.grpc.netty.shaded.io.grpc.netty.NettyChannelProvider not found at java.util.ServiceLoader.fail(ServiceLoader.java:239) at java.util.ServiceLoader.access$300(ServiceLoader.java:185) at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:372) at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404) at java.util.ServiceLoader$1.next(ServiceLoader.java:480) at io.grpc.ServiceProviders.loadAll(ServiceProviders.java:67) at io.grpc.ServiceProviders.load(ServiceProviders.java:42) at io.grpc.ManagedChannelProvider.(ManagedChannelProvider.java:37) at io.grpc.ManagedChannelBuilder.forAddress(ManagedChannelBuilder.java:39) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.init(ThermoRawFile.java:214) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.(ThermoRawFile.java:161) at crystalc.p_ReadData.LoadRawFile(p_ReadData.java:166) at crystalc.Run.ProcessPepXML(Run.java:70) at crystalc.Run.main(Run.java:51) I am using

openjdk version "1.8.0_272" OpenJDK Runtime Environment (build 1.8.0_272-b10) OpenJDK 64-Bit Server VM (build 25.272-b10, mixed mode)

Do you have any advice or is there more information I should provide?

Best

Jürgen

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[jayieh]

Hi Huiyin,

thank you so much for the instant reply!

You will find the requested files here:

https://uni-muenster.sciebo.de/s/OFXdO12LPKpfvQs

the link is only valid until may 5th... Let me know if you have not found the time until then and I can re-new the share.

This is just one pair of pepXML and raw (not mzML) - let me know if you need additional files from the dataset!

Best

Jürgen

[huiyinc]

Hi Jürgen,

Can you please also give me your fasta file? I have read the issue you report in MSFragger repo, and wondering if this Crystal-C issue is the same as the MSFragger issue (i.e., both fail when parsing the raw file). I will double check it after having the fasta file. Thanks!

Huiyin

jayieh @.***> 於 2021年5月3日 週一 下午9:04寫道：

Hi Huiyin,

thank you so much for the instant reply!

You will find the requested files here:

https://uni-muenster.sciebo.de/s/OFXdO12LPKpfvQs

the link is only valid until may 5th... Let me know if you have not found the time until then and I can re-new the share.

This is just set of pepXML and raw (not mzML) - let me know if you need additonal files from the dataset!

Best

Jürgen

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/Crystal-C/issues/5#issuecomment-831245693, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA5SKNUCKMGIODDFNX3TL2NOLANCNFSM44AQNWLA .

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[jayieh]

Hi Huiyin,

thanks again for looking into this!

I had a similar suspicion when troubleshooting the MSFragger issue with the help of Fengchao. I excluded the empty raw file from the analysis and the Crystal-C issue persists.

The raw file I uploaded contains MS2 spectra and PSMs can be identified from it.

You will find the fasta and also the MSFragger params under the same link as the other files!

[huiyinc]

Hi Jürgen,

Thanks for the prompt reply. I will check it and get back to you as soon as I can.

Best wishes,

Huiyin

jayieh @.***> 於 2021年5月4日 週二 下午2:37寫道：

Hi Huiyin,

thanks again for looking into this!

I had a similar suspicion when troubleshooting the MSFragger issue with the help of Fengchao. I excluded the empty raw file from the analysis and the Crystal-C issue persists.

The raw file I uploaded contains MS2 spectra and PSMs can be identified from it.

You will find the fasta and also the MSFragger params under the same link as the other files!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/Crystal-C/issues/5#issuecomment-831715059, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA6R2IMYNIWKVKARDMLTL6I3VANCNFSM44AQNWLA .

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[huiyinc]

Hi Jürgen,

We figure it out: It's because you need to manually include the Thermo raw library to parse raw files if you use command lines. Here is the command of Crystal-C for Thermo raw files: java -Dbatmass.io.libs.thermo.dir="D:\MSFragger-3.0\ext\thermo (please find the file path in your computer)" -Xmx53G -cp "CrystalC-1.2.1.jar" crystalc.Run crystalc.params *.pepXML

You may also use the dry run option in FragPipe to get the complete commands. Please feel free to let me know if this solves your problem. Thanks!

Huiyin

Chang Hui-Yin @.***> 於 2021年5月4日 週二 下午2:41寫道：

Hi Jürgen,

Thanks for the prompt reply. I will check it and get back to you as soon as I can.

Best wishes,

Huiyin

jayieh @.***> 於 2021年5月4日 週二 下午2:37寫道：

Hi Huiyin,

thanks again for looking into this!

I had a similar suspicion when troubleshooting the MSFragger issue with the help of Fengchao. I excluded the empty raw file from the analysis and the Crystal-C issue persists.

The raw file I uploaded contains MS2 spectra and PSMs can be identified from it.

You will find the fasta and also the MSFragger params under the same link as the other files!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/Crystal-C/issues/5#issuecomment-831715059, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA6R2IMYNIWKVKARDMLTL6I3VANCNFSM44AQNWLA .

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[jayieh]

hi,

Thanks for the replay, but this is what I was actually trying to do. This is the command I am running as part of a shell script - including the thermo library path, as pointed out in the CrystalC how-to:

java -Dbatmass.io.libs.thermo.dir=/home/j/jeirich/MSFragger-3.2/ext/thermo -Xmx175G -cp /home/j/jeirich/CrystalC/CrystalC-1.3.2.jar crystalc.Run /home/j/jeirich/CrystalC/CrystalC.params my.pepXML

I also excluded mono as a problem: as a first step, I am loading mono, running MSFragger (on the raw files) and then the CrystalC command. When NOT loading mono, I get an extra error...

Do I need to specify the path in a different way, as I am running on linux, maybe?

[huiyinc]

Hi,

Have you tried running Crystal-C in FragPipe? Do you still get the same error if using FragPipe? Thanks!

Huiyin

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jayieh @.***> 於 2021年5月4日 下午8:16 寫道：

 hi,

Thanks for the replay, but this is what I was actually trying to do. This is the command I am running as part of a shell script - including the thermo library path, as pointed out in the CrystalC how-to:

java -Dbatmass.io.libs.thermo.dir=/home/j/jeirich/MSFragger-3.2/ext/thermo -Xmx175G -cp /home/j/jeirich/CrystalC/CrystalC-1.3.2.jar crystalc.Run /home/j/jeirich/CrystalC/CrystalC.params my.pepXML

I also excluded mono as a problem: as a first step, I am loading mono, running MSFragger (on the raw files) and then the CrystalC command. When NOT loading mono, I get an extra error...

Do I need to specify the path in a different way, as I am running on linux, maybe?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

[jayieh]

I am not able to run FragPipe on that machine to the full extend. It's a HPC system and I can not run programs with X on the compute nodes. I need to submit jobs as scripts...

I did however do a dry run on the head node and saw, that the command in FragPipe contains more jar files after the -cp command, seperated by :

java -Dbatmass.io.libs.thermo.dir=/home/j/jeirich/MSFragger-3.2/ext/thermo -Xmx57G -cp /home/j/jeirich/fragpipe_15/tools/original-crystalc-1.3.2.jar:/home/j/jeirich/fragpipe_15/tools/batmass-io-1.22.1.jar:/home/j/jeirich/fragpipe_15/tools/grppr-0.3.23.jar crystalc.Run /home/j/jeirich/CrystalC/CrystalC.params /home/j/jeirich/rawfiles_on_scratch/MGA143/210409_C20_008_QHF1_TMTRev10#21_012_MGA144.pepXML

This was the key - CrystalC is running now :) Your hint with the dry run of FragPipe was essential!

Thank you guys so much for all the help and effort!