GNPSDocumentation Is the GNPS service down?

Hello! My data task has been running for nearly two hours and has not been completed. Is this a problem with the GNPS server? Before, the data results were obtained in more than 10 minutes.

Mar 04 '25 09:03 Yuan-666-lab

Yes...My dataset was still runing for a long time... Btw, I have some issues that I uploaded the dataset with failure showing "java.io.IOException: java.lang.RuntimeException: Could not execute requested link operation: /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML", but I have already convert the .d file to mzxml, so could you tell me how you made it? Thank you!

Mar 04 '25 14:03 Leyi-Xiao

https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/ Convert as in this link.

---- Replied Message ---- | From | @.> | | Date | 3/4/2025 22:40 | | To | @.> | | Cc | @.>, @.> | | Subject | Re: [CCMS-UCSD/GNPSDocumentation] Is the GNPS service down? (Issue #405) |

Yes...My dataset was still runing for a long time... Btw, I have some issues that I uploaded the dataset with failure showing "java.io.IOException: java.lang.RuntimeException: Could not execute requested link operation: /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML", but I have already convert the .d file to mzxml, so could you tell me how you made it? Thank you!

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Leyi-Xiao left a comment (CCMS-UCSD/GNPSDocumentation#405)

Yes...My dataset was still runing for a long time... Btw, I have some issues that I uploaded the dataset with failure showing "java.io.IOException: java.lang.RuntimeException: Could not execute requested link operation: /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML", but I have already convert the .d file to mzxml, so could you tell me how you made it? Thank you!

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

Mar 05 '25 01:03 Yuan-666-lab

I’m sorry I can’t read through this message

On Tue, Mar 4, 2025 at 5:27 PM Yuanyuan @.***> wrote:

https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/
Convert as in this link.

---- Replied Message ----
| From | @.> |
| Date | 3/4/2025 22:40 |
| To | @.> |
| Cc | @.>,
@.> |
| Subject | Re: [CCMS-UCSD/GNPSDocumentation] Is the GNPS service down? (Issue #405) |

Yes...My dataset was still runing for a long time... Btw, I have some issues that I uploaded the dataset with failure showing "java.io.IOException: java.lang.RuntimeException: Could not execute requested link operation: /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML", but I have already convert the .d file to mzxml, so could you tell me how you made it? Thank you!

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Leyi-Xiao left a comment (CCMS-UCSD/GNPSDocumentation#405)

Yes...My dataset was still runing for a long time... Btw, I have some issues that I uploaded the dataset with failure showing "java.io.IOException: java.lang.RuntimeException: Could not execute requested link operation: /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML", but I have already convert the .d file to mzxml, so could you tell me how you made it? Thank you!

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— Reply to this email directly, view it on GitHub https://github.com/CCMS-UCSD/GNPSDocumentation/issues/405#issuecomment-2699477399, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAXSEEEWS2OZ36H766FONL2SZHH5AVCNFSM6AAAAABYJAX2WOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOJZGQ3TOMZZHE . You are receiving this because you are subscribed to this thread.Message ID: @.> [image: Yuan-666-lab]Yuan-666-lab left a comment (CCMS-UCSD/GNPSDocumentation#405) https://github.com/CCMS-UCSD/GNPSDocumentation/issues/405#issuecomment-2699477399 https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/
Convert as in this link.

---- Replied Message ----
| From | @.> |
| Date | 3/4/2025 22:40 |
| To | @.> |
| Cc | @.>,
@.> |
| Subject | Re: [CCMS-UCSD/GNPSDocumentation] Is the GNPS service down? (Issue #405) |

Yes...My dataset was still runing for a long time... Btw, I have some issues that I uploaded the dataset with failure showing "java.io.IOException: java.lang.RuntimeException: Could not execute requested link operation: /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML", but I have already convert the .d file to mzxml, so could you tell me how you made it? Thank you!

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Leyi-Xiao left a comment (CCMS-UCSD/GNPSDocumentation#405)

Yes...My dataset was still runing for a long time... Btw, I have some issues that I uploaded the dataset with failure showing "java.io.IOException: java.lang.RuntimeException: Could not execute requested link operation: /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML", but I have already convert the .d file to mzxml, so could you tell me how you made it? Thank you!

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Mar 05 '25 02:03 mwang87

Hello! My data task has been running for nearly 20 hours and has not been completed. Is this a problem with the GNPS server? Before, the data results were obtained in more than 10 minutes. Looking forward to receiving your reply, thank you！

---- Replied Message ---- | From | Ming @.> | | Date | 3/5/2025 10:45 | | To | @.> | | Cc | @.>, @.> | | Subject | Re: [CCMS-UCSD/GNPSDocumentation] Is the GNPS service down? (Issue #405) | I’m sorry I can’t read through this message

On Tue, Mar 4, 2025 at 5:27 PM Yuanyuan @.> wrote:

> https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/ Convert
> as in this link. ---- Replied Message ---- | From |
> @.> | | Date | 3/4/2025 22:40 | | To | @.>
> | | Cc | @.>, @.> | | Subject | Re:
> [CCMS-UCSD/GNPSDocumentation] Is the GNPS service down? (Issue #405) | 
> Yes...My dataset was still runing for a long time... Btw, I have some
> issues that I uploaded the dataset with failure showing
> "java.io.IOException: java.lang.RuntimeException: Could not execute
> requested link operation:
> /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML",
> but I have already convert the .d file to mzxml, so could you tell me how
> you made it? Thank you! — Reply to this email directly, view
> it on GitHub, or unsubscribe. You are receiving this because you
> authored the thread.Message ID: @.> Leyi-Xiao left a
> comment (CCMS-UCSD/GNPSDocumentation#405) Yes...My dataset was
> still runing for a long time... Btw, I have some issues that I uploaded the
> dataset with failure showing "java.io.IOException:
> java.lang.RuntimeException: Could not execute requested link operation:
> /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML",
> but I have already convert the .d file to mzxml, so could you tell me how
> you made it? Thank you! — Reply to this email directly, view
> it on GitHub, or unsubscribe. You are receiving this because you
> authored the thread.Message ID: @.>
>
> —
> Reply to this email directly, view it on GitHub
> <https://github.com/CCMS-UCSD/GNPSDocumentation/issues/405#issuecomment-2699477399>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAAXSEEEWS2OZ36H766FONL2SZHH5AVCNFSM6AAAAABYJAX2WOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOJZGQ3TOMZZHE>
> .
> You are receiving this because you are subscribed to this thread.Message
> ID: @.>
> [image: Yuan-666-lab]Yuan-666-lab left a comment
> (CCMS-UCSD/GNPSDocumentation#405)
> <https://github.com/CCMS-UCSD/GNPSDocumentation/issues/405#issuecomment-2699477399>
> https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/ Convert
> as in this link. ---- Replied Message ---- | From |
> @.> | | Date | 3/4/2025 22:40 | | To | @.>
> | | Cc | @.>, @.> | | Subject | Re:
> [CCMS-UCSD/GNPSDocumentation] Is the GNPS service down? (Issue #405) | 
> Yes...My dataset was still runing for a long time... Btw, I have some
> issues that I uploaded the dataset with failure showing
> "java.io.IOException: java.lang.RuntimeException: Could not execute
> requested link operation:
> /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML",
> but I have already convert the .d file to mzxml, so could you tell me how
> you made it? Thank you! — Reply to this email directly, view
> it on GitHub, or unsubscribe. You are receiving this because you
> authored the thread.Message ID: @.> Leyi-Xiao left a
> comment (CCMS-UCSD/GNPSDocumentation#405) Yes...My dataset was
> still runing for a long time... Btw, I have some issues that I uploaded the
> dataset with failure showing "java.io.IOException:
> java.lang.RuntimeException: Could not execute requested link operation:
> /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML",
> but I have already convert the .d file to mzxml, so could you tell me how
> you made it? Thank you! — Reply to this email directly, view
> it on GitHub, or unsubscribe. You are receiving this because you
> authored the thread.Message ID: @.>
>
> —
> Reply to this email directly, view it on GitHub
> <https://github.com/CCMS-UCSD/GNPSDocumentation/issues/405#issuecomment-2699477399>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAAXSEEEWS2OZ36H766FONL2SZHH5AVCNFSM6AAAAABYJAX2WOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOJZGQ3TOMZZHE>
> .
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mwang87 left a comment (CCMS-UCSD/GNPSDocumentation#405) I’m sorry I can’t read through this message

On Tue, Mar 4, 2025 at 5:27 PM Yuanyuan @.> wrote:

> https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/ Convert
> as in this link. ---- Replied Message ---- | From |
> @.> | | Date | 3/4/2025 22:40 | | To | @.>
> | | Cc | @.>, @.> | | Subject | Re:
> [CCMS-UCSD/GNPSDocumentation] Is the GNPS service down? (Issue #405) | 
> Yes...My dataset was still runing for a long time... Btw, I have some
> issues that I uploaded the dataset with failure showing
> "java.io.IOException: java.lang.RuntimeException: Could not execute
> requested link operation:
> /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML",
> but I have already convert the .d file to mzxml, so could you tell me how
> you made it? Thank you! — Reply to this email directly, view
> it on GitHub, or unsubscribe. You are receiving this because you
> authored the thread.Message ID: @.> Leyi-Xiao left a
> comment (CCMS-UCSD/GNPSDocumentation#405) Yes...My dataset was
> still runing for a long time... Btw, I have some issues that I uploaded the
> dataset with failure showing "java.io.IOException:
> java.lang.RuntimeException: Could not execute requested link operation:
> /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML",
> but I have already convert the .d file to mzxml, so could you tell me how
> you made it? Thank you! — Reply to this email directly, view
> it on GitHub, or unsubscribe. You are receiving this because you
> authored the thread.Message ID: @.>
>
> —
> Reply to this email directly, view it on GitHub
> <https://github.com/CCMS-UCSD/GNPSDocumentation/issues/405#issuecomment-2699477399>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAAXSEEEWS2OZ36H766FONL2SZHH5AVCNFSM6AAAAABYJAX2WOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOJZGQ3TOMZZHE>
> .
> You are receiving this because you are subscribed to this thread.Message
> ID: @.>
> [image: Yuan-666-lab]Yuan-666-lab left a comment
> (CCMS-UCSD/GNPSDocumentation#405)
> <https://github.com/CCMS-UCSD/GNPSDocumentation/issues/405#issuecomment-2699477399>
> https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/ Convert
> as in this link. ---- Replied Message ---- | From |
> @.> | | Date | 3/4/2025 22:40 | | To | @.>
> | | Cc | @.>, @.> | | Subject | Re:
> [CCMS-UCSD/GNPSDocumentation] Is the GNPS service down? (Issue #405) | 
> Yes...My dataset was still runing for a long time... Btw, I have some
> issues that I uploaded the dataset with failure showing
> "java.io.IOException: java.lang.RuntimeException: Could not execute
> requested link operation:
> /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML",
> but I have already convert the .d file to mzxml, so could you tell me how
> you made it? Thank you! — Reply to this email directly, view
> it on GitHub, or unsubscribe. You are receiving this because you
> authored the thread.Message ID: @.> Leyi-Xiao left a
> comment (CCMS-UCSD/GNPSDocumentation#405) Yes...My dataset was
> still runing for a long time... Btw, I have some issues that I uploaded the
> dataset with failure showing "java.io.IOException:
> java.lang.RuntimeException: Could not execute requested link operation:
> /scratch/ccms-gnps/9439388747874618a4c5b475cadb35fc/filesummary/inputspectra/spec-00000.mzXML",
> but I have already convert the .d file to mzxml, so could you tell me how
> you made it? Thank you! — Reply to this email directly, view
> it on GitHub, or unsubscribe. You are receiving this because you
> authored the thread.Message ID: @.>
>
> —
> Reply to this email directly, view it on GitHub
> <https://github.com/CCMS-UCSD/GNPSDocumentation/issues/405#issuecomment-2699477399>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAAXSEEEWS2OZ36H766FONL2SZHH5AVCNFSM6AAAAABYJAX2WOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMOJZGQ3TOMZZHE>
> .
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Mar 05 '25 02:03 Yuan-666-lab

Yes.... I think so, my jobs are still runing from yesterday...

Mar 05 '25 16:03 Leyi-Xiao

@Yuan-666-lab @Leyi-Xiao Thanks for letting us know about this. If possible, please send an email to [email protected] about this problem, along with links to your stalled jobs. Screenshots are helpful, but links are better since that allows me to troubleshoot your specific jobs more easily.

@Leyi-Xiao The "Could not execute requested link operation" error was caused by a server issue that has been resolved. I apologize for this inconvenience. You should not be seeing this any more, so please let me know if you continue to see job failures like this.

Mar 05 '25 17:03 jjcarver