Analysis in platforma

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1

Hi, I am very familiar with MIXCR/4.7.0 and successfully analyzed my data and produced the clonotypes and some downstream analysis. However, i recently downloaded platforma for lineage tree analysis and built 2 blocks: samples and data, Mixcr-clonotyping, after loading my samples i wanted to run the built in preset, but I do not have built in present and the browser is browsing.
I want to run platforma for lineage tree analysis and mutational frequencies of replacement and silent mutation.

I am processing Bulk BCR seq fastq files R1 and R2 pared end reads, i want to assemble the clonotype by FR1 begin-FR4End, species is human
Also, i received 2 errors:
QuickJSUnwrapError: error in field presets of NG:0x5143: {“errorType”:“”,“message”:“"NG:0x5168" has 1 input errors:\n[I] "NG:0x5168/blob": "NG:0x5167" has 1 input errors:\n[I] "NG:0x5167/resource": "NG:0x517F" has 1 input errors:\n[I] "NG:0x517F/resource": "NG:0x517C" has 1 input errors:\n[I] "NG:0x517C/inputs": "NG:0x517D" has 1 input errors:\n[I] "NG:0x517D/workdir": working directory: "workdirs\\0x5198"\nfailed to run command: "java" exited with code 22.\nHere is the latest command output:\n\tLicense error: ConnectionError\r\n\tLicense manager thread died.\r\n”}
at resolveWithCommon (bundle.js:4121)
at resolve (bundle.js:4091)
at (bundle.js:5204)
at (bundle.js)
Host: Error: error in field presets of NG:0x5143: {“errorType”:“”,“message”:“"NG:0x5168" has 1 input errors:\n[I] "NG:0x5168/blob": "NG:0x5167" has 1 input errors:\n[I] "NG:0x5167/resource": "NG:0x517F" has 1 input errors:\n[I] "NG:0x517F/resource": "NG:0x517C" has 1 input errors:\n[I] "NG:0x517C/inputs": "NG:0x517D" has 1 input errors:\n[I] "NG:0x517D/workdir": working directory: "workdirs\\0x5198"\nfailed to run command: "java" exited with code 22.\nHere is the latest command output:\n\tLicense error: ConnectionError\r\n\tLicense manager thread died.\r\n”}
at QuickJSContext.unwrapResult (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/quickjs-emscripten-core/dist/chunk-JTKJZQYV.mjs:4:24443)
at file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:2488:19
at _Scope.withScope (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/quickjs-emscripten-core/dist/chunk-JTKJZQYV.mjs:4:402)
at Ze.runCallback (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:2483:17)
at Object.kernel (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:2964:17)
at L (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:366:17)
at S (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:441:13)
at I (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:387:14)
at S (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:441:41)
at I (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:387:14) {
cause: {
name: ‘Error’,
message: ‘error in field presets of NG:0x5143: {“errorType”:“”,“message”:“\“NG:0x5168\” has 1 input errors:\n[I] \“NG:0x5168/blob\”: \“NG:0x5167\” has 1 input errors:\n[I] \“NG:0x5167/resource\”: \“NG:0x517F\” has 1 input errors:\n[I] \“NG:0x517F/resource\”: \“NG:0x517C\” has 1 input errors:\n[I] \“NG:0x517C/inputs\”: \“NG:0x517D\” has 1 input errors:\n[I] \“NG:0x517D/workdir\”: working directory: \“workdirs\\\\0x5198\”\nfailed to run command: \“java\” exited with code 22.\nHere is the latest command output:\n\tLicense error: ConnectionError\r\n\tLicense manager thread died.\r\n”}’,
stack: ’ at resolveWithCommon (bundle.js:4121)\n’ +
’ at resolve (bundle.js:4091)\n’ +
’ at (bundle.js:5204)\n’ +
’ at (bundle.js)\n’
}
}

2

Hi,
Do you have UMIs or other barcodes in your library structure?

3

Hi Mark,
No, we do not have barcodes/UMIs in our library structure. We separate the cloen by cloneID based on the distinguished clonotype. In mixcr I analyzed the data wih generic amplicon.
Thank you
Divya

Cleveland Clinic is a nonprofit, multispecialty academic medical center that’s recognized in the U.S. and throughout the world for its expertise and care. Visit us online at for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

4

First, regarding the error you encountered, I have a few questions to better understand your setup:

  1. Which OS do you use for the App? (Windows/MacOS/Linux)
  2. Did you install a backend for Platforma on a server?
  3. How do you connect to the backend if you have one?
  4. Do you have any network restrictions on the machine running the app and the backend (if applicable)?

Could you check that the backend has access to the following endpoints?

This is in addition to the licensing IPs that should also be allowed:

75.2.96.100
99.83.215.63
2600:9000:a403:55e8:f9c1:f443:773b:4192
2600:9000:a51b:2483:639d:d5a9:270f:643

Also can you share a screenshot and the description of what you do when you get this error?

5

Hi Mark,
Yes, sure.

  1. System type: 64-bit operating system, x64-based processor,
    Edition Windows 11 Enterprise

  2. Version 23H2

  3. Installed on ‎10/‎1/‎2024

  4. OS build 22631.4890

  5. Experience Windows Feature Experience Pack 1000.22700.1067.0

I installed Platforma on my local Windows machine in the following location:

C:\Users\singhd6\AppData\Local\Programs\platforma\Platforma.exe
C:\Users\singhd6\Platforma\local\packages\installed\platforma-open\platforma-open\milaboratories.runenv-java-corretto\21.0.2.13.1\21.0.2.13.1-windows-x64.0x4636

Platforma is running on my local machine rather than on a server. The backend seems to be bundled with the software, as indicated by the directory path milaboratories.runenv-java-corretto, which is a Java runtime environment, and I think this would typically be local to the installation.

No, I did not install the backend on a separate server; it is running locally on my machine.

I am receiving the error at this step:

image.png1476×750 74.3 KB

Thank you
Divya
Cleveland Clinic is a nonprofit, multispecialty academic medical center that’s recognized in the U.S. and throughout the world for its expertise and care. Visit us online at for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

6

Do you have any network restrictions?

7

Yes.

Cleveland Clinic is a nonprofit, multispecialty academic medical center that’s recognized in the U.S. and throughout the world for its expertise and care. Visit us online at for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

8

From the error it looks like MiXCR inside the Platforma does not have an access to the licensing servers. The follwoing IPs should be allowed:
This is in addition to the licensing IPs that should also be allowed:

75.2.96.100
99.83.215.63
2600:9000:a403:55e8:f9c1:f443:773b:4192
2600:9000:a51b:2483:639d:d5a9:270f:643

I know you used MiXCR before, did you ever try to run MiXCR from the same machine (directly without connection to a remote server), did it work?

9

Hi Mark,
I am working at Cleveland Clinic, and most of our computers are Firewall secured, and admins regulate the activities of machines, so it could be possible my machine is also Firewall secured. However, I never used MIXCR on my local machine.

I will request my admin to allow all these IPs for Platforma.
Thank you
Divya
Cleveland Clinic is a nonprofit, multispecialty academic medical center that’s recognized in the U.S. and throughout the world for its expertise and care. Visit us online at for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

10

license error:
License error: ConnectionError
License manager thread died

PlErrorReport: resource: std/map:1, NG:0x5143

PlRunnerError:
command: java
exit code: 22
working directory: workdirs\0x5198
stdout:
License error: ConnectionError
License manager thread died.

full message:
“NG:0x5143” has 1 input errors:
[I] “NG:0x5143/presets”: “NG:0x5168” has 1 input errors:
[I] “NG:0x5168/blob”: “NG:0x5167” has 1 input errors:
[I] “NG:0x5167/resource”: “NG:0x517F” has 1 input errors:
[I] “NG:0x517F/resource”: “NG:0x517C” has 1 input errors:
[I] “NG:0x517C/inputs”: “NG:0x517D” has 1 input errors:
[I] “NG:0x517D/workdir”: working directory: “workdirs\0x5198”
failed to run command: “java” exited with code 22.
Here is the latest command output:
License error: ConnectionError
License manager thread died.

full error:
PlErrorReport: PlErrorReport: resource: std/map:1, NG:0x5143

PlRunnerError:
command: java
exit code: 22
working directory: workdirs\0x5198
stdout:
License error: ConnectionError
License manager thread died.

full message:
“NG:0x5143” has 1 input errors:
[I] “NG:0x5143/presets”: “NG:0x5168” has 1 input errors:
[I] “NG:0x5168/blob”: “NG:0x5167” has 1 input errors:
[I] “NG:0x5167/resource”: “NG:0x517F” has 1 input errors:
[I] “NG:0x517F/resource”: “NG:0x517C” has 1 input errors:
[I] “NG:0x517C/inputs”: “NG:0x517D” has 1 input errors:
[I] “NG:0x517D/workdir”: working directory: “workdirs\0x5198”
failed to run command: “java” exited with code 22.
Here is the latest command output:
License error: ConnectionError
License manager thread died.

at N (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-errors/dist/index.mjs:86:10)
at N (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-tree/dist/index.mjs:55:13)
at E.node (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-tree/dist/index.mjs:70:138)
at Object.operation (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:1923:34)
at yr (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:2338:32)
at Ss.J.makeRaw [as ___kernel___] (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:2394:13)
at L (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:366:17)
at S (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:441:13)
at I (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:387:14)
at S (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:441:41) {

fullMessage: ‘{“errorType”:“”,“message”:“\“NG:0x5143\” has 1 input errors:\n[I] \“NG:0x5143/presets\”: \“NG:0x5168\” has 1 input errors:\n[I] \“NG:0x5168/blob\”: \“NG:0x5167\” has 1 input errors:\n[I] \“NG:0x5167/resource\”: \“NG:0x517F\” has 1 input errors:\n[I] \“NG:0x517F/resource\”: \“NG:0x517C\” has 1 input errors:\n[I] \“NG:0x517C/inputs\”: \“NG:0x517D\” has 1 input errors:\n[I] \“NG:0x517D/workdir\”: working directory: \“workdirs\\\\0x5198\”\nfailed to run command: \“java\” exited with code 22.\nHere is the latest command output:\n\tLicense error: ConnectionError\r\n\tLicense manager thread died.\r\n”}’,
plErrorType: ‘’,
plMessage: ‘“NG:0x5143” has 1 input errors:\n’ +
‘[I] “NG:0x5143/presets”: “NG:0x5168” has 1 input errors:\n’ +
‘[I] “NG:0x5168/blob”: “NG:0x5167” has 1 input errors:\n’ +
‘[I] “NG:0x5167/resource”: “NG:0x517F” has 1 input errors:\n’ +
‘[I] “NG:0x517F/resource”: “NG:0x517C” has 1 input errors:\n’ +
‘[I] “NG:0x517C/inputs”: “NG:0x517D” has 1 input errors:\n’ +
‘[I] “NG:0x517D/workdir”: working directory: “workdirs\\0x5198”\n’ +
‘failed to run command: “java” exited with code 22.\n’ +
‘Here is the latest command output:\n’ +
‘\tLicense error: ConnectionError\r\n’ +
‘\tLicense manager thread died.\r\n’,
errors: [
g [PlRunnerError]: PlRunnerError:
command: java
exit code: 22
working directory: workdirs\0x5198
stdout:
License error: ConnectionError
License manager thread died.

full message:
"NG:0x5143" has 1 input errors:
[I] "NG:0x5143/presets": "NG:0x5168" has 1 input errors:
[I] "NG:0x5168/blob": "NG:0x5167" has 1 input errors:
[I] "NG:0x5167/resource": "NG:0x517F" has 1 input errors:
[I] "NG:0x517F/resource": "NG:0x517C" has 1 input errors:
[I] "NG:0x517C/inputs": "NG:0x517D" has 1 input errors:
[I] "NG:0x517D/workdir": working directory: "workdirs\\0x5198"
failed to run command: "java" exited with code 22.
Here is the latest command output:
	License error: ConnectionError
	License manager thread died.

    at m (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-errors/dist/index.mjs:130:72)
    at T (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-errors/dist/index.mjs:118:24)
    at N (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-errors/dist/index.mjs:85:41)
    at N (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-tree/dist/index.mjs:55:13)
    at E.node (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-tree/dist/index.mjs:70:138)
    at Object.operation (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:1923:34)
    at yr (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:2338:32)
    at Ss.J.makeRaw [as ___kernel___] (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/pl-middle-layer/dist/index.mjs:2394:13)
    at L (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:366:17)
    at S (file:///C:/Users/singhd6/AppData/Local/Programs/platforma/resources/app.asar/node_modules/@milaboratories/computable/dist/index.mjs:441:13) {
  fullMessage: '"NG:0x5143" has 1 input errors:\n' +
    '[I] "NG:0x5143/presets": "NG:0x5168" has 1 input errors:\n' +
    '[I] "NG:0x5168/blob": "NG:0x5167" has 1 input errors:\n' +
    '[I] "NG:0x5167/resource": "NG:0x517F" has 1 input errors:\n' +
    '[I] "NG:0x517F/resource": "NG:0x517C" has 1 input errors:\n' +
    '[I] "NG:0x517C/inputs": "NG:0x517D" has 1 input errors:\n' +
    '[I] "NG:0x517D/workdir": working directory: "workdirs\\\\0x5198"\n' +
    'failed to run command: "java" exited with code 22.\n' +
    'Here is the latest command output:\n' +
    '\tLicense error: ConnectionError\r\n' +
    '\tLicense manager thread died.\r\n',
  commandName: 'java',
  exitCode: 22,
  stdout: 'License error: ConnectionError\r\n\tLicense manager thread died.',
  workingDirectory: 'workdirs\\\\0x5198'
}

],
fieldName: undefined,
resource: 20803n,
resourceType: Object <[Object: null prototype] {}> {
name: ‘std/map’,
version: ‘1’
}
}

11

Hi,
Did you whitelist the IPs mentioned above?