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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
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A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'. #78

Closed Manuel-DominguezCBG closed 4 months ago

Manuel-DominguezCBG commented 4 months ago

I am trying to run Gemini


.dotnet/dotnet  /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/GeminiMulti.dll \
                                    -bam /home/dominm/install_dotnet/150REVERSE_fastq_.bam   \
                                    --exePath /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll \
                                    -genome  /home/dominm/references_files \
                                    -samtools  /home/dominm/install_dotnet/samtools-1.19.2/samtools \
                                    --outFolder ./results \
                                    --numProcesses  5 \

in a Linux machine (Linux 3.10.0-1160.108.1.el7.x86_64 x86_64 - CentOS Linux)

We installed dotnet Version: 2.1.818

and we are not able to make run Gemini (GeminiMulti).

This is the error message we get

(base) [dominm@bioinf-2u install_dotnet]$ ./run_multigemini.sh
---------------------------------------------------------------------------
GeminiMulti                                     Copyright (c) Illumina 2019
https://github.com/Illumina/Pisces                                5.2.10.49
---------------------------------------------------------------------------

19/02/2024 16:27 1  ************* Starting **************
19/02/2024 16:27 1  Version:  5.2.10.49.
19/02/2024 16:27 1  Command-line arguments: .
19/02/2024 16:27 1  "-bam /home/dominm/install_dotnet/150REVERSE_fastq_.bam --exePath /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll -genome /home/dominm/references_files -samtools /home/dominm/install_dotnet/samtools-1.19.2/samtools --outFolder ./results --numProcesses 5".
19/02/2024 16:27 3  PROCESS Gemini_chr1: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "0" --outFolder "./results/chr1"'.
19/02/2024 16:27 8  PROCESS Gemini_chr4: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "3" --outFolder "./results/chr4"'.
19/02/2024 16:27 5  PROCESS Gemini_chr3: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "2" --outFolder "./results/chr3"'.
19/02/2024 16:27 6  PROCESS Gemini_chr5: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "4" --outFolder "./results/chr5"'.
19/02/2024 16:27 4  PROCESS Gemini_chr2: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "1" --outFolder "./results/chr2"'.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
19/02/2024 16:27 6  PROCESS Gemini_chr5: ExitCode: 131.
19/02/2024 16:27 4  PROCESS Gemini_chr2: ExitCode: 131.
19/02/2024 16:27 4  PROCESS Gemini_chr7: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "6" --outFolder "./results/chr7"'.
19/02/2024 16:27 3  PROCESS Gemini_chr1: ExitCode: 131.
19/02/2024 16:27 8  PROCESS Gemini_chr4: ExitCode: 131.
19/02/2024 16:27 6  PROCESS Gemini_chr6: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "5" --outFolder "./results/chr6"'.
19/02/2024 16:27 5  PROCESS Gemini_chr3: ExitCode: 131.
19/02/2024 16:27 3  PROCESS Gemini_chr8: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "7" --outFolder "./results/chr8"'.
19/02/2024 16:27 8  PROCESS Gemini_chr9: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "8" --outFolder "./results/chr9"'.
19/02/2024 16:27 5  PROCESS Gemini_chr10: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "9" --outFolder "./results/chr10"'.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
19/02/2024 16:27 4  PROCESS Gemini_chr7: ExitCode: 131.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
19/02/2024 16:27 6  PROCESS Gemini_chr6: ExitCode: 131.
19/02/2024 16:27 4  PROCESS Gemini_chr11: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "10" --outFolder "./results/chr11"'.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
19/02/2024 16:27 6  PROCESS Gemini_chr12: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "11" --outFolder "./results/chr12"'.
19/02/2024 16:27 3  PROCESS Gemini_chr8: ExitCode: 131.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
19/02/2024 16:27 3  PROCESS Gemini_chr13: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "12" --outFolder "./results/chr13"'.
19/02/2024 16:27 8  PROCESS Gemini_chr9: ExitCode: 131.
19/02/2024 16:27 8  PROCESS Gemini_chr14: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "13" --outFolder "./results/chr14"'.
19/02/2024 16:27 5  PROCESS Gemini_chr10: ExitCode: 131.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
19/02/2024 16:27 5  PROCESS Gemini_chr15: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "14" --outFolder "./results/chr15"'.
19/02/2024 16:27 6  PROCESS Gemini_chr12: ExitCode: 131.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.
19/02/2024 16:27 4  PROCESS Gemini_chr11: ExitCode: 131.
19/02/2024 16:27 6  PROCESS Gemini_chr16: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "15" --outFolder "./results/chr16"'.
19/02/2024 16:27 4  PROCESS Gemini_chr17: Executing 'dotnet' with '"/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.dll" -bam "/home/dominm/install_dotnet/150REVERSE_fastq_.bam" -genome "/home/dominm/references_files" -samtools "/home/dominm/install_dotnet/samtools-1.19.2/samtools" --chromRefId "16" --outFolder "./results/chr17"'.
A fatal error was encountered. The library 'libhostpolicy.so' required to execute the application was not found in '/home/dominm/install_dotnet/GeminiMulti_5.2.10.49/'.
Failed to run as a self-contained app. If this should be a framework-dependent app, add the /home/dominm/install_dotnet/GeminiMulti_5.2.10.49/Gemini.runtimeconfig.json file specifying the appropriate framework.

We also tried to make this work in an HPC computer (NAME="Red Hat Enterprise Linux Server" VERSION="7.9 (Maipo)", Linux 3.10.0-1160.36.2.el7.x86_64 x86_64. And we got the same error.

On both computers, we install the same way, we download https://github.com/Illumina/Pisces/releases/download/v5.2.10.49/GeminiMulti_5.2.10.49.tar.gz, we uncompress and we run the code shown above.

are we doing something wring?

Thank

Manuel-DominguezCBG commented 4 months ago

With your last version (5.3.0.0) this problem is solved.