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Illumina / Pisces

Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
GNU General Public License v3.0
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GeminiMulti_5.2.11.163 crashes #45

Open hansenaw opened 5 years ago

hansenaw commented 5 years ago

I have pre-filtered a BAM file (with samtools view) to only include a region surrounding one gene on Chr2.

Running GeminiMulti (I could use Gemini, but trying to get the multi wrapper to work for another project...).

Script used to run GeminiMulti:

[dotnet/2.0.3/runtime/dotnet] /stornext/snfs4/gibbs/awhansen/software/illumina/pisces/GeminiMulti/GeminiMulti.dll -bam [bam_file] -genome [genome_folder] -exePath [gemini_path]/Gemini.dll -samtools [samtools] -outFolder [output] -numProcesses 10 
8/27/19 2:41 PM 1  WARNING:   Processing failed for Gemini_2. See error log for details.
8/27/19 2:41 PM 1  WARNING:   Processing failed for Gemini_5. See error log for details.

ERROR: Application failed: 2 tasks failed.

Stack trace:
   at GeminiMulti.GeminiMultiProcessor.ExecuteChromosomeJobs(ICliTaskManager cliTaskManager, Dictionary`2 chromRefIds, List`1 cmdLineList, String outMultiPath, String taskLogDir, String exePath, List`1 taskDirectories) in C:\Users\gberry\Downloads\Pisces5-release-Pisces_5_2_11_open\Pisces5-release-Pisces_5_2_11_open\src\exe\GeminiMulti\GeminiMultiProcessor.cs:line 228
   at GeminiMulti.GeminiMultiProcessor.Execute(ICliTaskManager cliTaskManager, Dictionary`2 chromRefIds, List`1 cmdLineList, ISamtoolsWrapper samtoolsWrapper) in C:\Users\gberry\Downloads\Pisces5-release-Pisces_5_2_11_open\Pisces5-release-Pisces_5_2_11_open\src\exe\GeminiMulti\GeminiMultiProcessor.cs:line 44
   at GeminiMulti.Program.ProgramExecution() in C:\Users\gberry\Downloads\Pisces5-release-Pisces_5_2_11_open\Pisces5-release-Pisces_5_2_11_open\src\exe\GeminiMulti\Program.cs:line 66
   at CommandLine.Application.BaseApplication`1.Execute() in C:\Users\gberry\Downloads\Pisces5-release-Pisces_5_2_11_open\Pisces5-release-Pisces_5_2_11_open\src\lib\CommandLine.Options\BaseApplication.cs:line 131

the output/2/ folder contains: 

GeminiLogs                                                                 out.bam_23_2_All_All_23_2_All_All_10000001_5_2_c3b9158b-76f3-4c50-869a-db599dd3f6d7
out.bam_0_2_All_All_0_2_All_All_7_7_0_95848a21-2708-4bd1-8a3a-7677e0e3df4d  out.bam_24_2_All_All_24_2_All_All_10000001_5_1_5354677c-73f1-451b-a0d7-f823b0cc7d5c

the output/5/ folder contains: GeminiLogs

hansenaw commented 5 years ago

I'll add that I'm not getting this issue at all with GeminiMulti_5.2.10.49