Gemini 5.3.0.0 Nullable object Error

[ShannonDaddy]

Hi

I got the Nullable object Error when I was using Gemini in Pisces 5.3.0.0, and I can't figure out why, please help me.

1/20/21 12:01 PM 1 * Starting ** 1/20/21 12:01 PM 1 Version: 5.3.0.0. 1/20/21 12:01 PM 1 Command-line arguments: . 1/20/21 12:01 PM 1 "--bam C2004235.flt.trim.bam --genome genome_db/hsa/Genome/ucsc/090520_hg19/SplitGenome/ --samtools samtools-1.9/samtools --outfolder Output/C2004235". 1/20/21 12:01 PM 1 Exception reported:
System.InvalidOperationException: Nullable object must have a value. at System.Nullable1.get_Value() at Gemini.BlockFactorySource.GetBlockProvider(Dictionary2 refIdMapping, String chrom, IWriterSource writerSource, ConcurrentDictionary2 progressTracker, ConcurrentDictionary2 categoryLookup, ConcurrentDic tionary2 masterIndelLookup, ConcurrentDictionary2 masterOutcomesLookup, ConcurrentDictionary2 masterFinalIndels, ChrReference chrReference) at Gemini.DataflowReadEvaluator.ProcessBam() at Gemini.GeminiWorkflow.Execute() at Gemini.Program.ProgramExecution() at CommandLine.Application.BaseApplication1.Execute(). 1/20/21 12:01 PM 1 **** Ending *****

The log file and input bam file are attached.

Thanks a lot! pisces.zip

[tamsen]

Hi!

I'm afraid I'm swamped right now and wont have the time to really dig into this until late March (sorry!). In the meantime, this new more linux-friendly version on this fork should be much more friendly to debug on your own if you are comfortable trying. (build instructions and compiler suggestion here: https://github.com/tamsen/Pisces/blob/master/README.md , go to Build instructions section)

I had a quick look at your log you attached and it seems like Gemini does not know its getting a bam. The samples object in GeminiOptions.used.json says "

"GeminiSampleOptions": { "InputBam": null, "OutputBam": null, "OutputFolder": null, "IntermediateDir": null, "RefId": null

So, the nulls in the above looks not good. Perhaps something is not right on your command line? Here's an example Gemini command that worked for me on a quick test, below. Maybe you can use this as an example to sort out your command line.

/rhome/tdunn011/pisces_all/Pisces_5.3.0/GeminiMulti --bam /rhome/tdunn011/bigdata/HomoSapiens/SampleSet1_Titration/12pct-NA12877-r1_S11.bam --genome /rhome/tdunn011/bigdata/Genomes/HomoSapiens/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta --samtools samtools --exePath /rhome/tdunn011/pisces_all/Pisces_5.3.0/Gemini --outFolder /rhome/tdunn011/bigdata/HomoSapiens/SampleSet1_Titration --numProcesses 24 --chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY

I'll check back in as soon as I have free time.

best Tamsen

[stephanflemming]

I had the same problem. --exePath was not set correctly. Maybe that helps.

[tamsen]

Hi ShannonDaddy,

I tested with your bam and had no issue with v5.3.0. Here is the command I used.

/rhome/tdunn011/shared/Pisces/Pisces_5.3.0/GeminiMulti --bam /rhome/tdunn011/bigdata/HomoSapiens/PICS8/C2004235.flt.trim.bam --genome /rhome/tdunn011/bigdata/Genomes/HomoSapiens/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta --samtools samtools --exePath /rhome/tdunn011/shared/Pisces/Pisces_5.3.0/Gemini --outFolder /rhome/tdunn011/bigdata/HomoSapiens/PICS8 --numProcesses 24 --chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY

I think this is a command-line issue as Stephen suggested. Please try v5.3.0 with the command line I suggest and see how it goes. I'm going to close this issue. But if you still have the issue, please let me know, and I will dig in some more.

best, Tamsen