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rapidjson internal assertion failure: IsObject()

Open AndreaGhiroldi opened this issue 1 year ago • 0 comments

I've installed Salmon and made the index, but once I run the analysis, I've got this error:

(salmon) andrea@Precision-7920-Tower:/hdd_a/andrea/Salmon$ sudo salmon quant -i GRCh38_salmon_index/ -l A -r /hdd_a/andrea/Salmon/Fastq/1_vehicle_R1.fastq.gz --validateMappings -o /Output/

salmon (mapping-based) v0.12.0

[ program ] => salmon

[ command ] => quant

[ index ] => { GRCh38_salmon_index/ }

[ libType ] => { A }

[ unmatedReads ] => { /hdd_a/andrea/Salmon/Fastq/1_vehicle_R1.fastq.gz }

[ validateMappings ] => { }

[ output ] => { /Output/ }

Logs will be written to /Output/logs [2024-02-21 09:49:04.094] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2024-02-21 09:49:04.094] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2024-02-21 09:49:04.094] [jointLog] [info] Usage of --validateMappings implies use of range factorization. rangeFactorizationBins is being set to 4 [2024-02-21 09:49:04.094] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 1. Setting consensusSlack to 1. [2024-02-21 09:49:04.094] [jointLog] [info] parsing read library format [2024-02-21 09:49:04.094] [jointLog] [info] There is 1 library. [2024-02-21 09:49:04.207] [jointLog] [info] Loading Quasi index Exception : [rapidjson internal assertion failure: IsObject()] salmon quant was invoked improperly. For usage information, try salmon quant --help Exiting.

Any suggestion? Thank you

AndreaGhiroldi avatar Feb 21 '24 08:02 AndreaGhiroldi