Exception : [rapidjson internal assertion failure: IsObject()]
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7 weeks ago
Andrea ▴ 10

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

salmon • 245 views
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sudo salmon

you should never run such tool as sudo

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thank you, solved!

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