[Error: The index version file /salmon_genome/BD_index/versionInfo.json doesn't seem to exist.

[CS791]

Hi!

An error pops in when I performed the salmon quantification for my data. The command and error is as follows: Command "salmon quant -i media/waqas/Chaudhary/BD_analysis/salmon_genome/BD_index -l A -1 /media/waqas/MG-ZDZ2D2R9/RNA_Seq_SC/Trimmed_BD/3/3_38_12_1_paired_R1.fastq.gz -2 /media/waqas/MG-ZDZ2D2R9/RNA_Seq_SC/Trimmed_BD/3/3_38_12_1_paired_R2.fastq.gz -o /media/waqas/Chaudhary/BD_analysis/Salmon_Out/3/3_38_12_1/"

Error: "Version Info: This is the most recent version of salmon.

salmon (mapping-based) v1.2.1

[ program ] => salmon

[ command ] => quant

[ index ] => { media/waqas/Chaudhary/BD_analysis/salmon_genome/BD_index }

[ libType ] => { A }

[ mates1 ] => { /media/waqas/MG-ZDZ2D2R9/RNA_Seq_SC/Trimmed_BD/3/3_38_12_1_paired_R1.fastq.gz }

[ mates2 ] => { /media/waqas/MG-ZDZ2D2R9/RNA_Seq_SC/Trimmed_BD/3/3_38_12_1_paired_R2.fastq.gz }

[ output ] => { /media/waqas/Chaudhary/BD_analysis/Salmon_Out/3/3_38_12_1/ }

Logs will be written to /media/waqas/Chaudhary/BD_analysis/Salmon_Out/3/3_38_12_1/logs [2020-05-30 17:22:09.253] [jointLog] [info] setting maxHashResizeThreads to 12 Exception : [Error: The index version file media/waqas/Chaudhary/BD_analysis/salmon_genome/BD_index/versionInfo.json doesn't seem to exist. Please try re-building the salmon index.] salmon quant was invoked improperly. For usage information, try salmon quant --help Exiting. [2020-05-30 17:22:09.253] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-05-30 17:22:09.253] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-05-30 17:22:09.253] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-05-30 17:22:09.253] [jointLog] [info] parsing read library format [2020-05-30 17:22:09.253] [jointLog] [info] There is 1 library."

Any help is much appriciated.

Thank you! Kind regards

CS

[rob-p]

Looks like you are missing a slash. I think this “ -i media/waqas/Chaudhary/BD_analysis/salmon_genome/BD_index” should be “ -i /media/waqas/Chaudhary/BD_analysis/salmon_genome/BD_index”. Let me know if that works.

[CS791]

Thank you! It is working now. Sorry I was so naive and didn't figure out such a simple error.

Kind regards CS

[rob-p]

No worries. Simple typographical errors are often difficult to see without an extra pair of eyes :).