problem with syntax of command line

[mocherry]

Dear all,

I am trying to analyze direct nanopore RNA sequencing data with salmon. Now I seem to have problems with getting the command line properly:

I use: salmon quant -i salmon_index -l r dmso_sham_4.fastq --validateMappings -o transcripts_quant

and get the following Version Server Response: Not Found

salmon (selective-alignment-based) v1.10.3

[ program ] => salmon

[ command ] => quant

[ index ] => { salmon_index }

[ libType ] => { r }

[ ] => { dmso_sham_4.fastq }

[ validateMappings ] => { }

[ output ] => { transcripts_quant }

Logs will be written to transcripts_quant/logs [2024-05-29 11:13:30.128] [jointLog] [info] setting maxHashResizeThreads to 24 Exception : [unknown library format string : R] salmon quant was invoked improperly. For usage information, try salmon quant --help Exiting. [2024-05-29 11:13:30.128] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2024-05-29 11:13:30.128] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2024-05-29 11:13:30.128] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. [2024-05-29 11:13:30.128] [jointLog] [info] parsing read library format

So, as far I can see, being a bloody beginner, the error: Exception : [unknown library format string : R] somehow suggests that the small letter r in my command line is interpreted as a capital letter??? Or is there anything else wrong with my command?

Help would be appreciated. Thanks and best, Matthias