Salmon quant produced an error

Question

[Mohamed Samir]

I am trying to produce quant.sf files from an indexed ref. transcripts (transcripts_index GCA_000195955.2_ASM19595v2_genomic.fa) against two of my samples (N2_trimmed_forward_paired.fq.gz & N2_trimmed_reverse_paired.fq.gz)

The command that I used is:

salmon quant \
--geneMap GCA_000195955.2_ASM19595v2_genomic.gtf \
--threads 2 -l A \
-i transcripts_index GCA_000195955.2_ASM19595v2_genomic.fa \
-1 N2_trimmed_forward_paired.fq.gz \
-2 N2_trimmed_reverse_paired.fq.gz -o N2

It produces an error : 

> --geneMap GCA_000195955.2_ASM19595v2_genomic.gtf \
> --threads 2 -l A \
> -i transcripts_index GCA_000195955.2_ASM19595v2_genomic.fa \
> -1 N2_trimmed_forward_paired.fq.gz \
> -2 N2_trimmed_reverse_paired.fq.gz -o N2
Version Info: This is the most recent version of salmon.
### salmon (selective-alignment-based) v1.4.0
### [ program ] => salmon 
### [ command ] => quant 
### [ geneMap ] => { GCA_000195955.2_ASM19595v2_genomic.gtf }
### [ threads ] => { 2 }
### [ libType ] => { A }
### [ index ] => { transcripts_index }
### [  ] => { GCA_000195955.2_ASM19595v2_genomic.fa }
### [ mates1 ] => { N2_trimmed_forward_paired.fq.gz }
### [ mates2 ] => { N2_trimmed_reverse_paired.fq.gz }
### [ output ] => { N2 }
Logs will be written to N2/logs
[2021-06-11 01:24:10.399] [jointLog] [info] setting maxHashResizeThreads to 2
[2021-06-11 01:24:10.399] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2021-06-11 01:24:10.399] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2021-06-11 01:24:10.399] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2021-06-11 01:24:10.399] [jointLog] [info] parsing read library format
[2021-06-11 01:24:10.399] [jointLog] [info] There is 1 library.
Exception : [Error: This version of salmon does not support indexing using the RapMap index.]
salmon quant was invoked improperly.
For usage information, try salmon quant --help
Exiting.

It produced the "N2" folder" but it dose not contain thje .sf files (the quant files).

Thanks

Answer 1

[ATpoint]

Exception : [Error: This version of salmon does not support indexing using the RapMap index.]

You probably have an index produced with an older version of salmon which is not supported in v1.4.0 anymore. Try to make a new index with that version you're using.

[Muffin Man]

That fixed it for me, nice!