SALMON produce gigantic standard output?

[yeodynasty]

Hi, just a quick check if it is normal for SALMON 1.3 to send > 100 Gb of output to the stdout, despite using the -quiet flag.

The quant mode appears to be running smoothly. A sample of the output at the end of file:

My command is as follow: /gpfsdata/apps/salmon-latest_linux_x86_64/bin/salmon quant \ -i /gpfshome/hockchuan/SALMON/GCF_900626175.2_cs10_index \ -l ISR \ -1 /gpfsdata/JangiLab/hockchuan/170302/2.Trimmomatic_output/clean_HEADBANDSTEM_1.fastq.gz \ -2 /gpfsdata/JangiLab/hockchuan/170302/2.Trimmomatic_output/clean_HEADBANDSTEM_2.fastq.gz \ --seqBias \ --gcBias \ --posBias \ --incompatPrior 0.0 \ --geneMap /gpfsdata/JangiLab/hockchuan/cs10_reference_genome/GCF_900626175.2_cs10_genomic.gtf \ --recoverOrphans \ --allowDovetail \ --threads $NSLOTS \ --dumpEq \ --minScoreFraction 0.65 \ --writeMappings /gpfshome/hockchuan/SALMON/MAP/HEADBANDSTEM \ --fldMean 250 \ --fldSD 25 \ --writeOrphanLinks \ --writeUnmappedNames \ --quiet \ -o /gpfshome/hockchuan/SALMON/HEADBANDSTEM_quant

[rob-p]

Hi @yeodynasty,

This is because of the unfortunate conventions regarding the parsing of command line options in the presence of a flag that has an implicit option. Specifically, the --writeMappings flag has an implicit option. Therefore, to provide an explicit option to the long-form argument flag, you must use the syntax --writeMappings=<outputdir>. So, your command would look something like:

/gpfsdata/apps/salmon-latest_linux_x86_64/bin/salmon quant
-i /gpfshome/hockchuan/SALMON/GCF_900626175.2_cs10_index
-l ISR
-1 /gpfsdata/JangiLab/hockchuan/170302/2.Trimmomatic_output/clean_HEADBANDSTEM_1.fastq.gz
-2 /gpfsdata/JangiLab/hockchuan/170302/2.Trimmomatic_output/clean_HEADBANDSTEM_2.fastq.gz
--seqBias
--gcBias
--posBias
--incompatPrior 0.0
--geneMap /gpfsdata/JangiLab/hockchuan/cs10_reference_genome/GCF_900626175.2_cs10_genomic.gtf
--recoverOrphans
--allowDovetail
--threads $NSLOTS
--dumpEq
--minScoreFraction 0.65
--writeMappings=/gpfshome/hockchuan/SALMON/MAP/HEADBANDSTEM
--fldMean 250
--fldSD 25
--writeOrphanLinks
--writeUnmappedNames
--quiet
-o /gpfshome/hockchuan/SALMON/HEADBANDSTEM_quant

let me know if this resolves your issue.

Best, Rob

[yeodynasty]

Thank you, will give a try.

[yeodynasty]

It works!

[rob-p]

Great!