RSEM Calculate Expression Error

Question

[mh9236183]

When using RSEM, I came across the error "Invalid number of arguments." Not sure where this arose from, since I separated the upstream and downstream reads with commas.

Usage: rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name

My Code: /u/local/apps/RSEM/1.3.3/gcc-4.9.3/bin/rsem-calculate-expression --paired-end /u/project/run434_1.fastq, /u/project/run434_2.fastq, /u/project/run437_1.fastq, /u/project/run434_T_1.fastq, /u/project/run434_T_2.fastq, /u/project/run437_T_1.fastq Aet_ref Aet_samp

Aet_ref is the reference name, and Aet_samp is the sample name. Let me know what I can do to resolve this issue! Thank you!

Answer 1

[MohammadAlkadi]

I think you left spaces between the file names. it should be A,B not A, B.

[mh9236183]

I tried running it with no spaces following the commas, but still no luck. Let me know if there is any other potential problems.

[MohammadAlkadi]

Sorry for late reply. "Invalid number of arguments"implied that you added more than the 4 arguments. the first arg is upstream_read_files (with no space and seperated by comma) then a space and writing the second argument downstream_read_file(s), then the third and fourth arguments