Hi, I am trying to run cuffquant (v2.2.1) on my RNA-seq data here is what I did :

1. cufflinks for my 6 samples : I retrieved a transcripts.gtf file
2. cuffmerge : I merged the 6 transcripts.gtf in a merged.gtf file.

I want now to run cuffquant with this command :

date="20171011"
Cond="A B"
Rep="Rep1 Rep2 Rep3"

for c in $Cond; do
        for r in $Rep; do
                cuffquant \     
                        -b MySpec.genome.tot.fa \
                        -u \
                        --no-update-check \
                        -M MySpec.ncRNA.gtf \
                        -p 16 \
                        -o ./${c}${r} \
                        ./merged_asm/merged.gtf \
                        sorted_${c}${r}_${date}.bam

                echo `pwd` ## To check if I am in the right dir

        done
done

Here are the errors I get (6 times) :

Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Error: cuffquant requires exactly 1 SAM/BAM file
/sge_spool/sl230lin12/job_scripts/2343232: line 93: -b: command not found

Question 1 : Why does cuffquant check for an update if I asked it not to do that with --no-update-check ?

Question 2 : Why can't cuffquant find my .bam files even if they are here in the rigth folder (as I checked with pwd) ?

Question 3 : Why does cuffquant say -b doesn't exist since here we can see that this option is allowed ?

Note : I know that cuffquant usage sends you to cuffdiff usage but I used the documentation from cuffquant website, here.

Thank you very much, and let me know if you have any clue !