Question: cuffquant command line error and question
gravatar for corend
18 months ago by
corend70 wrote:

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 :

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 \

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


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 (
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 !

ADD COMMENTlink modified 18 months ago by Pierre Lindenbaum119k • written 18 months ago by corend70
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

2343232: line 93: -b: command not found

i suspect there is an extra whitespace after an antislash....

ADD COMMENTlink written 18 months ago by Pierre Lindenbaum119k

Furthermore, here is a solution using a simple Makefile:

Cond=A B
Rep=Rep1 Rep2 Rep3 

define run

$(1)$(2):  sorted_$(1)$(2)_${date}.bam
    cuffquant -b MySpec.genome.tot.fa  -u \
          --no-update-check  -M MySpec.ncRNA.gtf  \
          -p 16  -o$$@  \
          ./merged_asm/merged.gtf \


all:$(foreach c,${Cond},$(foreach r,${Rep},${c}${r} ))
    echo Done

$(eval $(foreach c,${Cond},$(foreach r,${Rep},$(call run,$c,$r))))
ADD REPLYlink modified 18 months ago • written 18 months ago by Pierre Lindenbaum119k
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