Cuffdiff "No such file or directory" error

Question

[jammydodger123456]

I am trying to use the job script;

   cuffdiff -p 10 -L Egg,Metacercaria PRJEBWB9PAULAnnotations.gff3 EggB1/tophat_out/accepted_hits.bam,EggB2/tophat_out/accepted_hits.bam MetB1/tophat_out/accepted_hits.bam,MetB2/tophat_out/accepted_hits.bam,MetB3/tophat_out/accepted_hits.bam

However, I get the error;

  Error: cuffdiff requires at least 2 SAM files

And;

/EggB1/tophat_out/accepted_hits.bam,/EggB2/tophat_out/accepted_hits.bam: No such file or directory

I have checked the paths to these files and everything appears to be as it should for my script to work.

Any suggestions?

Thanks, Duncan

[GenoMax]

/EggB1/tophat_out/accepted_hits.bam

Why is cuffdiff looking for these under the / directory? Can you provide full paths for all the files?

[jammydodger123456]

EggB1 is one directory within my working directory. Here's my script;

#!/bin/bash
#$ -N EvM
#$ -o /mnt/scratch/users/40100371/Read_Files/Fhep/EggvMet.$JOB_ID

# send email when job begins end or aborts
#$ -M [e-mail] -m bea

#$ -pe smp-verbose 10

#load cufflinks module environment
module load apps/cufflinks

# set working directory to scratch space project folder
#$ -wd /mnt/scratch/users/40100371/Read_Files/Fhep

#cuffdiff [options]* <transcripts.gtf> <sample1_replicate1.sam,sample1_replicateN.sam> <sample2_replicate1.sam,sample2_replicateN.sam>
cuffdiff -p 10 -L Egg,Metacercaria PRJEBWB9PAULAnnotations.gff3
/EggB1/tophat_out/accepted_hits.bam,/EggB2/tophat_out/accepted_hits.bam /MetB1/tophat_out/accepted_hits.bam,/MetB2/tophat_out/accepted_hits.bam,/MetB3/tophat_out/accepted_hits.bam

I tried to run this without the / before each rep, but the same error message comes back

[GenoMax]

I assume these directories are in /mnt/scratch/users/40100371/Read_Files/Fhep? Can you try to explicitly say /mnt/scratch/users/40100371/Read_Files/Fhep/EggB1/tophat_out/accepted_hits.bam etc?

[jammydodger123456]

That worked! Thank you