Error While Running Cuffdiff for Groups

[bvk]

I'm trying to run cuffdiff for two groups. each has one sample for example I gave the following command:

cuffdiff -o diff_out3 -b ../genome/ce7.fa -p 2 -L em,la -u ../cufflinks/merged_asm/merged.gtf em/SRR493423_thout/accepted_hits.bam la/SRR872399_thout/accepted_hits.bam

[GenoMax]

This may sound odd but can you try replacing "em" and "la" with something else (longer names)?

[bvk]

This may sound odd but can you try replacing "em" and "la" with something else (longer names)?

nope that's not the problem