Question: Cuffdiff 2.2.1 Segmentation fault: 11
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9 months ago by
avillarreal.med0 wrote:

Hello!, I'm having problems with Cuffdiff analysis of gene Diff. expression. The code is:

cuffdiff -o (dir_output) --library-type=fr-firststrand -b ./dir/dir/file.fa -L Mock,Treated -u ./dir/file_gene_models.gtf

and followed by the inputs (with replicates).

In the terminal, the following is printed:

*Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (
[11:19:22] Loading reference annotation and sequence.
[11:19:23] Inspecting maps and determining fragment length distributions.
Segmentation fault: 11*

As a result, I get all expected files but with NO content (0 bytes).

Has anyone encountered such problem? I have a macbookpro with 8gb RAM and close to 140gb free space.


rna-seq software error • 305 views
ADD COMMENTlink modified 9 months ago by genomax83k • written 9 months ago by avillarreal.med0

Low memory, reported here: cuffdiff error: Segmentation fault: 11

Suggestions are to start from e.g. 10GB on: Memory and Runtime Cufflinks

Do you really need cufflinks, there are newer tools both differential gene and transcript level analysis that need far lower memory.

ADD REPLYlink written 9 months ago by ATpoint34k

You can use DEseq2 for the same as it is more updated method

ADD REPLYlink written 9 months ago by bioinfo_ga20
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