cufflinks/cuffdiff-segmentation error: 11

[Sataree]

Hi, I need your help.

I'm very new to this pipeline. I have just finished mapped my reads using tophat2 without any problems according to Alternate protocols for "Quantification of reference annotation only" from Nature Protocols paper (2012). I'm now trying to perform differential expression analysis and I keep getting the "segmentation error:11" almost immediately. I see other threads but they seem to have a different problem from me.

For example:
$ cufflinks -o test_clout 2064NIC51_thout/accepted_hits.bam
You are using Cufflinks v2.2.0, which is the most recent release.
[23:17:27] Inspecting reads and determining fragment length distribution.
Segmentation fault: 11

I am getting this message for both cufflinks and cuffdiff. I don't know what I'm doing incorrectly. I have run the test data and it seems fine.

$ cufflinks test_data.sam.txt
You are using Cufflinks v2.2.0, which is the most recent release.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File test_data.sam.txt doesn't appear to be a valid BAM file, trying SAM...
[23:18:37] Inspecting reads and determining fragment length distribution.
Processed 1 loci. [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct parameters (--frag-len-mean and --frag-len-std-dev) be provided.
Map Properties:
Normalized Map Mass: 102.50
Raw Map Mass: 102.50
Fragment Length Distribution: Truncated Gaussian (default)
Default Mean: 200
Default Std Dev: 80
[23:18:37] Assembling transcripts and estimating abundances.
Processed 1 loci. [*************************] 100%

I currently running the analysis on Mac OS X with 8 GB of RAM.

I will really appreciate any help I can get.

[therr]

I'm getting the same problem -- I'm also following the Nature Protocols paper and running OSX with 8 GB RAM.

I'm getting this error on a .BAM file that I obtained from ArrayExpress. If I run through the protocol using the demo data the paper references, it works properly with the .BAM that TopHat outputs. So, I suspect there's something wrong with the file.

Were you able to figure it out?

[Sataree]

I downloaded Cufflinks 2.1.1 and that version ran fine for me. I used Tophat2. I don't have experience with ArrayExpress, sorry.

[therr]

I downloaded Cufflinks 2.1.1 and that version ran fine for me. I used Tophat2. I don't have experience with ArrayExpress, sorry.

Thanks! I just tried 2.1.1, and it's working for me, too. I guess there's a bug in 2.2.0?

Oh, and ArrayExpress is a repository that has array and sequence data from published papers, so I was trying to analyze pre-prepared data. That's why it was strange to me that it didn't work!

https://www.ebi.ac.uk/arrayexpress/experiments/browse.html