Question: CuffDiff Hangs at same point
0
gravatar for Lauren Laboissonniere
2.6 years ago by
Iowa State University
Lauren Laboissonniere20 wrote:

Hi all,

I am currently encountering errors with CuffDiff because it appears to be stuck at the same locus for the past 48 hours and I was wondering if anyone else had this problem or had found a solution?

Here is my cuffdiff command line: cuffdiff -o diff_out -b index_mouse.fa -p 8 -L M1,M2 merged_asm/merged.gtf ./M1_1_3.th/accepted_hits.bam,./M1_2_13.th/accepted_hits.bam,./M1_2_14.th/accepted_hits.bam,./M1_2_15.th/accepted_hits.bam,./M1_2_17.th/accepted_hits.bam ./M2_1_2.th/accepted_hits.bam,./M2_2_8.th/accepted_hits.bam,./M2_2_23.th/accepted_hits.bam,./M2_2_24.th/accepted_hits.bam,./M2_2_26.th/accepted_hits.bam

The point where this command is stuck is under "Testing for differential expression and regulation in locus".

Thanks!

Lauren

rna-seq cufflinks cuffdiff • 623 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Lauren Laboissonniere20
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

I personally don't know of a specific known cause for this as a tool problem/error (suspect it is instead a content issue of some type that is triggering a compute-intensive cycle: region/s with many splices, fragmented assembly, etc), but you may have more luck with a post over at the general Biostars forum (this one is for Galaxy): https://www.biostars.org

I would suggest sharing a bit more about your data content when posting there. If you don't, will probably be asked to and this would help to attract constructive replies.

Take care, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
0
gravatar for Lauren Laboissonniere
2.6 years ago by
Iowa State University
Lauren Laboissonniere20 wrote:

Thank you!

ADD COMMENTlink written 2.6 years ago by Lauren Laboissonniere20
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