Question: (Closed) Cuffldiff is hanging at "99% complete"
gravatar for M K
5.0 years ago by
M K460
United States
M K460 wrote:

I am running cuffdiff but it is hanging at "99% complete", my commad as follows:

cuffdiff  -o /disk1//Diff_mouse  -b  /disk1/Mouse_genome/Bowtie2Index/genome.fa  -p 14  -L Brain,Heart,Kidney  -u Mouse_assemblies/merged.gtf   ./Mouse_brain/accepted_hits.bam,  ./Mouse_heart/accepted_hits.bam,  ./Alignment/Mouse_kidney/accepted_hits.bam

  > Map Properties:

   >       Normalized Map Mass: 72227841.38

   >       Raw Map Mass: 68981175.37

   >       Number of Multi-Reads: 11729580 (with 38235552 total hits)

   >       Fragment Length Distribution: Truncated Gaussian (default)

   >                     Default Mean: 200

   >                  Default Std Dev: 80

    [22:58:05] Calculating preliminary abundance estimates

> Processing Locus X:149357995-149358303       [************************ 99% ab@clyi:/disk1/Diff_mouse>

Then I tried to use the option  -M/--mask-file <mask.(gtf/gff)>  as follows: 

cuffdiff  -o /disk1//Diff_mouse  -b  /disk1/Mouse_genome/Bowtie2Index/genome.fa -p 14   -L Brain,Heart,Kidney  -M Mouse_assemblies/merged.gtf ./Mouse_brain/accepted_hits.bam, ./Mouse_heart/accepted_hits.bam,  ./Alignment/Mouse_kidney/accepted_hits.bam


but it gave me the following error

Cuffdiff Requires At Least 2 Sam Files. Please help

rna-seq • 1.5k views
ADD COMMENTlink modified 5.0 years ago by Istvan Albert ♦♦ 80k • written 5.0 years ago by M K460

Hello M K!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.


ADD REPLYlink written 5.0 years ago by Istvan Albert ♦♦ 80k

Hi Istvan,

I already posted this question and I got response with it by using the option 

-M/--mask-file <mask.(gtf/gff)> but with using this option the command doesn't work as I explained in this post, so please open this new post and close the old one that I posted yesterday.



ADD REPLYlink written 5.0 years ago by M K460

Asking the same question again with the same title twice can be very confusing. Imagine searching later for an answer.

You should put this into a comment or edit your original question.

Or if it is a different problem now then it needs to be asked as a different question. This now looks like an program invocation error that is about why the command does not recognize the bam files. It has nothing to do with the tool hanging at 99%/

ADD REPLYlink written 5.0 years ago by Istvan Albert ♦♦ 80k
gravatar for Istvan Albert
5.0 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:


See: Cuffldiff is almost done, but it seems to be hanging at "99% complete"

ADD COMMENTlink written 5.0 years ago by Istvan Albert ♦♦ 80k
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