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Cuffldiff is hanging at "99% complete"

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
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updated by Ram Ram • written by M K M K

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.

• 0 views • link
updated by Ram Ram • written by M K M K

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%/

• 0 views • link
written by Istvan Albert Istvan Albert

1 answer

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

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updated by Ram Ram • written by Istvan Albert Istvan Albert

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