Cuffdiff log file explanation

[jetspeeder]

Can anyone explain the following results to me

What do these errors and warnings mean? Thanks.

chr15:18938734-19082541 Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Quantitating samples in locus [ chr15:19158684-19167424 ]
Quantitating samples in locus [ chr15:19185685-19189691 ]
Quantitating samples in locus [ chr15:19234785-19239054 ]
Quantitating samples in locus [ chr15:21024266-21098894 ]
chr15:21024266-21098894 Warning: restimation failed, importance samples have zero weight.
Resorting to MLE and observed Fisher
chr15:21024266-21098894 Warning: restimation failed, importance samples have zero weight.
Resorting to MLE and observed Fisher
chr15:21024266-21098894 Warning: restimation failed, importance samples have zero weight.
Resorting to MLE and observed Fisher
chr15:21024266-21098894 Warning: restimation failed, importance samples have zero weight.
Resorting to MLE and observed Fisher
chr15:21024266-21098894 Warning: restimation failed, importance samples have zero weight.
Resorting to MLE and observed Fisher
chr15:21024266-21098894 Warning: restimation failed, importance samples have zero weight.
Resorting to MLE and observed Fisher
Quantitating samples in locus [ chr15:21098966-21205659 ]
chr15:21098966-21205659 Warning: restimation failed, importance samples have zero weight.
Resorting to MLE and observed Fisher
chr15:21098966-21205659 Warning: restimation failed, importance samples have zero weight.
Resorting to MLE and observed Fisher

[jdanderson]

Hello Jet Speeder,

Did you ever figure out/resolve this error code? I just received a similar print out.

Thank you for any guidance you might be able to give.

Regards,
Johnathon

[jetspeeder]

it's not an error, it's just telling you that there aren't enough reads to provide an estimation is what I was told

[jb2]

I am also getting the following error message and curious what exactly it means:

Error: sqrt(det(cov)) == 0, 0.000000 after rounding.

[glacierbird]

sam error msg here.

[marcora]

same here... any explanation?!?

[natinreg]

hi!

full of Error: sqrt(det(cov)) == 0, 0.000000 after rounding. here

[jb2]

I haven't heard anything, but at least it is nice to know that I am not the only one seeing this error.

[adarob]

From Cole:

Those are normal errors caused by too little data in complex genes. They get marked as FAIL in the expr and fpkm tracking files.

From Me:

You can try setting the min isoform fraction (-F) to be nonzero (0.1 is a good one). This will filter low-abundance isoforms and make the genes less complex.

[jb2]

Thanks for the help from you and Cole!

[kongantik]

I tried using cuffdiff and recieve the same error. I used the GTF output file from cuff compare and there is no option in cuffdiff to specify F