cufflinks error

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cufflinks error

jh yu
Dear all:

Recently I am using cufflinks to analyze differential expression between different conditions, but when using cufflinks an error occurred:

An error occurred running this job:cufflinks v1.0.3
cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat
Error running cufflinks. [bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this


However, when I used the same parameters to analyze another file, it worked well:

19,904 lines
format: gtf, database: rhodRHA1
Info: cufflinks v1.0.3
cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g /galaxy/main_database/files/002/991/dataset_2991920.dat


The only difference is the size of each file, the failed one input file is 23 G, while the succeeded one input file is 3.5 G, is the size causing failure?

Thank you in advance.



Best wishes!



Sincerely, Jinhai YU



Jinhai YU, Ph.D Candidate
010-64888521 
Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China



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Re: cufflinks error

Jeremy Goecks

An error occurred running this job:cufflinks v1.0.3
cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g =
/galaxy/main_database/files/002/991/dataset_2991920.dat
Error running cufflinks. [bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this

Hello,

Without seeing your analysis, it's difficult to determine what the problem is. My best guess is that:

(a) your SAM/BAM dataset is not compatible with Cufflinks for some reason, perhaps due to sorting?
(b) your gene annotation dataset is not compatible with Cufflinks.

Perhaps looking at the Cufflinks documentation will help you determine the error: http://cufflinks.cbcb.umd.edu/

If that doesn't work, you can report the problem by clicking on the bug icon next to the failed datasets.

Good luck,
J.
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Re: cufflinks error

Jen Hillman-Jackson
In reply to this post by jh yu
Hello Jinhai YU,

The error indicates that there was a problem with the BAM file/index.

When you loaded the larger file into Galaxy, did you use FTP? Was it
successful? Using a utility would allow you to track the progress, if
you are not certain. An incomplete load could generate an error like the
one you ran into. FTP help is at:
http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP

If the problem is confirmed to not be a data loading issue, it might be
a good idea to go back to the SAM file and convert to BAM again (if the
data was yours) or contact the owner/source of the BAM data and report
the problem to see what they think.

Apologies for the delay in reply,

Best,

Jen
Galaxy team

On 10/9/11 12:13 AM, jh yu wrote:

> Dear all:
>
> Recently I am using cufflinks to analyze differential expression between
> different conditions, but when using cufflinks an error occurred:
>
> An error occurred running this job:/cufflinks v1.0.3
> cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g
> /galaxy/main_database/files/002/991/dataset_2991920.dat
> Error running cufflinks. [bam_header_read] EOF marker is absent.
> [bam_header_read] invalid BAM binary header (this/
>
>
> However, when I used the same parameters to analyze another file, it
> worked well:
>
> 19,904 lines
> format: gtf, database: rhodRHA1
> Info: cufflinks v1.0.3
> cufflinks -q --no-update-check -I 1 -F 0.050000 -j 0.050000 -p 8 -g
> /galaxy/main_database/files/002/991/dataset_2991920.dat
>
>
> The only difference is the size of each file, the failed one input file
> is 23 G, while the succeeded one input file is 3.5 G, is the size
> causing failure?
>
> Thank you in advance.
>
>
>
> /Best wishes!/
> /
> /
> /
> /
> /
> /
> /Sincerely, Jinhai YU/
> /
> /
> /
> /
> /
> /
> /Jinhai YU, Ph.D Candidate/
> /010-64888521
> /
> /Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road,
> Chaoyang District, Beijing, 100101, China/
> /
> /
>
>
>
>
> ___________________________________________________________
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org