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




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