cufflinks. [bam_header_read] EOF marker is absent

[epistatic]

I am running RNA-seq samples on Galaxy and having problems running Cufflinks.

I upload the fastq file produced by CASAVA 1.8 and run through Tophat. Whenever I take this data from Tophat and run on Cufflinks, I get the following result. If the file needs formatting, it takes quite a bit of time to download the Tophat output, reformat, then upload for Cufflinks. Is there a step between Tophat and Cufflinks I am missing?

Thanks!

Cufflinks on data : gene expression
An error occurred running this job: cufflinks v1.0.3
cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 8
Error running cufflinks. [bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File /galaxy/main_database/files/

[maubp]

Cufflinks doesn't like your file. Try using this to peek at the start of the BAM file, replacing example.bam with your BAM filename.

hexdump -C example.bam | head

and:

cat example.bam | gunzip | hexdump -C | head

and please post the output here. Use the [ code ] tags (via the # button on the forum's advanced editor) to stop the forum formatting the output badly. That should let us check if it does look like a real BAM file or not.

[epistatic]

It turns out my file was too large to run on Galaxy. I normally analyzed multiplexed runs (30-50M reads/sample). This particular run was 1/2 lane on HiSeq v3. Once I split the file and ran, I had no problems.