HI @kdsung
It looks like the tool is detecting a problem with the BAM – maybe the format.
Are you able to click on the eye icon in the BAM dataset to open the peek view in the center panel? If yes, what does that plain text look like?
Another check is to confirm that the Upload process was complete. One simple way to do this is to compare the overall size of the file before and after. You could also do something like a checksum – use the tool Secure Hash / Message Digest (link at ORG) in Galaxy, run the same on your computer, and compare.
You could also back up and confirm that the file is intact on your computer, since an upstream transfer could have corrupted the file. Samtools is the general utility to use – if you install that on your own computer, it will make working with this file type much easier, even if just used for “sanity checks” like this. You don’t need to convert to SAM.
Given the size of the file, I would suggest that you put this into the larger storage space at UseGalaxy.org. You will be getting rid of this BAM once the sequences are extracted anyway. This post explains more about that space: What should I do if my data exceeds the given 250GB of storage?
And finally, the UseGalaxy.eu can sometimes process the largest data due to how they configure their public clusters. You cold try a cross-comparison to see what results. You can either Upload directly there, or attempt to transfer the data between servers. This might be needed for the Assembly step too but you won’t know until you try. The post above has instructions for moving data between servers.
SAM/BAM format (specification – an internet search will find much more)
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If the file is actually “sequence only”, these usually have a single header line, followed by data lines – one per sequence. All of the “mapping” statistics will have default placeholder values, and the nucleotide sequence and quality score “sequence” will both be present. The sequences are what you are extracting. Now, there might be some variation here, and source of the file may have more details about what to expect but the basic format constraints should be intact.
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If the file is from a prior alignment run, then you’ll have more header lines followed by data lines with statistics – one per alignment. This is what most of the online resources about the BAM/SAM formats are describing.
Please give those a check. It is hard to guess more without seeing the actual tool runs, and your file details.