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Topic: Invalid checksum (Read 4421 times) previous topic - next topic

Invalid checksum

Hi there,

I am having a problem after I submit my job, I get an error message that says MD5_FILE_CHECK_FAILED.

Looking at the files, it was the first file in the first dataset that caused the problem, the error message is "Invalid checksum".  I tried removing this file, but it I got the same problem with the next file too.

My job number is 1002782.

I have converted .raw files to .mzXML files and have been able to upload and process similar files previously.

Any suggestions welcome!

Katherine.

Re: Invalid checksum

Reply #1 –
We have been updating XCMS Online recently, specifically the data pre-processing modules to use sha1 instead of md5 checksums on certain files.  Unfortunately there was a bug in the way it was implemented that forced the system to check your files (stored MD5 checksum in database) with the locally-calculated sha1 checksum.  Since these values did not match, the system errored out the job.

I made a correction to the aforementioned check and reran the job 1002782 (with error) but now there is another problem - I only see 35 files in the source dataset #47917.  You would need to reupload the missing files or delete them from the dataset as they are not on disk.  On a bright note, I added an additional check to the stored datasets page to display a file as inactive if it is not physically on disk.  You can then re-upload the missing/corrupted files.

Duane
 

Re: Invalid checksum

Reply #2 –
Hi Duane,

Thanks for your reply.  I re-uploaded the problem files and re-submitted the job.  Almost all of the files have been fine, which is great.  However, I've an error message for 3 of them:

Error in xcmsRaw(file, profstep = 0) : Time for scan 7998 (3600) greater than scan 7999 (0.402)

Is there anything I can do about this?  It's only 3 samples out of over 200, but 2 of them in particular are quite important ones, I'd rather not just delete them.

Best,
Katherine.