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Mercator fatal error

Mercator fatal error
mercator fasta upload problem
Answer
2/24/15 6:04 PM
I tried to run Mercator, with a fasta file containing 2908 RNA-seq nucleotide sequences... although it recognised the correct number of sequences (in the file info box), I got a fatal error message:


FATAL
: FATAL ERROR: The input contains both nucleotide and protein sequences.
Please make sure the input only contains data of either type.
Number of sequence types found in input:
Protein : null
Nucleotide: 981


Is there a problem with my fasta file? I tried using the IS_DNA option, and got the same error message.

Best wishes,
Catherine

RE: Mercator fatal error
Answer
2/24/15 6:08 PM as a reply to Catherine Tetard-Jones.
Best check if you have any offending "nucleotide codes" in your sequence, this is mos often triggering this error.
E.g. ACGACGTACGACTGDACGATC

RE: Mercator fatal error
Answer
3/2/15 9:56 AM as a reply to Björn Usadel.
Thanks for this... indeed, my fasta sequences does contain some offending codes (ambiguous positions).

For those sequences that do contain an offending code, does the whole sequence need to taken out (or do people try to replace the offending code?)

RE: Mercator fatal error
Answer
3/2/15 10:27 AM as a reply to Catherine Tetard-Jones.
Hi Catherine
it really depends where they came from, if they are non IUPAC ambigous codes the question is how did they get inside and if this is iffy do you trust the pipeline they came from. In this case either re-run the pipeline with fixes (probably not always possible) or take the sequences out.

Otherwise you might be able to replace them with N. (actually in single occurences you could also replace them with random nucleotides, as it won't change the global scores miuch)


Cheers
björn

RE: Mercator fatal error
Answer
3/2/15 11:51 AM as a reply to Björn Usadel.
Thanks björn,

just trying to run it now with a sample of my data without ambiguous codes... my job goes into the queue, but then I get another fail / error message... I guess it doesn't like my fasta file?


Error: Mercator Scheduler failed: Error message appeared!

Mercator4d77fd49f6eaf5b7185d48255a2da549


Thanks,
Catherine

RE: Mercator fatal error
Answer
3/2/15 12:19 PM as a reply to Catherine Tetard-Jones.
Hi Catherine,

I took at quick look at you job and this is a know bug (which is fixed locally but not deployed).
Basically when the input is too small (less than 1000 characters), the code throws an exception.

I can e-mail you the results (the email address you used in when creating the job).

Sorry for the inconvenience,

Regards,
Marie.