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MapMan Bugs

mercator : Error: Sequence Check failed: String index out of range: -

HI all,
I'm experiencing a problem when trying to uplad cDNA sequences for mercator mappings.
shortly after having set the fasta database and chosen the mapping parameters and clicking start analysis,
the upload is terminated and the error is reported:

Error: Sequence Check failed: String index out of range: -1

aftter few attempts by correcting with a new cDNA dataset, I tested an old cDNA dataset which few months ago I was able to upload with no problems.: the same fasta file which worked in the past could not be uploaded today. any ideas?
thank for any hints


pb

RE: mercator : Error: Sequence Check failed: String index out of range: -
Answer
10/20/13 11:22 PM as a reply to paolo Bagnaresi.
hi,
many thanks for reporting this. We have put a new check in place to verify the fitness of the input sequence. This must have failed somehow.

We will investigate this tomorrow.

Axel

RE: mercator : Error: Sequence Check failed: String index out of range: -
Answer
10/21/13 12:16 PM as a reply to Axel Nagel.
Hi Paolo,

thanks again for your feed back. We are currently trying to investigate the problem you've reported.
Unfortunately we cannot reproduce the error because the sequence file you've tried to upload was,
due to the error that occurred during the upload, not saved on our server. We would be very grate-
ful if you could provide us with the sequence file so that we can find out what might have caused the
error message.

As Axel said, we've made the input data checker more strict - so it might be that a small irregularity
in your previously accepted file did now cause an error.
We are sorry for the inconvenience.

cheers,
Marc

RE: mercator : Error: Sequence Check failed: String index out of range: -
Answer
10/21/13 4:19 PM as a reply to Marc Lohse.
Hi Axel an Marc,
thanks for the prompt reply. I actually tested several files, includinf files that were happily loaded few months ago.
I'm confident the format of my fasta is OK since I generetaed the fasta wirh R dedicated funcions , starting from R DNA objects with a strict vocabulary. in any case, I also eliminated Ns (the only "anomaluos " bases present in my sequences) and got the same error. this happens in both my windows and ubuntu systems.

for reference I attch fasta 1, and fasta 2. the fasta 2 is a minimal dataset with only 3 sequences giving the error as well.
tahnks for any hints

Paolo

RE: mercator : Error: Sequence Check failed: String index out of range: -
Answer
10/21/13 4:22 PM as a reply to paolo Bagnaresi.
I'm not sure that the attachment were loaded, I can paste here the short file fasta 2: (only 3 sequences)


>VIT_02s0025g02100
TCCTAAGCACATTCTACCAACAACAACCATCGCAACACCAACAATGGTTCCCCATAGCAAAGCCTTAGTTTTCATCCTCC
TCTTACTCTTTGTTAGCTCATTTTCAGGCTGTGCAGATGGCTTCAAGGATGGAGCAAAGCTTCCATATCCAAATAGCTCG
GAGAATATCCAAATGATGGCGCGAAAGCTTATAGGAGTTGAAGCCCTGTTGGACTATGAAAAACCTGGATCTAATCCCTC
ACACACCCCAACTCCAGATAATGGTGGGAAAGACACCGGGGGAAAAACCCGCAAAGGAAGCAGTGTCAACAACTGAGTAA
CTCTACCTCATGTTACAGTTTGGTGAGTGCTTTGCTAAAATAAACGTCACTCTGACAGAAGGGTGACATTGTAAAACATC
TATTGGAAAAATGAAGAAAAAGGACCATGCCCATACTATATGTATTTCTACCGAAGAAAAGCAATAATAAGAAACTCATC
TCAGGCTCAAACCTGGCCTTAAATCATAAA
>VIT_11s0052g01280
ATGGCTTCTCCCTCTACTTCGAATCTGTCACCAAAGTTGCTCTTGATGTCTCTTCTGCTTGGTTCCTTTGTGGTTGCTTC
TGTTGGTAACTTGTACCAAGATTTTGATCTCACTTGGGGTGATGGCAGAGCCAAGATCCTCAACAATGGACAGCTTCTTA
CTCTCTCCCTTGACAAAGCCTCTGGCTCTGGCTTCCAGTCCAAGAATGAGTATCTGTTTGGGAAGATTGATATGCAGCTG
AAGCTTGTGCCTGGAAACTCTGCTGGCACTGTCACTGCCTACTATCTATCTTCACAAGGGCCTACCCATGATGAGATAGA
TTTTGAATTCTTGGGGAATCTCAGTGGTGATCCATACATTCTTCACACTAATGTGTTCAGCCAAGGAAAGGGAAACAGAG
AACAGCAGTTCTACCTCTGGTTTGACCCCACTGCTGATTTCCACACCTATTCCATCCTCTGGAATCCCCAGCGGATTATC
TTCTCTGTGGATGGCACCCCCATTAGAGAGTTCAAGAACTCTGAGTCCATTGGTGTTCCATTCCCAAAGAACCAGCCCAT
GAGGATATACTCCAGTCTCTGGAATGCAGATGACTGGGCAACAAGAGGTGGTCTTGTGAAGACAGACTGGAGCCAAGCAC
CTTTCACAGCCTCCTACAGGAACTTCAATGCCAATGCTTGTGTTTGGTCCTCTGGATCATCTTCTTGCAGTTCAACCTCT
CCATCTTCTACATCCACCAATAGTGGATGGTACTCACAAGAACTAGATTCCACAAGCCAAGAGAGAATGAAATGGGTGCA
GAAGAACTACATGATCTACAATTACTGCACAGACACAAAGAGATTCCCACAGGGCCTTTCCCCTGAATGCACTGCCACCA
CCACATCCTAGAGGAAACTCAACCTTAAAGGCCATTCAGTTAGATAGTTTGCCTCTGTAGGTTTCCTCAGTTCTGTTCTT
TCATTCTTTATCATTTTAGTCGGTATCACCACAGCTCATTGTTTA
>VIT_18s0001g00470
ATCCTCTCCCACTTGCAACTCCCCACCATCACCATCGCTCAAGAAATGGCCCTGAATTCTTTCCGGGCCTTTCTATCTAT
CTTTTCTCTCCTCTTCACCATTGTCGCCGCTGAAGATCCCTACAGATTCTTCACCTGGAATGTCACATTCGGCGACATTT
ATCCTCTTGGTGTTCGTCAACAGGGAATCTTGATCAATGGCCAATTCCCAGGTCCTGATATCTACTCCGTTACCAACGAT
AATCTCATTATCAACGTCTACAACAGCTTGACTGAGCCTTTTCTACTCTCCTGGAGTGGCGTTCAACAGAGGAGGAACTC
GTACGAAGATGGTGTGTACGGAACGACATGCCCAATCCCTCCGGGGAGGAACTTCACCTACATTCTCCAAGTGAAGGACC
AAATCGGAAGCTTCTTCTACTTCCCTTCTCTTGATTTCCACAAGGCCGCCGGCGGTTTCGGCGGCATCCGAATCCTCAGC
CGCCCTAGAATCCCTGTCCCCTTCCCCGATCCCGCCGGCGACATCACCGTCCTCATCGGAGATTGGTACAAAGCAAATCA
CACGACACTGAAGGCCATTCTAGACCGGGGTAAGAAGCTTCATTTTCCAGATGGGATCCTCATCAACGGCCGTGGTCCCA
ATGGAGTCTCTTTCACTGTGGAGCAAGGAAAAACATACAGGTTCAGGATATCAAATGTTGGGCTGCAAAATTCACTCAAC
TTCCGGATTCAAGATCACAAGATGGTGTTGGTTGAAGTGGAGGGAACACATACTCTCCAAACTACCTATTCCTCCCTTGA
TGTTCATGTTGGACAGTCCTACTCTGTGCTAGTGACTGCTGATCAGCCTGCCCAGGACTTCTACATTGTGGTCTCAACAC
GGTTCACCTCTCAGGTCCTCACCACCACCGGTATTCTCCGATACAGCAACTCTGCTGGTCCAGTCTCAGGCCCACCCCCA
GGTGGACCCACCATCCAAATTGACTGGTCCCTTAACCAGGCTCGCTCTATCAGGACTAATCTTACAGCAAGTGGACCAAG
GCCTAACCCACAAGGCTCTTACCACTATGGTATGATCACCACCTCCAGAACAATCAGGCTTGCAAGCTCTGCTGGTCAGG
TCAATGGCAAGCAAAGATATGCTGTTAATAGTGTATCCTATGTCCCAGGGGACACACCCCTAAAAGTTGCAGACTTCTTC
AAGATTGGAGGAGTTTTCCGTGTTGGAAGCATATCAGACAATCCTACTGGGGGAGGAGTATACCTTGATACTTCAGTTAT
GGGAGCTGACTTCAGAGCATTCGTAGAAATTGTGTTTGAAAATCCTGAGGACATCATACAGAGCTGGCACATCGATGGCT
ACTCTTTCTTTGTAGTCGGAATGGATGGAGGATTGTGGACAGCAAATAGTAGGAACCAGTACAATCTCCGTGATGCAGTT
GCCCGTTCCACTACTCAGGTATATCCCAAGTCATGGACTGCAATTTACGTGGCACTCGATAATGTGGGAATGTGGAACGT
GAGGTCTGAGTTCTGGGCAAGGCAATACCTAGGACAACAATTTTATCTACGGGTTTATTCGCCAGTAGAGTCTATCAGGG
ATGAATTCCCAATTCCAAAGAATGCACTGCTTTGTGGTAAGGCAAGTGGTCGACGAACAAGGCCCCTCTAAGAGCCAGCG
GCAAGCCACCAAAGCTCTGGAAGTGTTAGGGGAAACCTGTCTGGCATAGGAGGATTATTAAGAGTAGAGATATGCATATA
ATCTTTATGCGTGGGAGTTTAAATGACCTCAGCTCGAGGTCACATTCTTTTTTAACTAAAGGTTGTATTTTGTTTTGTTA
CTATTTATGTATTATGCCATTTTATAAAGAGAGGTGGTTAAAACTTATTAAATATCCTCTATTTGTAACAGCAACTTTGT
GTGTCTCTCTCTTTATAATAATATTAGGCAATTTACCTTGTTACCC

RE: mercator : Error: Sequence Check failed: String index out of range: -
Answer
10/21/13 4:27 PM as a reply to paolo Bagnaresi.
Hi Pablo,

thank you - unfortunately it seems like the attaching of the sequence files did not work. Anyhow,
we could reproduce the error using a different file and are currently testing the fix - in a few hours
(hopefully) the service will behave normally again and is a bit more permissive. The problem (at
least in our test file) was, that the input was not containing any description text after the identifier.
This is, according to the strictest interpretation of the format, not FASTA-compliant. Of course that
is impractical in real life and we are changing it now.

cheers,
Marc

RE: mercator : Error: Sequence Check failed: String index out of range: -
Answer
10/21/13 4:45 PM as a reply to Marc Lohse.
many thanks, indeed I routinely strip away descriptions from fasta headers !
Paolo