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Grice-Lab / HmmUFOtu

An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing
GNU General Public License v3.0
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new user problem #1

Open asantos01 opened 6 years ago

asantos01 commented 6 years ago

Hi, i am analyzing a MinION sequencer dataset that contains 16S gene sequences (1500 pb each) but i am having the next issue with the hmmufotu command :

MSA loaded HMM profile read CSFM-index loaded Phylogenetic tree loaded Determining read strand by alignment cost ... terminate called after throwing an instance of 'std::invalid_argument' what(): Your sequence contains invalid alphabet charactersCAGACGACTGCAAACGGAATCGGAGTCACGCACC Aborted (core dumped)

i have tried with another 16S small dataset from MinION and it worked well....

can someone help me please?

Thanks!

e00011027 commented 6 years ago

Hi, It may be caused by unprintable but illegal characters in your input file. Characters such as null ('\0'), Mac OS new line ('\r') may not be displayed but in the file. Try to open your input with vim or other text editors to find invalid characters.

Best Qi

On Wed, Sep 19, 2018 at 1:46 PM asantos01 notifications@github.com wrote:

Hi, i am analyzing a MinION sequencer dataset that contains 16S gene sequences (1500 pb each) but i am having the next issue with the hmmufotu command :

MSA loaded HMM profile read CSFM-index loaded Phylogenetic tree loaded Determining read strand by alignment cost ... terminate called after throwing an instance of 'std::invalid_argument' what(): Your sequence contains invalid alphabet charactersCAGACGACTGCAAACGGAATCGGAGTCACGCACC Aborted (core dumped)

i have tried with another 16S small dataset from MinION and it worked well....

can someone help me please?

Thanks!

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