Warning in Genemark and maker
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5.2 years ago
qazwsx88tt • 0

Thanks everyone After my training with Genemark, there are two kinds of warning in the "log" output file :

warning, error in input file format:

-9

warning, error in input file format:

-10

warning, error in input file format:

-11

gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR

gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR

gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR

gmhmme warning: index 41 is out of range for max 40 for key BP_ACC_DISTR

After this, I use the es.mod in 'maker' for training, the same warning appear in the error file again. I've check my .fa data for its ID and sequence, the software "formatdb" of blastall ran normally, and the sequence has no letters out of [ATCGN]. (ps: I've tried another sequence file .fa , these warnings didn't appear )

can someone help me with the problem? what does the warning mean? how can I deal with it? (genemark_es_linux64_v2.3d)

genemark software error maker • 1.6k views
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As you don't have any spurious nucleotides in you sequences and it works for an other fasta file, It looks like a problem with the header. Could be the length of the sequence names. As example, MAKER gives you a WARNING if the sequence name is over 78 (I don't remember exactly) characters. Maybe there is some limits with genemark that have hard time to handle long names over 41 characters. Just change the sequence names (shrink them) and try again.

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thank you , i've check my original seq name , but the longest one is just 17. I don't know whether there is some errors in the middle of the process.I am going to try the process again, especially the Genemark as the main warning is from the software

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